2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
2009 List of Proposals from the Department of Agriculture and Agri-Food Canada (AAFC)
(The List includes 49 proposals in total.)
Project ID
Contact
Project Title
Internship
(Use ‘CTRL+click’ on the ‘Project ID’ to follow the hyperlink to
(year_location_#)
(AAFC Scientist)
Duration
the proposal description)
(months)
David Ehret
Improving Nutritional Quality of Organic and Hydroponic
12
2009_Agassiz_01
Tomatoes
Todd Kabaluk
Yield increase of corn following treatment of seed with
12-24
2009_Agassiz_02
Metarhizium anisopliae: the identification of causal factors
David De Koeyer
Genomics-assisted potato breeding to meet global
12
2009_Fredericton_01
challenges
Rong Cao
Antioxidant properties and potential health benefits of
12
2009_Guelph_01
pigmented vegetables
John Shi
‘Green’ extraction process to produce functional food
12
2009_Guelph_02
ingredients from agricultural material
Alireza Navabi
Genotype by environment interaction and mega12
2009_Guelph_03
environment investigation in long term common bean
(Phaseolus vulgaris L.) regional variety testing in Ontario
Kangfu Yu
Coarse mapping of an F2 bean population BBSS x Jalo
24
2009_Harrow_01
EEP558 by Diversity Arrays Technology (DArT)
Les Shipp
Evaluation of bumble bees as vectors for microbial control
24
2009_Harrow_02
agents (viruses and fungi) for arthropod pest management
Vaino Poysa
EcoTILLING Molecular analysis of glycinin genes in
24
2009_Harrow_03
soybean (Glycine max) mutant lines.
Martin Kalmokoff
Manipulation of intestinal bacterial communities; an
12
2009_Kentville_01
investigation into the impact of dietary fibre and prebiotics.
Benoît Bizimungu
Identification and selection of potato clones with novel
24
2009_Lethbridge_01
starch properties for food and industrial uses
2009_Lethbridge_02
John Lu
Genetic engineering of cereal crops to produce novel starch
12-24
Ranjana Sharma
Assessment of molecular and genetic diversity in specific
12
2009_Lethbridge_03
bacterial population from beef cattle - Implications for the
Food safety
Wenzhu Yang
Develop alternative growth promoter in ruminant
12
2009_Lethbridge_04
production
Xiying Hao
Hydrogen energy production through bio-fermentation of
12
2009_Lethbridge_05
livestock manure
2009_London_01
Deena Errampalli
Management of postharvest diseases in tree fruits
19
2009_London_02
Aiming Wang
Developing Novel Genetic Resistance to Plum Pox Virus
24
Frédéric Marsolais
Functional genomic analysis of seed storage protein
24
2009_London_03
deficiency in common bean (Phaseolus vulgaris): regulation
of sulphur amino acid content.
George Lazarovits
Development of sustainable agricultural systems through an
12-24
2009_London_04
understanding of interactions between microorganisms in
the rhizosphere and corn roots
Mark Gijzen
Plant pathogenic Phytophthora: molecular determinants of
12
2009_London_05
virulence
Pervaiz A. Abbasi
Developing reduced-risk and biological-based strategies for
24
2009_London_06
management of soil-borne diseases of vegetable crops and
promotion of plant growth
2009_London_07
Rima Menassa
Characterizing plant-produced human interleukin-24
24
2009_Ottawa_01
Allen Xue
Biological management of fusarium head blight in wheat
12-24
2009_Ottawa_02
Lana M. Reid
Phytochemical Resistance Mechanisms to Corn Pests
12
Carlos Monreal
Management and total use of agricultural residues for
12-24
2009_Ottawa_03
biofuels, bioproducts and bioenergy
(Update: January 28, 2009)
Page 1 of 78
2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
Elizabeth Pattey
2009_Ottawa_04
2009_Quebec_01
Yves Castonguay
Eric van Bochove
2009_Quebec_02
Gaëtan Tremblay
2009_Quebec_03
2009_Quebec_04
2009_Saskatoon_01
2009_Saskatoon_02
2009_Saskatoon_03
2009_Saskatoon_04
2009_Saskatoon_05
2009_Sherbrooke_01
2009_Sherbrooke_02
2009_Sherbrooke_03
2009_SJSR_01
Marie-Josée Simard
Kevin Rozwadowski
Kevin Rozwadowski
Kevin Rozwadowski
Russell K. Hynes
Yong-Bi Fu
Lucie Masse
Luigi Faucitano
Daniel Ouellet
Shahrokh
Khanizadeh
Gaétan Bourgeois
2009_SJSR_02
2009_StHyacinthe_01
2009_StJohns_01
2009_Summerland_01
Byong H. Lee
Samir C. Debnath
Dan O’Gorman
Helene Sanfacon
2009_Summerland_02
2009_Summerland_03
2009_Summerland_04
Joan Cossentine
Howard Thistlewood
A. K. Singh
2009_Swift Current_01
2009_Winnipeg_01(Morden)
2009_Winnipeg_02
Anfu Hou
Mark Jordan
(Update: January 28, 2009)
Adapting micrometeorological techniques for verifying
GHG emissions from agricultural fields and paddocks to
desired conditions
Identification of functional markers associated to superior
freezing tolerance in alfalfa.
Develop a particulate phosphorus (PP) component for a risk
indicator of water contamination by P from Canadian
agricultural land
Fractions protéiques et glucidiques de diverses espèces
fourragères / Protein and carbohydrate fractions in different
forage species
Evaluation of invasive weed distribution and spread into
crop fields
Enhancing quality and function of recombinant proteins
produced in seeds
DNA recombination and repair in plants
Seed-based production of recombinant proteins
Formulation development for baculovirus
Molecular characterization of wheat adaptation genes
Ammonia recovery by volatilization and capture
Effect of vehicle design and transport distance on stress
response and carcass and meat quality of three pig lines
Factors influencing variations in milk protein constituents
Use phytochemical as marker to select strawberry and
raspberry lines for processing (juice & fruit wine)
Impact of climate change and variability on the productivity
of field grown vegetable crops: A bioclimatic modelling
approach
Overproduction of extremophilic bacterial enzymes (lactase
and lipase) for the industrial applications
Bioreactor micropropagation and genetic fidelity in berry
crops
Diagnostic Technologies and Management Strategies for
Trunk Disease of Grapevines in British Columbia
Evaluation of the breadth and durability of engineered
resistance to Plum pox virus based on the induction of RNA
silencing
Biological control of orchard insect pests
Landscape ecology and genetics of invasive pests in
orchards
Identification of molecular markers linked to disease
resistance through linakge analysis and association mapping
approaches in durum wheat
Genetic diversity and breeding use of dry bean (Phaseolus
vulgaris L.) germplasm
Novel molecular markers for wheat improvement
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Page 2 of 78
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2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID/NO DU PROJET: 2009_Agassiz_01
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PROJECT TITLE / TITRE DU PROJET : Improving Nutritional Quality of Organic and Hydroponic Tomatoes
Internship location in Canada/ Pacific Agri-Food Research Centre,
Internship Duration/Durée du
Emplacement du stage
Agassiz, British Columbia
stage: 12 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: david.ehret@agr.gc.ca
d’AAC) David Ehret
Phone/Téléphone: 1-604-796-1712
Name of Research Centre/Nom du Centre de Recherche : AAFC-Pacific Agri-Food Research Centre
Mailing address/Adresse postale du Centre : PO Box 1000, Agassiz, BC, Canada V0M 1A0
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Dr. David Ehret, Sustainable Production System
Other AAFC collaborators/Autre collaborateurs à AAC: Drs. W. Lin, K. Usher, M. Cliff, T. Papadopoulos and M. Dorais
University collaborators/Collaborateurs universitaires: Dr. A. Plant, Simon Fraser University, BC, Dr. E. Heuvelink,
Wageningen University, the Netherlands
Industry partners/Partenaires industriels: Gipaanda Greenhouses Ltd., BC.
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
Over the last 50 years, the nutritional quality of fruits and vegetables grown in North America has been shown to have
declined. Despite this, consumer demand for nutritious vegetables is continually growing. Consumption of organically-grown
foods is also at an all-time high. It is well-known that fruit and vegetable quality is influenced by growing conditions. The
remarkable control of environmental conditions which is possible for greenhouse crops presents opportunities to significantly
improve the nutritional quality of greenhouse vegetables.
Objective/Objectifs:
The goal of this project is to develop ways to improve the nutritional quality of greenhouse-grown tomatoes. The study will
examine the effects of specific environmental growing conditions and short-term environmental stress on nutritional
composition (vitamins, antioxidants and pigments), flavour, and shelf-life of hydroponic and organic greenhouse tomatoes.
Outcome expected/Résultats attendus:
Changes in fruit nutritional quality due to environmental conditions such as nutrient concentration, light, and water availability
will be related to the underlying physiology, biochemistry and molecular biology. Subtle changes in whole-plant function such
as growth rate and water uptake will be measured using novel automated monitoring technology and related to changes in fruit
quality. Since organically-grown vegetables are an increasingly important part of the Canadian diet, organic fertilizer regimes
will also being developed to promote higher nutritional quality in greenhouse-grown organic tomatoes. Finally, integrated fruit
quality models will be developed to provide a better understanding of nutritional quality in relation to environmental growing
conditions and the physiology of the crop.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
Dr. Ehret has experience in training and mentoring Canadian and foreign students. The program will provide the candidate with
a broad experience in technologically-advanced agricultural science and organic growing methods. Depending on the specific
aspect selected for study, the candidate will learn techniques and concepts in horticulture (organic and hydroponic), plant and
food chemistry, plant physiology, molecular biology, crop monitoring and modeling. The candidate will be given the
opportunity to write scientific papers for international science journals. Candidate qualifications include some combination of
knowledge and experience in horticulture, plant physiology, phytochemistry, food chemistry, molecular biology, statistics or
computer modeling.
(Update: January 28, 2009)
Page 3 of 78
2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID/NO DU PROJET: 2009_Agassiz_02
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PROJECT TITLE / TITRE DU PROJET: Yield increase of corn following treatment of seed with Metarhizium anisopliae:
the identification of causal factors
Internship location in Canada/ Pacific Agri-Food Research Centre,
Internship Duration/Durée du
Emplacement du stage
Agassiz, British Columbia
stage: 12-24 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: kabalukt@agr.gc.ca
d’AAC) Todd Kabaluk
Phone/Téléphone: 1-604-796-1710
Name of Research Centre/Nom du Centre de Recherche : AAFC-Pacific Agri-Food Research Centre
Mailing address/Adresse postale du Centre : PO Box 1000, Agassiz, BC, Canada V0M 1A0
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Dr. Todd Kabaluk, Biologist
Other AAFC collaborators/Autre collaborateurs à AAC: Dr. Tom Forge, Research Scientist
University collaborators/Collaborateurs universitaires:
Industry partners/Partenaires industriels: Novozymes Biologicals, Inc.
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
We have recently discovered that treating corn seed with conidia (spores) of the insect pathogenic fungus M. anisopliae
resulted in an 11% increase in stand density and a 20% increase in area fresh weight yield based on field trials at three locations
in 2006 (Kabaluk and Ericsson, 2007). The original purpose of the M. anisopliae corn seed treatments was to protect the corn
plants from wireworm herbivory, as M. anisopliae is an insect fungal pathogen and has been developed in other countries for
pest control. However, it is suspected that other factors are involved in causing the increase in corn yield. Based on the
assessment of data to date, the following causes are considered for exploration:
-wireworm mortality and subsequent protection of corn plants from wireworm herbivory
-repellency of wireworms from M. anisopliae-coated corn seed, protecting the corn from herbivory i.e. M. anisopliae is simply
by repelling them from germinating corn seedlings
-competition of M. anisopliae with seed-rotting fungi such as Pythium and Fusarium, preventing loss of stand and improved
plant health.
-interaction of the M. anisopliae applications with plant pathogenic nematodes, conferring protection to the crop plant
-colonization of corn rhizosphere with M. anisopliae, conferring an uptake of soil nutrients and improved emergence and plant
health
-M. anisopliae is digesting the corn seed coat, improving corn emergence and escape from wireworm herbivory
Kabaluk, J. T. and Ericsson, J. D. 2007. Metarhizium anisopliae seed treatment increases yield of field corn when applied for
wireworm control. Agronomy Journal. 99: 1377-1381.
The yield-increase of corn as a result of treating seeds with M. anisopliae is a truly interesting and novel scientific
phenomenon. Understanding the mode of action for the yield increase will represent a new contribution to science.
Commercialization of M. anisopliae, either as a pest control or plant growth enhancement will undoubtedly take place
following the research.
Objective/Objectifs:
The objective of this research is to understand why treating corn seed with M. anisopliae results in an increase in the yield of
field corn. The understanding will come from the identification of the causal factor(s) of the yield increase listed under
Background/Rational/Issue (above). This understanding is essential i) to make a meaningful contribution to science; ii) so that
confidence is established with the public when this technology is commercialized; iii) so the scientific information can be
further exploited to enhance the yield increase phenomenon; iii) to guide the use of the technology down a regulatory pathway
associated with either pest control or plant growth enhancement.
Outcome expected/Résultats attendus:
The primary deliverable of this project is scientific information relating the causality of the yield increase in corn as a result of
treating seeds with M. anisopliae. The information will be derived through scientific experimentation by the PDF, under the
(Update: January 28, 2009)
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2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
guidance of Todd Kabaluk and Tom Forge, AAFC, and Jarrod Leland, Novozymes Biologicals. At the end of the project, the
PDF will provide a summary of the work and its results to AAFC. Further research findings, as deliverables, will be assembled
in the form of scientific manuscripts for publication in peer-reviewed journals.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
This project is an excellent opportunity for the prospective PDF to generate new scientific information to advance his/her
scientific career aspirations to make a significant contribution to science. Discovering the mode of action for increased yield
will be a significant contribution to science: both the use of microbial insecticides and recent discoveries on beneficial effects
of certain insect-pathogenic fungi on plant growth are areas of interest in current science. The discovery and publication of the
mode of action will enable other researchers and industry to investigate and exploit the knowledge for further improvements to
agriculture and industry.
The PDF will have his/her own office, laboratory space, and access to a technician and students for assistance. According to
the needs of the project, equipment and apparatus will be available.
We require that the PDF have experience, interest, or ability to work in at least two of the following areas: plant physiology,
microbial ecology, entomology, entomopathology, microbiology. We require the PDF to be self-motivated and to possess a
strong work ethic.
(Update: January 28, 2009)
Page 5 of 78
2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID/NO DU PROJET: 2009_Fredericton_01
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PROJECT TITLE / TITRE DU PROJET : Genomics-assisted potato breeding to meet global challenges
Internship location in Canada/ Potato Research Centre,
Internship Duration/Durée du
Emplacement du stage
Fredericton, New Brunswick
stage: 12 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: David.DeKoeyer@agr.gc.ca
d’AAC) David De Koeyer
Phone/Téléphone: 1-506-452-4885
Name of Research Centre/Nom du Centre de Recherche : AAFC-Potato Research Centre
Mailing address/Adresse postale du Centre : 850 Lincoln Road, Fredericton, NB, CANADA E3B 4Z7
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Dr. David De Koeyer, Research Scientist
Other AAFC collaborators/Autre collaborateurs à AAC: Agnes Murphy, Helen Tai, Benoit Bizimungu, Larry Kawchuk
University collaborators/Collaborateurs universitaires: Karen Tanino, University of Saskatchewan; Walter De Jong, Cornell
University; Merideth Bonierbale, International Potato Center, Peru
Industry partners/Partenaires industriels: Andrjez Killian, Diversity Arrays Technology Pty Ltd, Australia; John Argall,
BioAtlantech
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue:
The potato is a key part of the global sustainable food system - the most significant vegetable crop in Canada and the world,
producing more food energy on less land than corn, wheat or rice. More than half of total production is generated from
developing countries, rendering it an important source of income to millions of farmers. Thus, the potato crop is a significant
economic mechanism for the production of food to address intensifying health needs and the delivery of new bioproducts, such
as bioplastics. To recognize the importance of the potato crop, the United Nations designated 2008 as the International Year of
the Potato.
Potato is susceptible to many pathogens and pests that result in economically significant disease losses globally. Global
warming is expected to increase the full range of abiotic stresses as well as disease losses as pathogens and vectors expand their
distributions. To develop ecologically and economically sustainable agricultural practices that reduce chemical and fossil fuel
inputs, we must develop varieties with more durable and generalized resistance. Emerging marker technologies and statistical
methods are required to access beneficial genetic variation related to stress tolerance from improved and unadapted germplasm
and integrate them into breeding programs.
Objective/Objectifs:
To combine improved phenotypic screening methods with new transcriptome, metabolome and epigenome data for
potato to identify candidate genes for abiotic and biotic stress resistance and novel bioproduct traits to contribute to marker
development
To generate natural allelic diversity information for marker development through targeted genome re-sequencing of
candidate genes and genome regions.
To identify and localize markers in the potato genome linked to economic and environmental traits using association
genetics based on dosage-sensitive candidate gene and whole-genome marker profiling.
To initiate Genomics-Assisted Breeding using markers for improving stress resistance and utilization traits in potato.
Outcome expected/Résultats attendus:
The proposed project will develop genomics tools for potato breeding programs with improved potato varieties for new and
existing markets that can be grown with reduced inputs and reduced loss from abiotic and biotic stress. The project will
integrate physiology, breeding and molecular approaches and produce a comprehensive Genomics-Assisted Breeding
Platform. Key outcomes from this project will include:
 Identification of genes involved in abiotic stress resistance, disease resistance, and quality traits.
 DNA markers tightly linked to genes influencing important traits.
 Dosage sensitive markers for quantitative assessment of allele dosage in tetraploid potatoes.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
(Update: January 28, 2009)
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2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
The postdoc will be part of a comprehensive research team that will be developing genomics tools for potato improvement.
The primary responsibilities of the candidate will be to develop high-resolution DNA melting (HRM) markers for candidate
genes, to genotype a germplasm panel with candidate gene markers, to integrate HRM data with DArT genotyping data; and to
conduct association genetics analysis. The expectation is that the candidate will have a doctoral degree in plant sciences,
genetics, agriculture, or molecular biology; have experience in a molecular laboratory; have a good understanding of statistics;
and have a willingness to learn new skills. The benefits to the intern will be conducting research within an applied genomics
laboratory; working with a large multi-disciplinary team; having excellent opportunities for publication of novel research; and
broadening skills in biotechnology and bioinformatics.
(Update: January 28, 2009)
Page 7 of 78
2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID/ NO DU PROJET: 2009_Guelph_01
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PROJECT TITLE / TITRE DU PROJET : Antioxidant properties and potential health benefits of pigmented vegetables
Internship location in Canada/ Guelph Food Research Centre,
Internship Duration/Durée du
Emplacement du stage
Guelph, Ontario
stage: 12 months/mois
Contact : Rong Cao (R. Tsao)
Email/Courriel: caor@agr.gc.ca
Phone/Téléphone: 1-519-827-0550
Name of Research Centre/Nom du Centre de Recherche : AAFC-Guelph Food Research Centre
Mailing address/Adresse postale du Centre : 93 Stone Road West, Guelph, Ontario N1G 5C9, Canada
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: Dr. Rong Cao, Functional Foods & Nutraceuticals Team
Other AAFC collaborators/Autre collaborateurs à AAC:
University collaborators/Collaborateurs universitaires: Dr. Mary-Ruth McDonald
Industry partners/Partenaires industriels: OMAFRA
B – Project Description: rational, objectives, outcome expected/
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
Consumption of fruits and vegetables has been related to significant reduction of chronic diseases, particularly cancer. This is
one of the five health claims approved by Health Canada. Phytochemicals are now considered to play a major role in the
prevention of cancer and cardiovascular diseases. Such physiological properties of vegetables have been attributed to the
strong antioxidant capacities of the phytochemicals instead of the essential vitamins such as vitamin C. Although in general
polyphenols and carotenoids are known as the major antioxidative phytochemicals, and compounds such as anthocyanins are
well know to be the major contributor to the antioxidant capacity of small berries e.g. blueberries and their various health
benefits, knowledge and information on the phytochemical profiles of different vegetables and factors affecting the
phytochemicals (genetics, environment, post-harvest and processing conditions etc) are largely unknown.
On the other hand, efforts in producing high antioxidant vegetables have been made. In the Province of Ontario, highly
pigmented vegetables with yellow, orange, red, blue and purple colours are being examined currently for their anthocyanin and
carotenoid compositions, and the effects of cultivar, geographic location and fertilizers. There is a need to develop validated
method for phytochemicals in such new vegetables, and examine their antioxidant capacities.
Objective/Objectifs:
1. To modify and develop method for the analysis of phytochemicals in most economically important vegetables in Ontario :
tomato, potato, cauliflower, cabbage, carrot, onion, broccoli
2. To further investigate the anthocyanin and carotenoid compositions and factors affecting of pigmented varieties (variety,
location, nitrogen, processing etc)
3. To investigate the antioxidant capacities using in vitro methods
Outcome expected/Résultats attendus:
1.
2.
3.
4.
Phytochemical database of major Ontario vegetable crops such as purple potatoes, purple cauliflowers, purple carrots.
Cultivars and best agronomic practice and processing conditions for maximized antioxidant capacities of Ontario vegetables
Information for consumers on the potential health benefits of the new and pigmented Ontario vegetables
Increased production and income by Ontario Vegetables farmers
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The program is to study highly pigmented vegetables and understand their health benefit (antioxidant potential). The intern
should be a PhD preferably in food /natural products/analytical chemistry with experiences in phytochemicals and antioxidants
research. The intern will be trained in a chemistry laboratory setting and will benefit from the following techniques including :
extraction of phytochemcials from different vegetables ; sample clean up and pre-concentration techniques such as solid phase
(Update: January 28, 2009)
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2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
extraction (SPE) ; analysis of total phenolic content using Folin-Ciocalteu method ; total anthocyanin/carotenoid content using
spectrophotometric detection ; analysis of phenolic compounds and carotenoids using HPLC (high performance liquic
chromatography) ; HPLC-MS (mass spectrometry), in vitro antioxidant capacity measurement using FRAP, ORAC, PCL, betaCLAMS, and cell-based antioxidant activity method (CAA).
(Update: January 28, 2009)
Page 9 of 78
2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID/ NO DU PROJET: 2009_Guelph_02
Back
PROJECT TITLE / TITRE DU PROJET: ‘Green’ extraction process to produce functional food ingredients from
agricultural material
Internship location in Canada/ Guelph Food Research Centre
Internship Duration/Durée du
Emplacement du stage
Guelph, Ontario
stage: 12 months/mois
Contact: (name of AAFC scientist / nom du chercheur Email/Courriel: shij@agr.gc.ca
d’AAC) John Shi
Phone/Téléphone: 1-519-780-8035
Name of Research Centre/Nom du Centre de Recherche: AAFC-Guelph Food Research Centre
Mailing address/Adresse postale du Centre : 93 Stone Road West, Guelph, Ontario N1G 5C9 Canada
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Dr John Shi, Functional Foods & Nutraceuticals Team
Other AAFC collaborators/Autre collaborateurs à AAC: Dr Elsayed Abdelaal, Dr Magda Kostrzynska, Dr Dan Ramdath,
University collaborators/Collaborateurs universitaires: University of Guelph (Dr Yukio Kakuda, Dr Gauri Mittal);
Industry partners/Partenaires industriels: Heinz Canada Co.; Joseph Natural Products, Ltd.
B – Project Description: rational, objectives, outcome expected/
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
The development of separation/ extraction/ concentration processes to produce high value-added functional food ingredients
from agricultural materials are now being recognized as one of the most important technological needs by agri-food industries.
The challenge is to develop “organic-solvent free” “green” extraction technologies to meet food safety regulations and to
economically preserve the bioactivity of health-promoting compounds. Supercritical fluid-based extraction (SFE) processes
have drawn much attention by extracting high-value compounds and opening new opportunities for innovative food products.
To achieve the goal for functional foods and ingredients that are free from chemical residues, an “organic-solvent free” “green”
separation/extraction process by supercritical-CO2 fluid –based technology, must be developed, optimized, and fully exploited
to produce the functional foods demanded by consumers. AAFC has considered development of functional foods by novel
separation technology as priority research area, and given full support in research activity. Dr. Shi and his research team have
launched projects related to extracting lycopene from tomatoes, β-carotene from pumpkin, sweet potatoes, and some berry
fruits, etc. He established collaborations with Heinz Co., Joseph Natural Products. Separation equipment such as supercritical
CO2 fluid extractors, microwave solvent extractor, molecular distillation separation apparatus, and membrane separation
equipment is available in Guelph. Advanced analysis facilities such as HPLC, GC, LC-Mass, GC-Mass, chemiluminescence
meter, etc. are also available. This team at AAFC has internationally recognized scientific expertise, is world class with broad
experience, international reputations.
Objective/Objectifs:
The Internship project is “Development of ‘organic-solvent free’ ‘green’ extraction processes by supercritical fluid-based
technologies to produce health-promoting functional food ingredients from agricultural plant material”: (a). development of an
optimum supercritical fluid extraction to provide high selectivity, solubility and yield, bioactivity stability; (b) development of
modeling methods to monitor the extraction process and product quality and bioactivity degradation of health-promoting food
ingredients;
Outcome expected/Résultats attendus:
The proposed project is to develop a new technology that will enhance the extraction of health-promoting components such as
carotenoid-rich functional food ingredients. It would be highly interested for the researcher to develop natural high-value-added
carotenoids-rich functional food ingredients for people health, and have high benefits for economic development. Dr Shi has
some classmates working as professors in universities.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
(Update: January 28, 2009)
Page 10 of 78
2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
Internship project: “Green” extraction process to produce functional food ingredients from agricultural material”
Methods:
1).Design of process conditions to extract carotenoids from selected carotenoid-rich materials by using SFE-CO2 equipment,
2). Modifiers (Co-solvents) design: water, ethanol, or food-grade-oils are used as co-solvents.
3).Optimization of operation parameters: to establish an optimized operation condition, experiments will be conducted to
determine the effect of extraction parameters and conditions such as pressure, temperature, moisture level, particle size, CO 2
flow rate, co-solvent, etc. on extraction yields and selectivity of the targeted component.
Work Plan and Outputs:
a) to prepare experimental plan (1st month),
b) to optimize operating condition for extracting selected materials(2-3th months),
c) to study effects of pre-treatments on yield of extracted products (4-5th month),
d) to determine solubility, mass transfer coefficients, and other engineering properties of extracts under different conditions (610th month),
e) to determine stability of bioactivity of caroteniod-rich functional foods under different conditions (9-11th month),
f) to develop optimal process condition and process modeling (9-12th month),
Post-doctoral fellow with background of food engineering, chemical engineering, food science and technology will well fit in
this project. They will be well –trained through the lab work activity and to gain sound knowledge and skill.
(Update: January 28, 2009)
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2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID/ NO DU PROJET: 2009_Guelph_03
Back
PROJECT TITLE / TITRE DU PROJET : Genotype by environment interaction and mega-environment investigation in
long term common bean (Phaseolus vulgaris L.) regional variety testing in Ontario
Internship location in Canada/ Universtiy of Guelph,
Internship Duration/Durée du
Emplacement du stage
Guelph, Ontario
stage: 12 months/mois
Contact : Alireza Navabi
Email/Courriel: alireza.navabi@agr.gc.ca
Phone/Téléphone: 1-519-824-4120 ext. 56829
Name of Research Centre/Nom du Centre de Recherche : AAFC-Greenhouse and Processing Crops Research Centre
Mailing address/Adresse postale du Centre : 2585 County Road 20, Harrow, ON, Canada N0R 1G0
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: Dr. Alireza Navabi, Research Scientist , Sustainable Production Systems
Other AAFC collaborators/Autre collaborateurs à AAC:
University collaborators/Collaborateurs universitaires: Dr. Istvan Rajcan, Universtiy of Guelph
Industry partners/Partenaires industriels: Ontario White and Colored Bean Growers Associations
B – Project Description: rational, objectives, outcome expected/
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
Multi-location and regional variety performance trials of common bean (Phaseolus vulgaris L.) in Ontario is performed
annually, in order to identify superior genotypes for commercial release and to provide growers with variety recommendations.
Like other multi-location variety trials, results of these tests are generally confounded by the presence of crossover genotype by
environment interaction, which complicates the process of variety selection and recommendation. In this research, we intend to
use long-term variety trial data from Ontario, along with agro-climatic data and to apply novel statistical models to test the
hypothesis that bean growing areas in Ontario may be dissected to subsets of regions with repeatable crossover interaction.
This may lead to identification of bean growing mega-environments in Ontario. We will also attempt to investigate if the
identified mega-environment(s) can be separated by agro-climatic indicators such as cumulative crop heat units during the
growing season, soil type etc.
Objective/Objectifs:
1) To study the genotype by environment interaction patterns in multi-location trials and
2) To perform mega-environment investigations using a long term dataset of common bean variety trials in Ontario.
Outcome expected/Résultats attendus:
Identification of bean growing mega-environments in Ontario and identification of sites that have historically been more
informative of the genotype by environment interaction patterns of bean genotypes in Ontario.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The intern will have the opportunity to work with the AAFC Bean Breeding Program at the University of Guelph in Guelph,
Ontario. The program is currently working on a variety of objectives, including breeding for high yield, high quality, resistance
to major bean diseases and the canopy structure suitable for direct combining.
For the purpose of this research, a dataset of long-term variety trials in Ontario is being put together. The internship program
will provide the PDF with experience in application of novel statistical models in plant breeding data analysis.
For this position, prior training in plant breeding, knowledge of advanced statistics, genotype by environment interaction
analyses and SAS programming is required.
The PDF will have the opportunity to learn a range of novel approaches in statistical analysis of multi-location data. The intern
may also bring along data from crop breeding programs of the home country and perform similar tests on a dataset from his/her
country. It is expected that this research result in at least one scientific publication in peer-reviewed journals.
(Update: January 28, 2009)
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2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID/ NO DU PROJET: 2009_Harrow_01
Back
PROJECT TITLE / TITRE DU PROJET : Coarse mapping of an F2 bean population BBSS x Jalo EEP558 by Diversity
Arrays Technology (DArT)
Internship location in Canada/ Greenhouse and Processing Crops Research Centre,
Internship Duration/Durée du
Emplacement du stage
Harrow, Ontario
stage: 24 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: yuk@agr.gc.ca
d’AAC) Kangfu Yu
Phone/Téléphone: 1-519-738-1207
Name of Research Centre/Nom du Centre de Recherche : AAFC-Greenhouse and Processing Crops Research Centre
Mailing address/Adresse postale du Centre : 2585 County Road 20, Harrow, ON, Canada N0R 1G0
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Dr. Kangfu Yu, Sustainable Production Systems
Other AAFC collaborators/Autre collaborateurs à AAC: Drs : Navabi, Alireza; Marcus Shi
University collaborators/Collaborateurs universitaires: Drs : William B. Crosby; Peter Pauls
Industry partners/Partenaires industriels: Ontario White and Colored Bean Growers Associations
B – Project Description: rational, objectives, outcome expected/
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
Common bacterial blight (CBB) of common bean is a significant bacterial pathogen that is endemic to the $280 Million annual
processing bean production industry in Canada. At present, cultivation of CBB resistance cultivars is the only effective and
environmentally sound approach to management of this disease in bean production. Application of marker-assisted selection
(MAS) can significantly increase the selection efficiency in bean breeding program. However, the whole bean genome is not
sequenced yet and the high-throughput genotyping method, Diversity Arrays Technology (DArT), is also not established in
bean. DArT is a novel large-scale genotyping technique that has been very attractive to breeders due to its low cost and high
throughput, as well as its ability to generate reproducible molecular markers with no prior DNA sequence information.
Objectives/Objectifs:
1) To establish the DArT technology in common bean genetics;
2) To apply DArT for high-throughput genotyping and linkage mapping of an F2 population derived from the BBSS
(resistant) x Jalo EEP558 (susceptible) cross.
Outcomes expected/Résultats attendus:
1) To produce the Bean Diversity Array containing ≥1,500 DArT markers; 2) To genotype 52 lines including two parent lines
and 50 individual F2 lines; 3) To construct a coarse map of the F2 BBSS x Jalo EEP558 population with ≥100 markers.
C –Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The internship program will focus on preparing genomic representations from Jalo EEP558 and generating the Bean Diversity
Array. For this position, prior training in plant genetics and plant molecular biology is preferred. Experience with plant
pathology will also be a plus.
The internship will have the opportunity to learn a range of cutting-edge genomics techniques, such as, enriched DNA library
construction, macroarray-based hybridization, and microarray data analysis. Upon completion of this training program, the
intern could adapt these technologies to improve bean production in the home country.
(Update: January 28, 2009)
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2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID/ NO DU PROJET: 2009_Harrow_02
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PROJECT TITLE / TITRE DU PROJET : Evaluation of bumble bees as vectors for microbial control agents (viruses and
fungi) for arthropod pest management
Internship location in Canada/ Greenhouse and Processing Crops Research Centre,
Internship Duration/Durée du
Emplacement du stage
Harrow, Ontario
stage: 24 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: shippl@agr.gc.ca
d’AAC) Les Shipp
Phone/Téléphone: 1-519-738-1235
Name of Research Centre/Nom du Centre de Recherche : AAFC-Greenhouse and Processing Crops Research Centre
Mailing address/Adresse postale du Centre : 2585 County Rd. 20, Harrow, Ontario, Canada
N0R 1G0
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Dr. Les Shipp, Environmental Health
Other AAFC collaborators/Autre collaborateurs à AAC: Drs. Bruce Broadbent (London) and Martin Erlandson (Saskatoon)
University collaborators/Collaborateurs universitaires: Dr. Peter Kevan, University of Guelph
Industry partners/Partenaires industriels: Biobest Canada, Novozymes Biologicals Inc. and NSERC Canadian Pollination
Initiative Network
B – Project Description: rational, objectives, outcome expected/
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
Traditionally, microbial control agents have been applied to crops for pest control using standard chemical spray application
technology. It has been known for a long time of the ability of bees to carry microscopic particles such as pollen. Dr. Shipp
and colleagues have developed a “Pollinator Biocontrol Vector Technology” for using bee pollinators to deliver fungal control
agents for insect pest control and plant disease suppression using the agents, Beauveria bassiana and Chlonostachys rosea.
Greenhouse cage trials have shown that bee-vectored B. bassiana can cause substantial mortality of Lygus, whiteflies, thrips
and aphids (up to 80% mortality) when tested on greenhouse tomato and sweet pepper. The bees deliver the fungal spores
directly to the flowers and leaves where the pests are found. This approach reduces the amount microbial agent applied,
minimizes human handling of the fungal control agents, eliminates the use of pesticides for insect control and is more
environmentally-friendly and cost effective than the application of chemical pesticides. Since bumble bees are the standard
pollination method in greenhouse vegetables, you can combine pollination and pest control activities together. In addition,
preliminary greenhouse cage trials have found that bumble bees can simultaneously deliver both a pest fungal biocontrol agent
(B. bassiana) and a plant inoculum (C. rosea) to sweet pepper for Lygus (ca. 80% infection) and grey mould (45-55%
suppression) control. The impact of these fungal agents on bumble bees appears to be minimal. The next steps in developing
this technology is to evaluate the ability of bumble bees to deliver insect viruses for pest control and assess the ability of bees
to vector other entomopathogenic fungi, such as Metarhizium anisopliae.
This project involves a multidisciplinary team approach consisting of AAFC, a Canadian university and industry partners. The
overall objective of this project is to develop an effective, environmentally-friendly method for application of microbial control
agents using bee pollinators for pest control of greenhouse vegetable crops. The end result will be safer food products for the
consumer through the elimination of insecticides.
Objective/Objectifs:
1. Evaluate the effectiveness of using bumble bee pollinators for delivery of the entomopathogenic fungus, M. anisopliae, for
pest control.
2. Evaluate the use of bumble bees as a delivery system for baculoviruses for control of lepidopteran pests.
Outcome expected/Résultats attendus:
 Determination of the ability of the commercially-reared bumble bee, Bombus impatiens, as a new application method for
delivering M. anisopliae for pest control to crops.
 Development of a new methodology for the application of insect viruses to crops for pest control.
C –Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
(Update: January 28, 2009)
Page 14 of 78
2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
Internship Program:
Intern will assist in conducting greenhouse cage trials:
 to determine the optimal bee-vectored concentration ratio of M. anisopliae for pest control (whitefly, thrips and
aphids) on greenhouse tomato and sweet pepper
 to determine the impact of bee vectored M. anisopliae on non-targets hosts (ie, bumble bees and biological control
agents)
 to determine the amount of M. anisopliae deposited on plant structures (flowers and leaves)
 to determine the effectiveness of using bee vectoring to deliver baculoviruses to crops for control of lepidopteran pests
(ie. cabbage looper)
 to improve the design of the inoculum dispenser.
Expected qualifications of the intern:
Experience in entomology and integrated pest management. Knowledge of greenhouse pests, bumble bees and insect
pathology is an asset, but not essential.
Benefits to the intern:
 Gain experience with a new novel IPM strategy of using pollinators to deliver microbial control agents for control
arthropod pests and diseases in greenhouse crops.
 Gain experience in IPM in Canadian greenhouse vegetable crop production systems. The main emphasis of
greenhouse vegetable IPM in Canada is biological control.
 Be part of a greenhouse IPM/pollination team that is recognized as a world leader in this area of research.
 Broaden their network of contacts in entomology and pest management.
(Update: January 28, 2009)
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2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID: 2009_Harrow_03
Back
PROJECT TITLE / TITRE DU PROJET : EcoTILLING Molecular analysis of glycinin genes in soybean (Glycine max)
mutant lines.
Internship location in Canada/ Greenhouse and Processing Crops Research Centre,
Internship Duration/Durée du
Emplacement du stage
Harrow, Ontario
stage: 24 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: poysav@agr.gc.ca
d’AAC) Vaino Poysa
Phone/Téléphone: 1-519-738-1260
Name of Research Centre/Nom du Centre de Recherche : AAFC-Greenhouse and Processing Crops Research Centre
Mailing address/Adresse postale du Centre : 2585 County Rd. 20, Harrow, Ontario, Canada
N0R 1G0
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Dr. Vaino Poysa, Research Scientist – Soybean Breeding and Genetics
Other AAFC collaborators/Autre collaborateurs à AAC: Drs. K. Yu & S. Jegadeesan
University collaborators/Collaborateurs universitaires: Dr. Peter Pauls, U of Guelph
Industry partners/Partenaires industriels: Ontario Soybean Growers
B – Project Description: rational, objectives, outcome expected/Description du projet: rationnel, objectifs, résultats attendus
Background, Rationale, Issue / Context, Rationale, Problématique: Soy food quality is determined largely by soy seed
protein content and composition. Together glycinin (11S) and β-conglycinin (7S) proteins account for about 70% of the total
soybean seed proteins, with glycinin accounting for about 40%. Functional properties of soy proteins, such as gelation and
emulsification, are determined by the total and relative amounts of the different 11S and 7S protein subunits or peptides. Since
glycinin plays such an important role in the properties of foods made from soybean, the soy breeding program at Harrow has
developed lines with different protein subunit compositions. Understanding the genetic control for the presence or absence of a
specific protein subunit would help us to develop soybean varieties with optimal combinations of the protein subunits.
Glycinin has five subunits, coded for by five genes, divided into group-1(Gy1, Gy2 and Gy3) and group-2 (Gy4 and Gy5). We
have shown that the absence of the A4 peptide is conditioned by a single recessive null allele resulting from one base pair
mutation in the Gy4 gene. The absence of the A4 peptide has been associated with superior nigari tofu quality, while the
absence of A4 and 7S ά results in superior GDL tofu quality. We have developed a series of unique soy lines with various
protein subunit compositions, including lines lacking all 11S subunits and the 7S ά subunit, as well as various combinations of
the 11S subunits. The availability of the complete soy genome sequence combined with reverse genetics will facilitate the
identification of novel genetic variations in any gene affecting the phenotype. Targeting Induced Local Lesions IN Genomes
(TILLING) and EcoTILLING techniques are being used to discover polymorphisms in specifics gene in mutated and natural
populations respectively, providing guidelines to develop new strategies for genetic improvement of soybean.
Objective/Objectifs: (1) To study genetic variation behind different glycinin subunit mutant lines.
(2) To understand whether INDELs of structural genes or mutations of regulatory genes are involved in regulating expression
of glycinin genes. (3) To associate genetic variation (SNPs and INDELs) with protein subunit polymorphisms contributing to
improved soy food quality.
Outcome expected/Résultats attendus: New SNPs and other genetic variations identified in this study could be used as
genetic markers in breeding programs for quality improvement. Understanding the genetic control of soy protein subunits will
allow breeders to combine specific protein subunits to develop superior soybean cultivars for soy food production.
C –Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The internship at Harrow will be integrated into the soy breeding and molecular genetics labs, providing the PDF with an
opportunity to learn new techniques and improve their skills in breeding and molecular genetics. The candidate should have a
Ph.D. in molecular biology, plant breeding, plant biochemistry, plant biology or in a related field. The selected applicant will
be involved in the identification of SNPs and other genetic polymorphisms in soybean, cloning the different protein subunit
polymorphic gene(s), and sequencing the genes. The PDF will also assist in associating the polymorphism with protein quality.
The PDF will have the opportunity to learn more about Canadian agriculture and to observe a wide range of research activities
in a progressive AAFC Research Center.
(Update: January 28, 2009)
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2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID/ NO DU PROJET: 2009_Kentville_01
Back
PROJECT TITLE / TITRE DU PROJET: Manipulation of intestinal bacterial communities; an investigation into the
impact of dietary fibre and prebiotics.
Internship location in Canada/ Atlantic Food and Horticulture Research Centre,
Internship Duration/Durée du
Emplacement du stage
Kentville, Nova Scotia
stage: 12 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: KalmokoffM@agr.gc.ca
d’AAC) KALMOKOFF, Martin
Phone/Téléphone: 1-902-679-5374
Name of Research Centre/Nom du Centre de Recherche : AAFC-Atlantic Food and Horticulture Research Centre
Mailing address/Adresse postale du Centre : 32 Main St., Kentville, Nova Scotia, Canada B4N 1J5
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Dr. Martin Kalmokoff (Research Scientist), Food Safety and Quality
Other AAFC collaborators/Autre collaborateurs à AAC: Steve Brooks (Acting Chief, Bureau of Nutritional Research, Food
Directorate, Health Canada, Ottawa)
University collaborators/Collaborateurs universitaires: Julia Green-Johnson (Professor Immunology, University of Ontario
Technical Institute), Brent Selinger (Professor Microbiology, University of Lethbridge)
Industry partners/Partenaires industriels: Advanced Food and Materials Network (AFMnet)
B – Project Description: rational, objectives, outcome expected/
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
Emerging evidence indicates that the bacterial community associated with the gastro-intestinal tract plays an important role in
the health status of the host. Over the last decade there has been significant market growth in food products and ingredients
having health claims pertaining specifically to gut-health. These products represent a source for significant additional
economic value from the commodity food chain. However, health related claims require regulatory approval and it has been
recognized that current regulatory framework is inadequate to assess gut-health claims associated with these new and novel
food products. Furthermore, current approaches used by industry to justify health claims lack a firm scientific basis.
Traditional approaches for the analyses of gastro-intestinal communities are based on cultivation. Not surprisingly, many
foods having purported gut-health promoting properties base their health claims on the ability of these substrates to alter the
numbers of certain readily cultivable bacterial genera as proof of positive impacts on gut health. However, it is now recognized
that the vast majority of colonic bacteria have yet to be cultivated, and that cultivation alone provides a very limited and
skewed perspective on change within these microbiologically complex communities. Over the last five years molecular based
approaches have largely superseded cultivation-based community analysis. While these new phylogenetics-based approaches
have provided new insights into the complexity and composition of the communities found in a wide variety of animals, these
studies remain largely descriptive.
Objective/Objectifs: There are few studies which have used molecular based methods to analyze gut-community change in
response to dietary fibre, prebiotics or probiotics. However there is a need for functional-based studies so that change within
the colonic flora may ultimately be correlated with other indicators of gut-health. Our objectives are to understand how
different dietary fibre sources alter the colonic community and impact the immunological status of the host.
Outcome expected/Résultats attendus: Data generated from different dietary fibre sources using a single animal model will
establish a baseline useful to assess the properties of new and novel functional fibre sources. Understanding how dietary fibre
alters colonic communities will allow a more realistic basis to assess health claims and begin to correlate improvements in gut
health with colonic community composition. This data will be used by regulatory agencies to assess functional claims and by
industry to identify and characterization the activities of new functional dietary fiber sources.
C –Internship: Describe the internship program, qualifications of and the benefits to the expected intern / Stage:
Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The PDF will participate in an ongoing national collaboration aimed at elucidating the impact of different dietary fibre sources
on colonic community composition and the impact on the immunological state of the host using a rat nutrition model. It would
be advantageous for the PDF to have some previous experience in microbiology or molecular biology, although this is not an
(Update: January 28, 2009)
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2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
absolute requirement as we are willing to provide training. The PDF will participate in on-going animal feeding trials
involving various dietary fibre sources and interact with scientists and technicians at various locales in Canada. Change within
the colonic community in response to these fibre sources will be assessed using both cultivation dependent (anaerobic
cultivation) and cultivation-independent methods (16S rRNA libraries, DGGE). The PDF will gain experience in current
molecular methodologies useful for the analysis of complex microbial communities, where ever they may originate from.
Within the context of this main project are additional opportunities to carry out basic and applied research on a number of
related topics. Examples of this include studies on the characterization of new anaerobic bacteria, studies on structure/function
in anaerobic bacteria, metagenomic-based analysis of colonic communities and the genetic and physical characterization of
new fibre hydrolytic enzymes.
(Update: January 28, 2009)
Page 18 of 78
2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID/ NO DU PROJET: 2009_Lethbridge_01
Back
PROJECT TITLE / TITRE DU PROJET : Identification and selection of potato clones with novel starch properties for
food and industrial uses
Internship location in Canada/ Lethbridge Research Centre,
Internship Duration/Durée du
Emplacement du stage
Lethbridge, Alberta
stage: 24 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: BizimunguB@agr.gc.ca
d’AAC) Benoît Bizimungu
Phone/Téléphone: 1-403-317-2276
Name of Research Centre/Nom du Centre de Recherche : AAFC-Lethbridge Research Centre
Mailing address/Adresse postale du Centre : 5403- 1 Avenue S. P.O Box 3000, Lethbridge AB T1J 4B1
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) : Dr. Benoît Bizimungu, Research Scientist (potato breeding)
Other AAFC collaborators/Autre collaborateurs à AAC: Drs. Qiang Liu (Guelph) and Xiu-Qing Li (Fredericton)
University collaborators/Collaborateurs universitaires: Prof. Alan Sullivan and Prof. Ming Fan (U.Guelph), and Prof. Thomas
Wolever (U. Toronto)
Industry partners/Partenaires industriels:
B – Project Description: rational, objectives, outcome expected/
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique :
Potato has recently risen to the third rank among the most important food crops worldwide, with more than half of total
production generated from developing countries. To recognize the importance of the potato crop, the United Nations had
designated 2008 as the International Year of the potato. Potato is also a high value crop in Canada, and one of the most
important sources of dietary starch for many Canadian diets. Potatoes account for about 39 per cent of all fresh and processed
vegetables consumed in Canada, representing a total annual consumption of about 72.69 kg per capita. The newly ABIP funded BioPotato Network seeks to deliver bioproducts that address key issues concerning human and environmental health,
including the development of a low glycemic index potato, functional foods, and industrial starch. The production of new
potato germplasm high in slowly digestible or resistant starches and fibre content, tailored for the food sector which have
proven health benefits to the consumer, would be beneficial to the health and well-being of Canadians and increase the
markets of Canadian-based food industries and producers.
Objective/Objectifs: To develop new screening tools (including NIR spectrometry and/or molecular markers) for use in potato
breeding to develop germplasm with novel starch properties for food and industrial applications.
Outcome expected/Résultats attendus: Improved potato germplasm with low glycemic index, germplasm with novel starch
properties for food or industrial applications, new screening tools for the development of germplasm with altered starch
characteristics.
C –Internship: Describe the internship program, qualifications of and the benefits to the expected intern / Stage:
Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The candidate will be expected to participate in the screening and the development of potato germplasm with altered starch
characteristics for food and industrial uses, using NIR spectrometry and/or molecular markers. Ph.D. degree specializing in
plant/food science and familiarity with starch analysis and molecular markers are desirable.
(Update: January 28, 2009)
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2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID/NO DU PROJET: 2009_Lethbridge_02
Back
PROJECT TITLE / TITRE DU PROJET : Genetic engineering of cereal crops to produce novel starch
Internship location in Canada Lethbridge Research Centre,
Internship Duration/Durée du
Emplacement du stage
Lethbridge, Alberta
stage: 12 -24 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: luj@agr.gc.ca
d’AAC)
John Lu
Phone/Téléphone: 1-403-381-0118
Name of Research Centre/Nom du Centre de Recherche : AAFC-Lethbridge Research Centre
Mailing address/Adresse postale du Centre : 5403 - 1st Ave. S. Lethbridge, AB T1J 4B1 Canada
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Dr. John Lu, Bio-Products and Bio-Processes
Other AAFC collaborators/Autre collaborateurs à AAC: Drs. A. Laroche, D. Gaudet, F. Eudes
University collaborators/Collaborateurs universitaires: University of Alberta, University of Lethbridge
Industry partners/Partenaires industriels:
B – Project Description: rational, objectives, outcome expected/
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
Cereal crops represent one of the most important economic forces over the world. Scientists at Lethbridge Research Centre
have been working on improvement of wheat yield and quality for many years and already made significant contributions to
wheat production in Canada. Starch is the most abundant and renewable polysaccharide in cereal grains and can be produced
cost-effectively in vast quantities by using modern agronomic systems. Genetic modifications of cereal genotypes create a new
platform to produce value-added starches for carbohydrate-based industrial applications.
Objective/Objectifs:
Our research objective will be focused on genetic modifications of wheat and triticale genotypes to produce value-added
starches, such as amylose-free starches (waxy starches) and high-amylose starches (resistant starches), for industrial
applications.
Outcome expected/Résultats attendus:
This research project will turn out measurable and deliverable bioproducts (e.g. waxy and resistant starches) and biotechnology
(e.g. novel delivery system for genetic modification). Such outcomes can benefit the economy and also advance our knowledge
in plant sciences.
C –Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The post-doctor under this internship program will have the opportunity to employ the latest techniques for studying gene
isolation, expression, transient and whole plant transformation, quantitative real-time PCR, RNAi, and all other ancillary
biotechnologies. He/she will use these techniques to isolate and characterize the conserved domains of cereal starch syntheses
genes, to construct the expression vectors for RNAi function, to conduct the target gene transformations, to develop transgenic
wheat and triticale genotypes, and to evaluate the transformants for determining novel starch properties. The post-doctor will
be trained to conceive research objectives, design experimental approaches, conduct the independent researches, and analyze
the experimental results. He/she is required to have strong communication skills on speaking, reading, and writing in English,
and would be expected in preparation and presentation of experimental results at local or national conference and in preparation
of a manuscript on the work carried out in our labs.
(Update: January 28, 2009)
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PROJECT ID/ NO DU PROJET: 2009_Lethbridge_03
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PROJECT TITLE / TITRE DU PROJET : Assessment of molecular and genetic diversity in specific bacterial population
from beef cattle - Implications for the Food safety
Internship location in Canada/ Lethbridge Research Centre,
Internship Duration/Durée du
Emplacement du stage
Lethbridge, Alberta
stage: 12 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: sharmar@agr.gc.ca
Phone/Téléphone: 1-403-317-2232
d’AAC) Ranjana Sharma
Name of Research Centre/Nom du Centre de Recherche : AAFC-Lethbridge Research Centre
Mailing address/Adresse postale du Centre : 5403-1Ave. S, PO BOX 3000, Lethbridge, AB T1J 4B1, Canada
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Dr. Ranjana Sharma, Biotechnologist, Sustainable Production Systems
Other AAFC collaborators/Autre collaborateurs à AAC: Drs. Ed Topp, Tim McAllister,
University collaborators/Collaborateurs universitaires: Drs. L. Brent Selinger, James Thomas, Marie Louie, Ron Read (located
at Universities of Lethbridge and Calgary).
Industry partners/Partenaires industriels: awaiting confirmation
B – Project Description: rational, objectives, outcome expected/
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
The proposed research project is part of initiative of Agriculture and Agri-Food Canada (AAFC) aimed at assessing the
sustainability of current farming practices for livestock production and factors that enhance the food safety. The results from
the research will be of direct consequence to safe agri-food productions and at finding sustainable beef production practices
that are ecologically and environmentally sustainable. The proposed project will be focussed on Assessment of molecular and
genetic diversity in specific bacterial population from beef cattle – and has Implications for the Food safety. The
proposed research will address the impact of production environment and practices on the bacterial populations. The research
will use the bacterial isolates being currently collected from an ongoing animal trial at AAFC, Lethbridge.
Objective/Objectifs:
To quantify the specific bacterial population from the feces and rumen digesta samples from animals.
Specific objectives :
1) quantify specific bacterial populations from animal feces destined for the food chain using Real-Time PCR. Correlate the
quantification between samples derived from rumen vs. feces to understand the stability of specific population.
2) assess present role of diets and farming practices in affecting beneficial bacteria and identifying factors and/or conditions
that supports their growth.
Outcome expected/Résultats attendus:
The research will provide an integrated knowledge of beef production system with regards to specific bacterial quantification
and persistence in the food chain. These results will be useful in devicing food safety practices. The methods developed in the
study will provide diagnostic tools to detect, monitor and control bacterial related hazards in the food chain and environment.
The results from the study will provide data to better manage on-farm spread of specific bacteria. There is a need to establish
the prevalent methods of spread of antibiotic-resistant (AR) bacteria before we can develop and plan for mitigation strategies.
The results will identify ways to limit and and contain AR in food production.
The results will be applicable to agricultural industry since it has agricultural production base (meat and fish). The molecular
diagnostic techniques used in the proposed study are versatile and are applicable for addressing related food safety concerns.
Relevance to AAFC strategic priorities:
This proposal is closely aligned with two of the AAFC research priorities; namely “Enhancing environmental performance of
the Canadian agricultural system” and “Enhancing the quality of food and the safety of the food system”.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
Internship Program: The selected individual will be involved in molecular research using fecal samples derived from
(Update: January 28, 2009)
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animals. He/She would work in the laboratory of the PI with the aim of addressing the proposed objectives. The individual will
conduct experiments, compile and analyze data and will work on writing and presenting results for scientific audience.
Expected Student Qualification: The candidate must either have a Ph. D degree or in the final phase of completion of the
degree. Trained in Microbiology and Molecular Biology with knowledge of DNA/RNA extraction, PCR and Real-time PCR
analysis.
Benefits to the student: The individual will add to his/her abilities and skills in terms of experimental procedures and
techniques. He/She will get training in molecular fingerprinting and molecular quantitative techniques for specific bacteria.
These techniques are versatile in their application and can be applied for diagnostics and food safety issues such as bacterial
tracking through food chain. Application of these techniques will help to understand the critical mitigation points and the
measures required for safe food supply and reducing environmental pollution.
Apart from the technical skills, the individual will get adept with the scientific writing. Hence the work term will be highly
beneficial to the incumbent.
(Update: January 28, 2009)
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2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID/ NO DU PROJET: 2009_Lethbridge_04
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PROJECT TITLE / TITRE DU PROJET : Develop alternative growth promoter in ruminant production
Internship location in Canada/ Lethbridge Research Centre,
Internship Duration/Durée du
Emplacement du stage
Lethbridge, Alberta
stage: 12 months/mois
Contact: Wenzhu Yang
Email/Courriel: yangw@agr.gc.ca
Phone/Téléphone: 1-403-317-3427
Name of Research Centre/Nom du Centre de Recherche : Lethbridge Research Centre
Mailing address/Adresse postale du Centre : 5403-1 Ave. S. Box 3000, Lethbridge, AB, Canada T1J4B1
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: Dr. Wenzhu Yang, Sustainable Production Systems
Other AAFC collaborators/Autre collaborateurs à AAC: Dr. Maolong He
University collaborators/Collaborateurs universitaires: Dr. Burim Ametaj, University of Alberta
Industry partners/Partenaires industriels:
B – Project Description: rational, objectives, outcome expected/Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique: Rare earth elements (REE) including La, Ce and other
lanthanides are a group of elements with many similarities in chemical and biochemical characters. The REE have been used as
feed additives in animal production for more than twenty years in China, and have been recently shown, in Europe, improved
growth performance of pigs, poultry and calves. In Canada, we are the first to have conducted the studies using the REE in
animal nutrition. Our results indicated that supplementation of REE in media culture stimulated proliferation of 3T3-L1
preadipocytes, and affected the fatty acid composition in lipids accumulated in the cells. Supplementation of REE in the diet of
feedlot cattle increased dry matter disappearance in vitro that was resulted mainly from the increased of digestibility of fibre.
Including REE in the culture medium also stimulated ConA-induced splenocyte proliferation. The finding suggests a dietary
REE-mediated enhancement of immunological function that may contribute to improved immune response and possibly
prevent from disease. Given their potential but very limited information on their mode of action in animal, these elements
should be considered for a series of examination in vitro or in vivo to understand their potential activities.
Objective/Objectifs: to elucidate the mode of action of REE under continuous flow rumen environment or in animal, and to
define the optimum dosage of REE that could be safely used under feedlot cattle management system.
Outcome expected/Résultats attendus: The expected results of this project are to enhance the efficiency of feed utilization,
lower the cost of production, ameliorate immune status and animal health, and improve animal welfare. Another important
outcome of the proposed research is to decrease feedlot industry reliance on in-feed antimicrobials, lower the risk of antibiotic
resistance and its consequences to human health. The outcomes of the proposed work will have significant implications on the
sustainability of dairy and beef cattle production systems. The proposed research project is part of a larger and longer research
program aiming at developing nutraceuticals as new alternatives to in-feed antibiotics for use in livestock production systems.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The potential candidate will become a member of our integrated research team and is expected to have an in-depth knowledge
of biochemistry, ruminant nutrition, and immunology. More specifically, the student will be expected to: 1) use in vitro, in vivo
and molecular (Real-time PCR) techniques as research tools to assess the effects of REE on rumen bacterial composition and to
define the optimum conditions for application of these novel additives; 2) conduct in vivo studies to assess the effects of REE
on rumen fermentation, animal performance and modulation of immune status; 3) participate and learn diverse methods of data
entry and statistical analysis and report results in peer-reviewed scientific journals; 4) have good communication skills in both
oral and written English; and 5) work efficiently and effectively under minimum supervision.
The student will participate in a research program that consists of multiple-disciplinary scientists that closely collaborate with
research institutes and universities. The proposed work would allow the potential student to get acquainted with research
activities at a Canadian National Research Laboratory. The student will be trained how to establish a database and work with
them statistically, how to write and publish scientific papers in English peer-reviewed journals and present the data to
colleagues at scientific conferences.
(Update: January 28, 2009)
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PROJECT ID/ NO DU PROJET: 2009_Lethbridge_05
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PROJECT TITLE / TITRE DU PROJET: Hydrogen energy production through bio-fermentation of livestock manure
Internship location in Canada/ Lethbridge Research Centre,
Internship Duration/Durée du
Emplacement du stage
Lethbridge Alberta
stage: 12 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: haoxy@agr.gc.ca
d’AAC) Xiying Hao
Phone/Téléphone: 1-403-317-2279
Name of Research Centre/Nom du Centre de Recherche : Lethbridge Research Centre
Mailing address/Adresse postale du Centre : 5403 1st ave S, Lethbridge, Alberta, Canada T1J 4B1
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre): Dr. Xiying Hao, Environmental Health
Other AAFC collaborators/Autre collaborateurs à AAC: Drs. Chi Chang and Tim McAllister
University collaborators/Collaborateurs universitaires: Dr. Angus Chu, University of Calgary
Industry partners/Partenaires industriels: Canadian Cattlemen Association
B – Project Description: rational, objectives, outcome expected/
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
With the increase in Canadian intensive livestock production, animal manure management is often problematic and has been
associated with environmental problems such as water and air pollution, resulting in negative public reaction. If animal manure
could be used for bio-hydrogen production, this would not only contribute to better animal manure management practices but
also produce a clean fuel that reduces greenhouse gas emissions. Traditionally, animal manure is used to produce methane
through fermentation. However, unlike methane, hydrogen used as a fuel source will produce only H 2O, not CO2. Therefore,
there are advantages in producing hydrogen rather than methane from animal manure. More research is needed to investigate
the anaerobic fermentation conditions for different waste substrates and combinations, and to analyze the efficiency of mixed
waste sources for hydrogen production.
By understanding how the process works for various types of wastes and waste mixtures, schemes for the best utilization of
these different organic wastes will be developed. This will also provide data that is fundamental to the engineering of any fullscale facility designed to bioprocess waste for the generation of hydrogen, thereby contributing to Canadian bio-based energy
systems and technologies and reducing our reliance on fossil fuel.
Objective/Objectifs:
This research investigates optimal conditions to produce hydrogen gas using livestock manure and other organic waste.
The objectives of this project are to:
1) explore the factors affecting hydrogen production and optimize fermentation conditions and feedstock composition for
hydrogen production
2) explore the feasibility of applying 2-phase anaerobic digestion to hydrogen and methane production
3) genetically “finger print” the microbial community responsible for hydrogen production and explore potential use of
bacteria to increase hydrogen production
Cattle feedlot manure, liquid potato processing waste, and meat processing by-products (specified risk materials: SRM) will be
tested as substrates in this H2 fermentation study.
Outcome expected/Résultats attendus:
1) Recommendations for optimal conditions for hydrogen production using livestock manure and other organic waste.
2) 1 to 2 scientific manuscripts addressing hydrogen production through bio-fermentation of livestock manure.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
(Update: January 28, 2009)
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2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
Program:
The cattle feedlot manure will be incubated alone and in co-incubations in a continuously-stirred batch process at various
temperatures. Gas samples will be collected daily and the concentrations of H 2 and other gaseous products (CO2, N2, CH4)
will be determined. Slurry samples will also be taken throughout the fermentation process and analyzed to determine total
organic nitrogen, total organic carbon, available nitrogen, total carbohydrates, volatile suspended solids and microbial
community composition.
Experiments will be conducted to investigate (1) the effect of substrate:inoculum ratios used for co-fermentation of various
organic wastes with cattle manure on hydrogen production, (2) the effect of temperature shifts on hydrogen production,
and (3) the feasibility of applying 2-phase anaerobic digestion to hydrogen and methane production.
Anaerobic digestion will be divided into two stages; the first will emphasize hydrogen production (as in Experiment 1),
while the second will utilize the effluent from the first stage as a substrate for methane production. By using two digestion
stages, usable bio-energy in the form of hydrogen and methane is being produced, while increasing the stability of the
effluent generated. This will increase the total energy yield obtained while reducing the potential environmental impact of
effluent from the system.
Microbial analysis focusing on ‘genetic fingerprints’ of the overall community composition will be performed utilizing
denaturing gradient gel electrophoresis techniques targeting PCR-amplified 16S rRNA gene fragments. This will allow
comparisons between trials, aiding in the interpretation of the results obtained from chemical and physical analyses.
Qualification:
Ph.D. specializing in soil science, agronomy, biology or environmental chemistry.
Benefit to student:
The new PDF will interact and work side-by-side with other researchers in this group and gain first-hand knowledge on how to
conduct agronomical and environmental research. This includes how to design and plan the logistics to conduct rigorous
scientific experiments. The PDF will learn how to prepare, extract and digest livestock manure and other organic waste samples
and techniques to analyze these samples using an auto-analyzer, atomic absorption machine, and ion chromatograph and
analyze gas samples on gas chromatography (GS). The PDF will learn proper data management and record keeping and how to
conduct statistical analysis. Finally, the PDF will learn how to write scientific papers in English for publication. Being able to
work in an English environment and write papers in English is important to future international collaboration and ensures that
results are disseminated to the widest possible audience.
For the Lethbridge Research Centre, the opportunity to bring in top potential researchers from all over world helps us build
ongoing collaborations and international networks. These PDFs could be our research collaborators for many years to come.
(Update: January 28, 2009)
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PROJECT ID/ NO DU PROJET: 2009_London_01
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PROJECT TITLE / TITRE DU PROJET : Management of postharvest diseases in tree fruits
Internship location in Canada Southern Crop Protection and Food Research Centre Internship Duration/Durée du
Emplacement du stage
Vineland Station, Ontario
stage: 19 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: errampallid@agr.gc.ca
d’AAC) Deena Errampalli
Phone/Téléphone: 1-905-562-4113 ext. 234
Name of Research Centre/Nom du Centre de Recherche : AAFC-Southern Crop Protection Food Research Centre,
Mailing address/Adresse postale du Centre : 4902 Victoria Ave. N., Vineland Station, Ontario, L0R 2E0, Canada
Website/site Web: http://www4.agr.gc.ca/AAFC-AAC/display-afficher.do?id=1180640801098&lang=e
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) : Dr. Deena Errampalli,
Other AAFC collaborators/Autre collaborateurs à AAC: Dr. Peter Sholberg, AAFC, Summerland, BC
University collaborators/Collaborateurs universitaires: Dr. Jennifer DeEll, OMAFRA/University of Guelph
Industry partners/Partenaires industriels: Grape and Tenderfuit Ontario Ltd.
B – Project Description: rational, objectives, outcome expected/
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique: Field based horticultural crop production represents a
significant component of agriculture in Canada. To enable the year long supply of the fresh produce, producers from the
southern hemisphere countries were able to directly export their produce to the northern hemisphere countries and vice versa.
Long distance marketing for the horticultural crops was made possible by improved technologies in extending storage life of
the commodity, storage facilities and faster and better transport systems.
One such development in the recent years is the use of 1-methylcyclopropene (1-MCP) to preserve the quality of fresh produce.
1-MCP is an ethylene inhibitor. Ethylene is the precursor for disease resistance genes in plants. Dr. Errampalli’s research has
shown that the effect of 1-MCP depends on apple cultivars (Errampalli et al. 2007). One of the issues to be addressed is the
effect of 1-MCP on pears and peaches.
The second issue that affects the fruit quality is the postharvest diseases. Significant crop losses attributed to storage rots have
been reported worldwide. The control of postharvest diseases of apples and pears stored commercially depends on fungicides
applied as postharvest dips or drenches. Thiabendazole (TBZ, Mertect) was the only registered postharvest fungicide for apples
(until 2005) and the extensive use of this fungicide over two decades has resulted in the development of TBZ-resistant strains
of storage rot pathogens (Errampalli and Brubacher 2006). One of the fungicide resistance management strategies is to
alternate or combine fungicides with different modes of action. In recent years biological control agents, and new chemistries
that have different mode of action than the TBZ are being developed.
Objective/Objectifs: To determine the effect of 1-MCP on the management of postharvest diseases of tree fruits (apples, pears
and peaches) with a biological control agent and two reduced risk fungicides.
Outcome expected/Résultats attendus:
1) the effect of 1-MCP on diseases of apples, pears and peaches will be determined and 2) the efficacy of the control agents
against postharvest diseases of tree fruits in the presence of 1-MCP will be assessed.
References:
Errampalli. D., and Brubacher, N.R. 2006. Biological and integrated control of blue mold (Penicillium expansum) of apples
by Pseudomonas syringae and cyprodinil Biological Control 36:49-56.
Errampalli, D., DeEll, J. and Murr, D. 2005. Effect of 1-Methylcyclopropene treatment on postharvest decay in apple cvs.
Empire and McIntosh. Canadian Journal of Plant Pathology 27:467.
(Update: January 28, 2009)
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C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
Internship Program:
19 months:
August & September 2009 –May 2010:
A) Peach, pear and apple fruit will be harvested at the optimum commercial maturity required for long-term storage, and
treatment with 1-MCP. Fruit will be treated with reduced-risk fungicides and biological agent and stored for 8 months. All of
the pears and apples will be evaluated for disease incidence at monthly intervals (Lab and cold storage).
June-July 2010:
C) Data analysis from above experiments
August 2009-December 2010
D) Detection and identification of the pathogens with traditional and molecular techniques & data analysis.
E) Preparation of a research publication to be submitted to International scientific journal; will present results at a regional
conference.
Expected student qualifications : Ph.D. in Plant Pathology or Plant Sciences
Benefits to the student: The student will have an opportunity to work on a multi-disciplinary project (plant pathology and
plant physiology) and learn traditional and molecular techniques in the detection of the pathogens and identification of
diseases of tree fruits; 2) will prepare a report and have an opportunity to make research presentation at a regional conference
and finally, 3). will develop skills of collaboration and team work in a research laboratory in Canada.
(Update: January 28, 2009)
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2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID/ NO DU PROJET: 2009_London_02
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PROJECT TITLE / TITRE DU PROJET: Developing Novel Genetic Resistance to Plum Pox Virus
Internship location in Canada/ Southern Crop Protection and Food Research Centre,
Internship Duration/Durée du
Emplacement du stage
London, Ontario
stage: 24 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: wanga@agr.gc.ca
d’AAC) Aiming Wang
Phone/Téléphone: 1-519-457-1470 ext. 313
Name of Research Centre/Nom du Centre de Recherche: AAFC-Southern Crop Protection and Food Research Centre
Mailing address/Adresse postale du Centre: 1391 Sandford ST, London, Ontario N5V 4T3, Canada
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre): Dr. Aiming Wang, Genomics and Biotechnology
Other AAFC collaborators/Autre collaborateurs à AAC:
University collaborators/Collaborateurs universitaires: University of Western Ontario
Industry partners/Partenaires industriels:
B – Project Description: rational, objectives, outcome expected/
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
Plum pox virus (PPV) is the causal agent of the most devastating viral disease on many stone-fruit species (Wang et al. 2006).
It has been found in many fruit-producing countries. Currently there is no effective way to control the virus. No natural
resistance can be introduced into conventional breeding programs. The development of genetic resistance to PPV through
biotechnology becomes an attractive approach to the control of the virus. Like other plant viruses, PPV has a small genome and
thus must rely on host gene products (host factors) for translation, replication and infection. Mutation or silencing of these host
factors, yet dispensable for plant biology, will generate novel recessive resistance to PPV. Identification of host factors is
critical for the development of novel strategies against PPV.
Objective/Objectifs:
Recently using a number of genomics tools such as EST, cDNA-AFLP and microarray, the Wang lab has identified a few
hundred of candidate genes for host factors (Wang et al. 2005; Babu et al. 2008). The objective of this research is to screen for
recessive resistance genes from these candidate genes and further characterize these genes using Arabidopsis mutant lines.
Outcome expected/Résultats attendus:
This proposed project will advance our understanding of molecular PPV-host interactions and identify target genes for the
development of novel genetic resistance against PPV. Agriculture/horticulture development will directly benefit from this
research. The findings resulting from this research will be presented in academic conferences and submitted to peer-reviewed
journals for publication.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
This postdoctoral internship program will provide a postdoctoral scientist to work in this genomics and molecular virology
laboratory. Aiming at academic excellence, the hosting lab resides in a research centre equipped with state-of-the-art facility
for research in the areas of plant molecular biology, genomics, biotechnology and biochemistry. The hosting lab has extensive
experience in training technicians, postdoctoral scientists and graduate students with multicultural background. . The
postdoctoral scientist must be fluent in English and have basic knowledge and lab experience in plant molecular biology or
virology or microbiology. Under Dr. Wang’s direct supervision, the postdoctoral scientist will team up with an NSERC
Visiting Fellow and a molecular biology technician to conduct the project. Thus the postdoctoral scientist will receive extensive
training in the area of plant molecular biology/virology and biotechnology.
(Update: January 28, 2009)
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PROJECT ID/ NO DU PROJET: 2009_London_03
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PROJECT TITLE / TITRE DU PROJET : Functional genomic analysis of seed storage protein deficiency in common bean
(Phaseolus vulgaris): regulation of sulphur amino acid content.
Internship location in Canada/ Southern Crop Protection and Food Research Centre,
Internship Duration/Durée du
Emplacement du stage
London, ON
stage: 24 months/mois
Contact: Frédéric Marsolais
Email/Courriel: marsolaisf@agr.gc.ca
Phone/Téléphone: 1-519-457-1470 ext. 311
Name of Research Centre/Nom du Centre de Recherche : AAFC-Southern Crop Protection and Food Research Centre
Mailing address/Adresse postale du Centre : 1391 Sandford St., London, ON, N5V 4T3, Canada
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Dr. Frédéric Marsolais, Genomics and Biotechnology
Other AAFC collaborators/Autre collaborateurs à AAC: Dr. Sangeeta Dhaubhadel
University collaborators/Collaborateurs universitaires: Raju Datla, Gopalan Selvaraj, NRC-PBI, Saskatoon
Industry partners/Partenaires industriels: Saskatchewan Pulse Growers
B – Project Description: rational, objectives, outcome expected/
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue: In the past 15 years, Canadian acreage of pulses has grown by 400%, because of their high
value as export commodity, and significant environmental benefit due to reduced need for nitrogen fertilizer. Among pulses,
common bean (Phaseolus vulgaris) is dominant for human consumption worldwide, and an important source of vegetable
protein. Canada is the world’s second exporter of common bean. Despite their importance, common bean and other pulses lack
the genomic resources available for other major crops. This proposal will contribute to address this gap, while focusing on an
important seed quality trait.
The contents of sulphur amino acids in seeds of common bean and other grain legumes are suboptimal for nutrition. A
distinctive feature of Phaseolus and several Vigna species is the accumulation of high levels of a non-protein sulphur amino
acid, S-methyl-cysteine, in part as a γ-glutamyl dipeptide. S-Methyl-cysteine cannot substitute for methionine or cysteine in the
diet. In common bean, a deficiency in the major seed storage proteins, phaseolin, phytohemagglutinin and arcelin, results in a
significant increase in sulphur amino acid content, particularly cysteine (ca. 2-fold), mostly at the expense of S-methyl-cysteine
(Taylor et al. 2008 J. Agric. Food Chem. 56, 5647-5654). This increase brings the methionine and cystine content to levels
slightly above FAO guidelines on amino acid requirements for human nutrition.
Objectives: The objectives of this proposal are to achieve a detailed understanding of the S-methyl-cysteine metabolic
pathway, and the regulation of sulphur amino acid levels in developing seeds of common bean. To attain this objective, we will
develop a core platform for transcript profiling in pulse seeds, a 90K CombiMatrix microarray. Using this microarray,
transcripts will be profiled in developing seeds of two genetically related lines differing in seed storage protein composition,
and contrasted in S-methyl-cysteine and sulphur amino acid content. Five stages will be profiled, selected according to the
developmental profile of S-methyl-cysteine accumulation. Candidate genes will be validated and further characterized.
Outcome expected: The results of these studies will identify key biosynthetic genes controlling S-methyl-cysteine
accumulation, based on differential transcript accumulation among the two genetic lines. This research will provide insight into
how protein demand for sulphur regulates the levels of sulphur amino acids. The identity of associated metabolite signals will
be investigated. The microarray results will constitute a core resource to investigate other important seed traits and related
biochemical pathways, including raffinose oligosaccharides, vitamins and minerals, resistant starch and protein composition.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’ineterne.
The postdoctoral intern will participate in functional genomic research, including transcript profiling using a custom microarray
platform, data analysis and validation by quantitative RT-PCR. The derived hypotheses will be tested using a viral induced
gene silencing system, by the characterization of recombinant enzymes, and targeted biochemical analyses of metabolites. The
candidate should have a strong background in plant molecular biology and biochemistry. Dr. Frédéric Marsolais’ research
program focuses on the protein chemistry of pulse crops, and the metabolism of nitrogen and sulphur in developing seeds. Drs.
(Update: January 28, 2009)
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2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
Datla and Selvaraj at NRC-PBI will be responsible for the development and production of the Combimatrix array. Dr.
Dhaubhadel will provide support for the transcript profiling experiments. The intern will benefit from training in a research
centre having a strong track record and expertise in functional genomics of crops. The centre is located in a state-of-the-art
facility, equipped with all necessary instrumentation to carry out the research project.
(Update: January 28, 2009)
Page 30 of 78
2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID/ NO DU PROJET: 2009_London_04
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PROJECT TITLE / TITRE DU PROJET : Development of sustainable agricultural systems through an understanding of
interactions between microorganisms in the rhizosphere and corn roots
Internship location in Canada Southern Crop Protection and Food Research Centre,
Internship Duration/Durée du
Emplacement du stage
London, Ontario
stage: 12-24 months/mois
Contact: George Lazarovits
Email/Courriel: Lazarovitsg@agr.gc.ca
Phone/Téléphone: 1-519-457-1470 ext. 293
Name of Research Centre/Nom du Centre de Recherche : AAFC-Southern Crop Protection and Food Research Centre
Mailing address/Adresse postale du Centre : 1391 Sandford Street, London, Ontario, Canada, N5V 4T3
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor: Dr. George Lazarovits, Plant Sciences and Plant Protection
University collaborators: Dr. Manish Raizada, University of Guelph
Industry partners: Ontario Ministry of Agriculture and Food
B – Project Description: rational, objectives, outcome expected
Background, Rational, Issue:
We aim to reduce the cost of production of major crops of Canada, specifically corn, by reducing the need for chemical
fertilizers that continue to increase in price. This will also allow Canadian producers of corn to be more economically viable as
based on the Brazilian sugarcane model. We identified several root-associated microorganisms from Ontario-grown corn that
enhance the nutrient flow to corn roots, directly or indirectly. This can minimize the use of extraneous fertilizer and is useable
by organic growers. In greenhouse and field tests the bacteria consistently improved the growth of corn and also vegetable
crops. In initial tests, the growth promoting ability of the microbes appears to be cultivar-specific but not plant specific. Current
methods used to screen and measure microbial nitrogen fixation are time consuming and expensive. In this project we will
screen potential beneficial endophytic microbes using polymerase chain reaction assay (PCR) to identify microbes that have
potential biological activities such as N fixation, antibiotic production, phosphate solubilization, etc. The microbes selected will
bet tested in model assays for growth promotion under low N and P inputs, under disease pressures form various root
pathogens etc. For such information we will develop soil microbial inoculants as biofertilizers.
Objective :
1) Create a collection of known and potential microorganisms from the rhizosphere of corn and potato; 2) Identify potential
agents for plant growth promotion using known genes associated with such functions eg. N fixation, antibiosis etc. ; 3) Screen
such agents using model systems having low nutrient inputs and high disease pressures; 4) Develop some sense of mode of
action for the microbes using gnotobiotc assays where plants are grown in various substrates under limited nitrogen conditions;
5) Create consortia that may enhance plant growth; 6) Mark microbes with tags for rapid identification on/in root systems
Outcomes expected:
This project addresses the critical need for low cost biomass production based on ecological principles for plant cultivation. We
expect to identify an array of biological agents that enhance the fertility of various biofuel and food crops, developed novel
screening tools as to how to identify and quantify organisms in the rhizosphere, develop methods to bring them to commercial
use, and implement agricultural systems to maintain their populations in soil. We expect to enhance the science of soil
microbiology and the economic health of the biofuels and food production industry by delivering highly effective biofertilizers
for diverse crops.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne
The intern will participate in all aspects of our laboratories’ activity. Their specific tasks will be to isolate microbial agents
from the root zone and screen them using gene specific probes and PCR for specific genes considered beneficial to plant
growth. Using plant growth as an indicator they will screen these bacteria for growth promotion by exposing plants directly to
such agents and then growing them under various stress conditions. Consortia and individual microorganisms will then be field
tested for yield benefits. The candidate should have experience in microbiology, sterile technique and handling of plants for
growth assays. Some experience in molecular biology would be useful but is not a necessity. There will be opportunities to
interact with two postdoctoral fellows, graduate and udnergradute students.
(Update: January 28, 2009)
Page 31 of 78
2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID/ NO DU PROJET: 2009_London_05
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PROJECT TITLE / TITRE DU PROJET : Plant pathogenic Phytophthora: molecular determinants of virulence
Internship location in Canada/ Southern Crop Protection and Food Research Centre,
Internship Duration/Durée du
Emplacement du stage
London, Ontario
stage: 12 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: gijzenm@agr.gc.ca
d’AAC) Mark Gijzen
Phone/Téléphone: 1-519-457-1470 ext 280
Name of Research Centre/Nom du Centre de Recherche : AAFC-Southern Crop Protection and Food Research Centre
Mailing address/Adresse postale du Centre : 1391 Sandford Street, London, ON, Canada N5V 4T3
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Dr. Mark Gijzen, Genomics and Biotechnology
University collaborators/Collaborateurs universitaires: University of Western Ontario
Industry partners/Partenaires industriels: Ontario Soybean Growers, Soy20/20
B – Project Description: rational, objectives, outcome expected/
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue:
Plant pathogens destroy crops and impede production of food, fiber, and biofuels. Pathogens may also be invasive organisms
that damage natural ecosystems, parkland, and urban landscapes. Overall, plant pathogens threaten our security and quality of
life. Proper control of plant pathogens relies on a multitude of monitoring, diagnostic, and eradication techniques. Safer and
more effective control strategies for many plant pathogens are required, since these organisms are often overlooked and
understudied. This research is aimed at developing better management strategies for plant diseases caused by oomycetes,
especially species from the genus Phytophthora.
Objective/Objectifs:
This research is on a disease problem that affects all soybean growing areas. The disease is caused by a soil borne pathogen
Phytophthora sojae. It produces a root and stalk rot of soybean that reduces the yield and quality of the crop. The objective of
the research is to discover the molecular and genetic factors that mediate this host-pathogen interaction, for the purpose of
developing better diagnostic and control measures. Soybean losses due to Phytophthora root rot impact production wherever
soybeans are grown. Many other crops, ornamental plants, and even natural environments are damaged by Phytophthora
species, since these organisms are all destructive and invasive plant pathogens. The study of the interaction between P. sojae
and soybean additionally provides a model for other Phytophthora diseases.
Outcome expected/Résultats attendus: The expected outcome for the Postdoctoral candidate will be co-authorship on a
publication derived from the research project.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern / Stage:
Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The Postdoctoral candidate will be engaged in functional genomics work, using genome sequence information from the
pathogen (Phytophthora sojae) and from the host (Glycine max) to find targets for functional characterization. The genome
sequences of P. sojae and soybean (G. max) are now available and offer new opportunities for discovery. The candidate will
use bio-informatics to mine sequence and gene expression databases to select candidate genes that are likely to be important
determinants in the P. sojae - soybean interaction. For example, P. sojae genes that determine race-cultivar compatibility are
known as avirulence (Avr) genes. It is necessary to identify all the P. sojae Avr genes because this will greatly aid breeding and
diagnostics. Other genes that are crucial for pathogen growth in the host, and for soybean resistance to P. sojae, also need to be
identified. Candidate genes will be systematically chosen form genome sequence data and compared among different strains of
the pathogen or host cultivars. Bioassays will be preformed to measure the effect on the virulence and aggressiveness of the
pathogen, or level of resistance of the host. The work may also involve genetic mapping using molecular markers, and
expression of proteins in E. coli for purification and characterization. The candidate will benefit from working in a modern
biochemical laboratory engaged in molecular genetic and genomic research. The organisms under study are economically
important. The research is practically driven. The candidate will learn how to conduct experiments, assembly the results, draft a
manuscript, and carry this through to publication in a major international journal.
(Update: January 28, 2009)
Page 32 of 78
2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID/ NO DU PROJET: 2009_London_06
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PROJECT TITLE / TITRE DU PROJET: Developing reduced-risk and biological-based strategies for management of soilborne diseases of vegetable crops and promotion of plant growth
Internship location in Canada/ Southern Crop Protection and Food Research Centre,
Internship Duration/Durée du
Emplacement du stage
London, Ontario
stage: 24 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: Pervaiz.Abbasi@agr.gc.ca
d’AAC) Pervaiz A. Abbasi
Phone/Téléphone: 1-519-457-1470 ext. 696
Name of Research Centre/Nom du Centre de Recherche : AAFC-Southern Crop Protection & Food Research Centre
Mailing address/Adresse postale du Centre : 1391 Sandford Street, London, ON, Canada N5V 4T3
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) : Dr. Pervaiz A. Abbasi, Plant Sciences and Plant Protection
Other AAFC collaborators/Autre collaborateurs à AAC:
University collaborators/Collaborateurs universitaires:
Industry partners/Partenaires industriels:
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
Production of vegetables is vital to the economic health of a country. Plant diseases caused by various bacterial and fungal
pathogens are one of the key limiting factors in vegetable production with estimated annual losses of 8-23% or more in terms
of the yield and quality of the produce. Organic amendments animal by-products, poultry by-products, fish by-products, plantbased products, manures, and composts play an important role in organic production systems both as nutrient source and
disease management tools. It is now a well known fact that soil-borne plant diseases are less severe in organically-managed
soils than in conventionally-managed soils. Organic amendments can also provide an ideal matrix for delivery of bio-control
agents and can enhance the performance of a microbial product in the field. The main constraint in using organic amendments
for control of soil-borne diseases is the inconsistent field efficacy results and high rates of applications. Our focus is to
minimize this field inconsistency, enhance disease control effects, and reduce high application rates of organic amendments by
formulating them with known or other biological control agents. The organic amendments we are interested in include fish
emulsion, corn distillery products, composts, and any other products which are readily available in large quantities. Once
suitable combination of biological control agents and organic materials are established through growth room bioassays with
target soil-borne pathogens, efficacy of the formulated products can be tested under micro-plot or field conditions. We also
anticipate to tag our key bio-control agent with antibiotic resistance and GFP markers for monitoring its populations in the soil
and plant and to study its interactions with pathogens in the presence of organic materials.
Objective/Objectifs: Evaluate reduced-risk and biological-based strategies for managing damping-off, root rots, and wilts of
vegetable crops and enhance disease control effect of organic amendments with bio-control agents.
Outcome expected/Résultats attendus: The ultimate aim is to reduce pesticide use and minimize health impacts on humans
and environment, and to provide control measures for soilborne diseases in the organic production systems.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The applicant is expected to possess a Ph. D degree in Plant Pathology or any related discipline in Biological Sciences. The
internship will involve: developing or modifying or setting up plant bioassays, perform molecular biology techniques, isolate
and screen potential new biological control agents, and formulation work. The applicant will learn new techniques and the
internship will increase his/her knowledge and understanding.
(Update: January 28, 2009)
Page 33 of 78
2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID/ NO DU PROJET: 2009_London_07
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PROJECT TITLE / TITRE DU PROJET : Characterizing plant-produced human interleukin-24
Internship location in Canada/ Southern Crop Protection and Food Research Centre,
Internship Duration/Durée du
Emplacement du stage
London, Ontario
stage: 12 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: menassar@agr.gc.ca
d’AAC) Rima Menassa
Phone/Téléphone: 1-519-457-1470 ext 270
Name of Research Centre/Nom du Centre de Recherche : AAFC- Southern Crop Protection and Food Research Centre
Mailing address/Adresse postale du Centre : 1391 Sandford St, London, ON, Canada N5V 4T3
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Dr. Rima Menassa, Genomics and Biotechnology
Other AAFC collaborators/Autre collaborateurs à AAC:
University collaborators/Collaborateurs universitaires:
Industry partners/Partenaires industriels: Plantigen Inc.
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
The human interleukin-24 gene is being developed for the treatment of various cancers in humans, as it targets and causes
apoptosis specifically in cancer cells but not in normal cells. The gene has been shown to successfully reduce the size of
tumors when applied as gene therapy in an adenoviral vector. However, this delivery method does not provide enough IL-24 to
the tumors, and it is thought that applying enough recombinant protein directly to the tumors might achieve a stronger effect.
We have produced the human interleukin-24 protein in plants and plant cell lines. We would like now to characterize this
protein by determining its glycosylation patterns and biological activity. This characterization will allow us to define the
possible applications in cancer treatment of this recombinant protein.
Objective/Objectifs:
To determine expression levels of the recombinant protein in the plant cell lines
To purify the recombinant IL-24 from high expressing plant cell lines
To determine the glycosylation levels and patterns of plant-produced IL-24
To determine the biological activity of plant-produced IL-24 in cancer cell lines
Outcome expected/Résultats attendus:
One or two publications are expected to be published from the results obtained. We already have filed a patent application for
the production of IL-24 in plants. Further, a major outcome of this project will allow us to determine if plant-produced IL-24
can be used for the treatment of cancer
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The fellow will work within a broad program in molecular biology and biotechnology at the Agriculture Canada Research
Station in London, Ontario, which houses state of the art facilities for molecular biology research. The fellow will work
independently within a multidisciplinary team composed of plant scientists, immunologists and medical doctors to develop the
potential use of interleukin-24 as a cancer therapy. This position requires a strong background in protein expression and
purification, basic knowledge in immunology and cell culture, and an excellent mastery of the English language. This position
will allow the fellow to develop their scientific potential, and should lead to the publication of at least one scientific article.
(Update: January 28, 2009)
Page 34 of 78
2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID/ NO DU PROJET: 2009_Ottawa_01
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PROJECT TITLE / TITRE DU PROJET : Biological management of fusarium head blight in wheat
Internship location in Canada/ Eastern Cereal and Oilseed Research Centre,
Internship Duration/Durée du
Emplacement du stage:
Ottawa, Onatario
stage: 12 -24 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: axue@agr.gc.ca
d’AAC) Allen Xue
Phone/Téléphone: 1-613-759-1513
Name of Research Centre/Nom du Centre de Recherche : AAFC-Eastern Cereal and Oilseed Research Centre (ECORC)
Mailing address/Adresse postale du Centre : KW Neatby Building, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Dr. Allen Xue, Research Scientist, Plant Pathology
Other AAFC collaborators/Autre collaborateurs à AAC: Drs. M. Savard, H. Voldeng, G. Fedak
University collaborators/Collaborateurs universitaires: Dr. Tom Hsiang, University of Guelph
Industry partners/Partenaires industriels: Ontario Wheat Producers Marketing Board
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
Wheat is the largest crop in both Canada, and fusarium head blight (FHB) has been a devastating disease that causes extensive
yield and quality losses to wheat in both countries. Wheat cultivars with high levels of resistance to FHB are not yet
commercially available, and foliar application of fungicides has been the only mean to combat the disease in both countries.
However, the fungicide treatment is not desirable due to some adverse effects on the environment and ecosystem, and an
improved FHB management system with reduced fungicide use is urgently needed.
Since 2005, Dr. Xue at ECORC has led studies in identifying a more natural and environmentally acceptable alternative to the
existing chemical treatment methods. His research demonstrated that a strain of Clonostachys rosea, ACM941, and a strain of
Trichoderma harzianum, Tr14, and a strain of Bacillus subtilis ACO071 are effective bioagents against FHB pathogens in vitro
and in greenhouse and field conditions. A further in-depth research is underway to examine the mechanisms of these bioagents
against FHB pathogens, the population dynamics in various wheat production systems and their impact on reduction of initial
inoculum of FHB after foliar application, and the compatibility of bioagents with registered fungicides for potentially enhanced
effectiveness for the control of FHB. Research on the development of experimental commercial formulations are underway in
collaboration with Cornell University to make new biocontrol products more stable, effective, safe, and cost-effective.
Objective/Objectifs:
The objectives of this project are to evaluate selected microbe bioagents and formulated products of these bioagents for their
efficacy in reducing the initial inoculum by suppressing the perithecium production in various wheat production systems and in
reducing FHB disease severity, Fusarium damaged kernels, and Mycotoxin levels in kernels by foliar application, in
comparison with Folicur (tebuconazole) fungicide.
Outcome expected/Résultats attendus:
The successful completion of this project will lead to the development of commercial formulations of the bioagents. The new
technologies will be transferred to the grain industries through licences and technology transfer agreements to interested
companies. Results will be published in at least two peer-reviewed articles in scientific journals.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The PDF will work with members of the Crop Pathology Team at ECORC conducting majority of the research experiments to
evaluate and validate the efficacy of selected bioagents in controlling FHB. Depending on the PDF’s experience, training may
be provided in data collection, statistical analysis, and preparation of research reports and manuscripts. The PDF will also have
the opportunity to interact with a number of excellent scientists in cereal breeding, cytogenetics, mycotoxin, and molecular
biology at ECORC and University of Guelph. Candidates with some background training and experience in biological control
of plant diseases would be desirable.
(Update: January 28, 2009)
Page 35 of 78
2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID/ NO DU PROJET: 2009_Ottawa_02
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PROJECT TITLE / TITRE DU PROJET : Phytochemical Resistance Mechanisms to Corn Pests
Internship location in Canada/ Eastern Cereal and Oilseed Research Centre,
Internship Duration/Durée du
Emplacement du stage
Ottawa, Onatario
stage: 12 months/mois
Contact: Lana M. Reid
Email/Courriel: reidl@agr.gc.ca
Phone/Téléphone: 1-613-759-1619
Name of Research Centre/Nom du Centre de Recherche : AAFC-Eastern Cereal and Oilseed Research Centre (ECORC)
Mailing address/Adresse postale du Centre : Bldg. 99-Central Experimental Farm, 960 Carling Ave., Ottawa, ON, Canada
K1A 0C6
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) : Dr. Lana M. Reid, Research Scientist, Corn Breeding
Other AAFC collaborators/Autre collaborateurs à AAC: Xiaoyang Zhu, Biologist, Corn Pathology
University collaborators/Collaborateurs universitaires: Dr. John T. Arnason, University of Ottawa
Industry partners/Partenaires industriels:
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue: AAFC has developed many corn varieties with improved resistance to eight of the major
diseases of corn found in Canada. These resistant varieties were developed with conventional breeding protocols. In some
cases, it is not clear what the underlying mechanism of resistance to a given disease is. Understanding these mechanisms will
lead to the development of rapid screening tools to assist in the development of higher levels of resistance and a greater
understanding of the genetics of this resistance. Dr. Reid and Dr. Arnason have a long standing collaborative research program
to investigate phytochemical resistance mechanism in corn. Dr. Reid, as a corn breeder, and Mr, Zhu, as a corn pathologist,
breed and identify the resistant germplasm; Dr. Arnason, as a phytochemist, conducts the laboratory analysis of the potential
phytochemical resistance factors.
Objective/Objectifs: To further our investigations into the role of phytochemicals in resistance to corn diseases, with an
emphasis on di-ferulates and resistance to Fusarium species.
Outcome expected/Résultats attendus: Increased co-operation to further the development of corn varieties resistant to major
economically important diseases in both countries.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
In the summer and fall, the student will work primarily in the experimental plots of AAFC with Dr. Reid to learn corn breeding
and specifically, breeding for pest resistance. The PDF/student will learn how to inoculate plants with diseases, assess
resistance and collect plant tissue samples. In the winter months, the student will work at the University of Ottawa with Dr.
Arnason to conduct a phytochemical analysis of the samples he/she collected in the field. The intern will return to the home
country with a greater understanding of North American corn breeding and phytochemisty; the intern will learn how to
integrate this new knowledge into improving corn or other crop production in the home country.
Candidates should have some basic understanding of plant genetics and breeding and/or chemistry.
(Update: January 28, 2009)
Page 36 of 78
2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID/ NO DU PROJET: 2009_Ottawa_03
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PROJECT TITLE / TITRE DU PROJET: Management and total use of agricultural residues for biofuels, bioproducts and
bioenergy
Internship location in Canada/ Eastern Cereal and Oilseed Research Centre,
Internship Duration/Durée du
Emplacement du stage
Ottawa, Onatario
stage: 12-24 months/mois
Contact: Carlos Monreal
Email/Courriel: monrealc@agr.gc.ca
Phone/Téléphone: 1-613-759-1053
Name of Research Centre/Nom du Centre de Recherche : AAFC-Eastern Cereal and Oilseed Research Centre (ECORC)
Mailing address/Adresse postale du Centre : KW Neatby Building, 960 Carling Ave., Ottawa, ON, Canada K1A 0C6
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) : Dr. Carlos Monreal, Research Scientist, Environmental Health
Other AAFC collaborators/Autre collaborateurs à AAC: Drs. M. Schnitzer, R. Lemke, T. Huffman, E. Pattey, R. Desjardins
University collaborators/Collaborateurs universitaires: University of Ottawa and Carleton University in Canada, and other
foreign universities.
Industry partners/Partenaires industriels: Advanced Biorefineries Inc., Highmark Renewables, Enerkem Inc.
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
Agricultural residues, especially animal manures and crop residues, have no economic value in spite of their high nutrient and
energy content. The pathogens existing in animal residues create health related problems to humans and wildlife. Agricultural
residues may also contribute to environmental contamination with excess nutrients and GHG emissions. The disposal of the
latter residues in municipal landfills increases the cost of their disposal and the cost of food production to farmers and the agrifood industry and translates into higher food prices for consumers. In comparison, the use, conversion and processing of
agricultural residues alone or in combination with municipal, food, of forest residues into biofuels and bioproducts create new
economic opportunities in Rual communities by creating new value-added bioproducts in biorefineries.
Objective/Objectifs: a) to establish benefitial management practices for the handling of animal manures in the intern’s home
country; b) create value-added for agricultural residues through the production of bioenergy, biofuels and bioproducts derived
from the conversion of agricultural and other biomass; b) enhance knowledge on the carbon and nitrogen cycles associated with
agriculture in the northern and southern hemispheres; c) support the commercialization of leading-edge Canadian technologies
for the conversion of agricultural residues; and c) to enhance the environmental, economic and social performance of
agriculture.
Outcome expected/Résultats attendus: production of: i) second generation biofuels (i.e., biooil and biogas), ii) bioenergy
(electrical and thermal), and iii) bioproducts (i.e., polyesters for bioplastics, biofertilizers); ii) scientific R&D networks for
enhancing knowledge on the carbon and nitrogen cycles associated with cultivated land and food production systems; iii)
scientific and technical networks for the utilization of residues, and the reduction and monitoring of net greenhouse gas
emissions; iv) development and commercialization of Canadian technologies and bioprocesses.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The Post-doctoral fellow(s) will spend time in the lab of Dr. Monreal and others at AAFC and universities enhancing
knowledge of complex living and chemical systems, learning new techniques of nano- and bio-technology and developing new
knowledge and bioprocesses that will contribute to better manage carbon and nitrogen during food production and the
successful establishment of biorefineries in rural communities. Arrangements will be made with industry for the Post-docs to
spend time with Canadian industry and farmers for getting acquainted with leading-edge primary biomass conversion
technologies of pyrolysis, anaerobic digestion and gasification useful to farm operations and rural communities.
(Update: January 28, 2009)
Page 37 of 78
2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
PROJECT ID/ NO DU PROJET: 2009_Ottawa_04
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PROJECT TITLE / TITRE DU PROJET: Adapting micrometeorological techniques for verifying GHG emissions from
agricultural fields and paddocks to desired conditions
Internship location in Canada/ Eastern Cereal and Oilseed Research Centre,
Internship Duration/Durée du
Emplacement du stage
Ottawa, Onatario
stage: 24 months/mois
Contact: Elizabeth Pattey
Email/Courriel: elizabeth.pattey@agr.gc.ca
Phone/Téléphone: 1-613-759-1523
Name of Research Centre/Nom du Centre de Recherche : AAFC-Eastern Cereal and Oilseed Research Centre (ECORC)
Mailing address/Adresse postale du Centre : KW Neatby Building, 960 Carling Ave., Ottawa, ON, Canada K1A 0C6
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Dr. Elizabeth Pattey, Research Scientist, Environmental Health
Other AAFC collaborators/Autre collaborateurs à AAC: Dr. Ray Desjardins, Ward Smith, Dave Dow, Stuart Admiral
University collaborators/Collaborateurs universitaires: Dr. Ian Strachan
Industry partners/Partenaires industriels
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
National greenhouse gas (GHG) inventory calculation are developed using IPCC methodology. Countries are encouraged to
develop their own sets of emission factors which better accounts for the influence of environmental conditions and
management practices. This is referred as Tier 2 methodology in IPCC. The country-specific methodology can be further
refined by using process-based modelling in mass balance approach, which corresponds to a Tier 3 methodology. Using a
country-specific methodology is particularly important for calculating the nitrous oxide emissions from the agricultural sector.
Indeed, the complexity of biological and physical controls on microbial processes that generate N 2O in soils and animal wastes
has caused huge uncertainty in estimating N2O emissions from agricultural sources. More site-specific N2O emission factors
are needed for GHG inventories that account for variability caused by climate, soil and manure management, and topography.
Moreover, these site-specific datasets can be used to verify process-based models in preparation of Tier 3 approach. Any new
emission factors should be scientifically documented and peer-reviewed to be accepted in IPCC.
Nitrous oxide emissions are well-known to be highly variable over space and time. These emissions are driven by both
nitrification and denitrification processes. The latter takes place under anaerobic conditions and usually leads to higher N 2O
production. In order to capture the spatial and temporal variability at the scale of the production unit, (e.g., field, paddock,
manure storage facility), micrometeorological techniques need to be adapted to these appropriate scales and conditions. They
can provide N2O emissions on a continuous basis and with lower uncertainty than using a chamber approach alone, which
usually integrate emissions over a square meter or less, thus requiring scaling-up. Our laboratory has a long experience in
developing and refining micrometeorological techniques. The laboratory has four tunable diode lasers, all the software for
supporting the various techniques, more than a decade of experience in measuring N 2O emissions as testified by the scientific
publications on the topic. We also calculate the national GHG emisisons from the Canadian agricultural sector.
Objective/Objectifs:
Provide a post-doctoral internship on measuring N2O emissions from diffuse agricultural sources using several
micrometeorological techniques, in order for the target country to develop specific N2O emissions factors and verify the
performance of process-based models under the wide range of climate and soil environments that prevails in the target country.
Outcome expected/Résultats attendus:
This project will allow the training of highly qualified personnel in trace gas flux measurement using both tower and chamber
approaches. This expertise will be useful to setup a trace gas flux laboratory in the target country and establish collaborative
work with us.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The emphasis will be put on the micrometeorological approach and the PDF will become familiar with the operation of a
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tunable diode laser and other instruments used to measure fluxes from diffuse sources (such as sonic anemometers and infrared
gas analyzers). The intern will have the opportunity to use chambers and gas chromatograph for measuring GHG fluxes and to
analyze datasets from chambers and towers. The internship will cover the various phases of the experimentation, from setting
up and operating the equipment, acquiring and processing the data, analyzing the emissions with regard to the environmental
conditions and comparing the N2O emissions with estimates from models. The candidate will have the opportunity to be
exposed on how we compute the agro-environmantal indicator on GHG emission of Canada. The PDF should have a good
background in physics or meteorology, gas laws, statistics, ecology, knowledge in agricultural practices. The PDF will join a
team made of scientists, research professionals and a technician with complementary expertise, providing an opportunity to
cover the various phases of the research including the submission of scientific manuscript.
(Update: January 28, 2009)
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PROJECT ID/ NO DU PROJET: 2009_Quebec_01
Back
PROJECT TITLE / TITRE DU PROJET : Identification of functional markers associated to superior freezing tolerance
in alfalfa.
Internship location in Canada/ Soils and Crops Research and Development Centre,
Internship Duration/Durée du
Emplacement du stage
Québec City, Québec
stage: 12 months/mois
Contact: Yves Castonguay
Email/Courriel: yves.castonguay@agr.gc.ca
Phone/Téléphone: 1-418-210-5012
Name of Research Centre/Nom du Centre de Recherche : AAFC-Soils and Crops Research and Development Centre
Mailing address/Adresse postale du Centre : 2560 HOCHELAGA BLVD., QUÉBEC, QC, CANADA, G1V 2J3
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: Dr. Yves Castonguay, Scientist in Environmental Physiology, Sustainable Production Systems
Other AAFC collaborators/Autre collaborateurs à AAC: Dr. Annick Bertrand (biochemistry), Dr. Serge Laberge (molecular
biology), and Dr. Réal Michaud (forage breeding)
University collaborators/Collaborateurs universitaires:
Industry partners/Partenaires industriels:
B – Project Description: rational, objectives, outcome expected/
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
Alfalfa (Medicago sativa L.) is the most extensively used forage legume with 32 million hectares cultivated worldwide and 15
million hectares in North America. Alfalfa’s attributes include genetic variability/adaptability, growth on alkaline soils and
under reduced moisture, and a deep nitrogen-fixing taproot which improves soil structure and health. In addition to its large
economic value as a staple used by dairy and beef livestock producers, it is a strong biomass candidate for sustainable
production of ligno-cellulosic biofuel. However, cultivars currently available in Canada, suffer from recurrent winterkill as a
result of insufficient tolerance to subfreezing temperatures. In recent years, our group has applied an indoor screening method
to develop alfalfa populations selectively improved for their tolerance to freezing (TF populations). Several cycles of recurrent
phenotypic selection have been performed in various cultivars and large increases in freezing tolerance that translated into
superior field survival in the spring were documented. Further acceleration of the breeding process could be achieved by the
identification of DNA markers. For that purpose, the identification of functional markers derived from polymorphic sites
within genes associated to the trait will be required for the fixation of alleles in different genetic backgrounds without
additional calibration.
Objective/Objectifs: Using the Sequence Related Amplified Polymorphism (SRAP) technique, we have recently identified
several anonymous genomic DNA polymorphisms that increase in frequency with the number of cycles of selection for
improved freezing tolerance. Although the SRAP technique is a random PCR-based approach, primers are designed to
preferentially target coding sequences. Using already identified SRAP polymorphisms, the candidate will perform parallel
amplification with genomic DNA and cDNA templates from cold-acclimated plants in order to identify polymorphisms located
within functional sequences. DNA polymorphism putatively located within coding sequences will be cloned, sequenced and
analyzed for heir homology with sequences in databank. Candidate sequences will be validated for their linkage with freezing
tolerance using segregating genotypes individually scored for their freezing tolerance.
Outcome expected/Résultats attendus: Combination of unique genetic resources and molecular genetics techniques will
allow the identification of markers that can trace functional cold tolerance alleles during introgression into germplasm of high
agronomic value.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
Program: The project will be conducted over a one year period and will proceed according to the following schedule :
1- First trimester: Make an inventory of SRAP polymorphisms uncovered using populations recurrently selected for
superior freezing tolerance. Clone and sequence several (10-20) fragments that are polymorphic among populations
recurrently selected for superior freezing tolerance and that are equally amplified with genomic DNA and cDNA
templates.
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2- Second trimester: Search for homologies with sequences in data bank. Analyze correlation between the inheritance of
functional sequences and segregation of freezing tolerance within populations. Conduct multivariate analyses
(principal component and/or discriminant analyses) to identify groups of polymorphisms that are closely associated to
superior freezing tolerance.
3- Third trimester: Finalize analyses, write a scientific manuscript and prepare final report.
Expected qualifications: The candidate should have completed a PhD program in agricultural plant science in a recognized
university. She/he should have a background in plant breeding and have a good knowledge of the field of molecular genetics.
She/he should have expertise in PCR analyses, gene cloning and sequence analyses with bioinformatics software (BLAST,
FASTA). She/he should be familiar with data analyses including correlation and multivariate analyses using specialized
statistical software (e.g. SAS, Genstat). She/he should also have English language skills in speech and writing.
Benefits to post-doctoral candidate: The project will provide an excellent opportunity for the candidate to be trained to field
of molecular genetics for species with complex genome within a multidisciplinary environment involving a physiologist, a
biochemist, a molecular biologist and a plant breeder. She/he will have access to the latest techniques and equipment and will
work with a research team with a recognized expertise in forage breeding and physiology. The candidate will also have access
to data and genetic resources (genotypes, DNA, RNA samples) that are already available to initiate the project. This project
provides a good opportunity to learn techniques in molecular breeding of species with complex genomes.
(Update: January 28, 2009)
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PROJECT ID/ NO DU PROJET: 2009_Quebec_02
Back
PROJECT TITLE / TITRE DU PROJET : Develop a particulate phosphorus (PP) component for a risk indicator of water
contamination by P from Canadian agricultural land
Internship location in Canada/ Soils and Crops Research and Development Centre,
Internship Duration/Durée du
Emplacement du stage
Québec City, Québec
stage: 12 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: eric.vanbochove@agr.gc.ca
d’AAC) Eric van Bochove
Phone/Téléphone: 1-418-210-5050
Name of Research Centre/Nom du Centre de Recherche : AAFC-Soils and Crops Research and Development Centre
Mailing address/Adresse postale du Centre : 2560 Hochelaga Blvd, Québec, QC, G1V 2J3, Canada
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Dr. Eric van Bochove, Research Scientist in Water Quality
Other AAFC collaborators/Autre collaborateurs à AAC: Georges Thériault, Jean-Thomas Denault, Marie-Line Leclerc
University collaborators/Collaborateurs universitaires: Pr. Suzanne Allaire, Laval University, Quebec, QC; Pr. David Lobb,
University of Manitoba, Winnipeg, MB; Pr. Brad Joern, Purdue University, Indiana, USA
Industry partners/Partenaires industriels: None
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
Excessive amounts of P in surface fresh water contribute to eutrophication of rivers and lakes and to Cyanobacteria blooms.
The contamination of water is of greatest concern in areas where soil tests show high P levels, ability of soils to retain P is low,
susceptibility to runoff is high, macropore flow is high, soil erosion is high; and where connectivity to surface water and
artificial drainage are dense. Phosphorus from agricultural land is transported by surface runoff and drainage in variable
proportions of dissolved P (DP) and particulate P (PP). The Government of Canada has undertaken evaluation of the
performance of its agriculture and reporting on agri-environmental indicators. The indicator of risk of water contamination by
phosphorus (IROWC-P) has been recently developed at the national scale.
The IROWC_P algorithm aims to integrate both annual risks of water contamination by DP and PP for the agricultural land of
Canada at the watershed scale. IROWC_P is a multiplicative equation between phosphorus source (P_Source) and transporthydrology (T_H) components. P_Source represents the proportion of DP that can be potentially desorbed by agricultural soils
of a watershed during a Census of agriculture year. The T_H component integrates both DP and PP transport processes (surface
runoff, drainage and water erosion) as well as other factors accounting for hydrological connectivity between P source and
water bodies (topographic index, tile drainage, surface drainage and preferential flow). The total proportion of PP is indirectly
estimated by the amount of soil sediments removed by water erosion and transported to streams as a function of P saturation
expressed by P_Source. The P_Source component is a function of a 30-year cumulative P_Balance (1976 to 2006) and soil P
saturation. Final IROWC_P modified values were associated to five vulnerability classes (very low, low, moderate, high and
very high) on the basis of their respective distribution in 2006 to obtain a corresponding magnitude of risk for each agricultural
watershed at the scale of Fundamental Drainage Areas for all Census years. Finally, the risk was calculated for 279 watersheds
having more than 5% agricultural land to identify critical areas across Canada and temporal trend of P risk loss over 25 years
period (from 1981 to 2006).
Objective/Objectifs:
Develop the methodology to better estimate the risk of PP and bioavailable PP that can be released from agricultural land of
Canada by runoff events using available soil and watershed datasets at the national scale.
Outcome expected/Résultats attendus:
Literature review, concept and methodology integrating the new PP component to the IROWC-P indicator.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The post-doctoral fellow will be integrated in a bilingual team (French/English) of two research scientists, four research
professionals, post-doctoral fellows and graduate students with access to a laboratory of water quality and soil analyses and
GIS facilities working in collaboration with governmental organizations and universities across the country.
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The candidate should have a background and/or knowledge on the phosphorus cycle and/or soil science and/or soil hydrology.
Experience with risk indicators development and/or modeling will be an advantage.
The post-doctoral work will be integrated within a 4-yr national project and contribute significantly to the indicator
development leading to publication of peer-reviewed scientific papers in collaboration with the team of scientists partner in the
project.
(Update: January 28, 2009)
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PROJECT ID/ NO DU PROJET: 2009_Quebec_03
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TITRE DU PROJET : Fractions protéiques et glucidiques de diverses espèces fourragères
PROJECT TITLE: Protein and carbohydrate fractions in different forage species
Internship location in Canada/ Soils and Crops Research and Development Centre,
Internship Duration/Durée du
Emplacement du stage
Québec City, Québec
stage: 12 months/mois
Contact: Gaëtan Tremblay
Email/Courriel: tremblaygf@agr.gc.ca
Phone/Téléphone: 1-418-210-5048
Name of Research Centre/Nom du Centre de Recherche : AAC-Centre de recherche et de développement sur les sols et les
grandes cultures / AAFC-Soils and Crops Research and Development Centre
Mailing address/Adresse postale du Centre : 2560 Boulevard Hochelaga, Québec, QC, Canada G1V 2J3
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: Gaëtan Tremblay. Ph.D., Chercheur, Valeur nutritive des aliments du ruminant / Research Scientist,
Nutritive value of feedstuffs.
Other AAFC collaborators/Autre collaborateurs à AAC: Drs. Gilles Bélanger (agronomie et physiologie des plantes fourragères
/ forage crop physiology and agronomy), Yves Castonguay (physiologie végétale / plant physiology), Annick Bertrand
(biochimie / biochemistry), et/and Réal Michaud (génétique des plantes fourragères / forage breeding).
University collaborators/Collaborateurs universitaires: Dr. Guy Allard (agronomie des plantes fourragères / forage crop
agronomy), Université Laval, Québec.
Industry partners/Partenaires industriels: Novalait inc. (Corporation créée conjointement par les producteurs et les
transformateurs laitiers du Québec / A private corporation owned by Québec milk producers and processors).
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Contexte, Rationnel, Problématique: La dégradation intensive et rapide des protéines, combinée à une faible teneur en
énergie rapidement fermentescible dans les fourrages, causent une faible utilisation de l’azote des fourrages par les ruminants,
ce qui résulte en un excès d’azote excrété dans l’environnement.
Background, Rational, Issue : Intensive and rapid degradation of proteins combined with insufficient readily fermentable
energy in forages contributes to the poor forage N utilization by ruminants and, consequently, results in an excess of nitrogen to
be excreted in the environment.
Objectifs: Le projet global vise à augmenter l’énergie et l’azote protéique (fractions B2 et B3) des fourrages pour ainsi
améliorer les performances du ruminant via une augmentation de la prise alimentaire et de l’efficacité d’utilisation de l’azote,
causant du même coup une réduction des pertes d’azote dans l’environnement. Un des objectifs spécifiques est de caractériser
les fractions protéiques et glucidiques dans les espèces fourragères cultivées dans l’Est du Canada.
Objective : The overall project aims at increasing the content in energy and protein-nitrogen (fractions B2 and B3) of forages
with the ultimate goal of improving the performance of ruminants through an increase in intake and nitrogen utilisation
efficiency while reducing nitrogen losses to the environment. One of the specific objectives is to characterize protein and
carbohydrate fractions in different forage species grown in Eastern Canada.
Résultats attendus: L’estimation des fractions protéiques et glucidiques des différentes espèces fourragères, faites par
spectroscopie dans le proche infrarouge, sera utilisée par l’industrie pour formuler les rations des ruminants au Canada.
Outcome expected: Estimation of protein and carbohydrate fractions in different forage species, made using near infrared
reflectance spectroscopy (NIRS), will be used by the industry to formulate ruminant rations in Canada.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne :
Pour le stagiaire, le projet représente une excellente opportunité de faire partie d’une équipe multidisciplinaire dans le domaine
de la physiologie, de l’agronomie et de la valeur nutritive des plantes fourragères. Il travaillera dans un laboratoire utilisant de
l’équipement de pointe. Il utilisera les techniques de laboratoire permettant de doser les fractions protéiques et glucidiques,
ainsi que la technique de prédiction de ces fractions en utilisant la spectroscopie dans le proche infrarouge (SPIR). Le projet
sera réalisé entre octobre 2009 et octobre 2010 :
Octobre 2009-Février 2010: Balayage par SPIR des échantillons de fourrages prélevés au cours des étés 2007 et 2008.
(Update: January 28, 2009)
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2009 Postdoctoral Internship at AAFC / Stage postdoctoral 2009 à AAC
Analyses en laboratoire des fractions protéiques (Cornell Net Carbohydrate and Protein System,
Sniffen et al. 1992) et des fractions glucidiques (acides organiques, mono- et oligo-saccharides,
amidon, et fibres solubles dans un détergent neutre, Hall et al. 1999. J. Sci. Food Agric. 79:2079)
dans un certain nombre d’échantillons.
Mars 2010:
Calibration SPIR pour prédire les fractions protéiques et glucidiques dans tous les échantillons.
Avril 2010-Mai 2010:
Revue de littérature et analyse statistiques des données.
Juin 2010- Septembre 2010: Rédaction d’un manuscrit scientifique.
Le candidat sélectionné devra détenir un doctorat en phytologie ou en sciences animales avec expérience en laboratoire, dans
l’utilisation de la spectroscopie dans le proche infrarouge, et dans l’analyse statistique des données. Il devra avoir une bonne
connaissance de l’anglais parlé et écrit. La connaissance du français est un atout.
Internship: Describe the internship program, qualifications of and the benefits to the expected intern
The project will be an excellent opportunity for the postdoctoral student to be part of a multidisciplinary team in the area of
plant physiology, agronomy, and nutritive value of forage crops. She/he will work in the laboratory using the latest equipment.
The postdoctoral student will also use techniques for determination of protein and carbohydrate fractions, and for their NIRS
predictions. The project is scheduled from October 2009 to October 2010 and will be organized as follows:
October 2009-February 2010: NIRS scanning of forage species samples collected during the 2007 and 2008 summers.
Laboratory analyses of protein fractions (Cornell Net Carbohydrate and Protein System,
Sniffen et al. 1992) and carbohydrates fractions (organics acids, mono- and oligo-saccharides,
starch, and neutral detergent-soluble fiber, Hall et al. 1999. J. Sci. Food Agric. 79:2079) in a
subset of samples.
March 2010:
NIRS calibration to predict protein fractions and carbohydrates in all collected samples.
April 2010-May 2010:
Literature review, data and statistical analyses.
June 2010- September 2010:
Completion of a scientific manuscript.
The selected postdoctoral student should have a Ph.D. in plant or animal science with some experience in laboratory, NIRS
equation development, and in statistical data analyses. She/he should also have English language skills in speech and writing.
Having French language skills would be an asset.
(Update: January 28, 2009)
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PROJECT ID/NO DU PROJET: 2009_Quebec_04
Back
PROJECT TITLE / TITRE DU PROJET : Evaluation of invasive weed distribution and spread into crop fields
Internship location in Canada/ Centre de recherche et de développement sur les sols et les
Internship Duration/Durée du
Emplacement du stage
grandes cultures/Soils and Crops Research and Development stage: 12 months/mois
Centre, Québec, Québec
Contact: Marie-Josée Simard
Email/Courriel: marie-josee.simard@agr.gc.ca
Phone/Téléphone: 1-418-210-5044
Name of Research Centre/Nom du Centre de Recherche : AAC-Centre de recherche et de développement sur les sols et les
grandes cultures / AAFC- Soils and Crops Research and Development Centre
Mailing address/Adresse postale du Centre : 2560 boul. Hochelaga, Québec, QC, G1V 2J3, Canada
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: Dr. Marie-Josée Simard/Plant Ecologist-Weed Scientist
Other AAFC collaborators/Autre collaborateurs à AAC: Drs. Robert Nurse and Stephen Darbyshire
University collaborators/Collaborateurs universitaires: Dr. Claude Lavoie
Industry partners/Partenaires industriels:
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte/Rationnel/Problématique:
A striking number of invasive species are plants (Pimentel et al. 2005). Darbyshire (2002) estimated that 1-2 new species of
weeds become established in Canada every year and that this rate is increasing. Agriculture (new crops such as biofuels and
seed contaminants) is an important pathway of plant introduction into Canada (CFIA 2008). Nevertheless, the agricultural
linkage (as source of new propagules and as source of landscape) of plant invasions receives limited attention from invasion
ecologists that mainly study natural systems, or from weed scientists who typically investigate weed control in fields.
Pastinaca sativa L. (wild parsnip) is an invasive species of increasing agronomic importance in Canada whose landscape
dynamic deserves attention.
Pastinaca sativa is a biennial species that has spread from Eurasia into the American continent. The species, occasionally
referred to as Pastinaca sativa subspecies sylvestris, probably escaped from fields of the edible crop at the beginning of the
twentieth century (Rousseau 1968; Averill and DiTommaso 2007). Wild populations of Pastinaca sativa contain
furanocoumarins which cause severe skin photo-activated dermatitis in humans and livestock (Mitchell and Rook 1979) and
suppress herbivory (Berenbaum 1981; Zangerl and Nitao 1998). The species invades reduced-tillage cropping systems in
eastern Canada and is considered a noxious weed in Ontario (Darbyshire 2003) and several U.S. states. The presence of this
poisonous weed in hay severely decreases forage quality for on-farm use and closes or restricts markets for high-value eastern
Canadian hay commodities. Abundant along roadsides in eastern Canada, road networks could be contributing to the spread of
the species into crops and associated agricultural landscapes (DiTommaso pers. comm.). An evaluation of the historical and
current spread of the species could be used to test this hypothesis (Lavoie et al. 2005; Amor and Stevens 2008).
Objective/Objectifs:
Evaluate the historical distribution of Pastinaca sativa in Canada using herbarium records of the species and of other weeds.
Compare the historical distribution of Pastinaca sativa with that of other weeds not found along roadsides.
Evaluate the potential for spread by water along roadsides and by soil transport during road construction/refection.
Outcome expected/Résultats attendus:
Documenting the spread of the species in Canada will provide information on the interactions and dynamics of roadside weeds
with agro-ecosystems.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
Internship program description: The project (training) will be organized as follows:
Four months of herbarium data collection and literature update (September to December 2009);
Three months of herbarium data analyses (January to April 2010) and
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Four months of manuscript writing and occasional field work (participation in different phases of the field project, A-Base
funding) (May to August 2010).
Expected qualification:
The selected applicant should have a Ph. D. in weed science, plant ecology or botany or equivalent from a recognized
university. The selected intern should have a good knowledge of weed biology/dynamics, of statistical data analyses and of
science. The selected intern should also have some experience in computer mapping (GIS) and in the conduct of field
experiments.
Benefits for the student: The project will be an excellent opportunity for the intern to be trained with a multidisciplinary team
in the area of weed science, plant ecology and botany. He/She will have the opportunity to consult different national (Ottawa),
university (Québec) and provincial (Québec, Montréal) herbariums, use state of the art computer programs, write a manuscript
and participate in field experiment in Canada.
(Update: January 28, 2009)
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PROJECT ID/ NO DU PROJET: 2009_Saskatoon_01
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PROJECT TITLE / TITRE DU PROJET : Enhancing quality and function of recombinant proteins produced in seeds
Internship location in Canada/ Saskatoon Research Centre,
Internship Duration/Durée du
Emplacement du stage
Saskatoon, Saskatchewan
stage: 12 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: RozwadowskiK@agr.gc.ca
d’AAC) Kevin Rozwadowski
Phone/Téléphone: 1-306-956-7692
Name of Research Centre/Nom du Centre de Recherche : AAFC-Saskatoon Research Centre
Mailing address/Adresse postale du Centre : 107 Science Place, Saskatoon, Saskatchewan, Canada S7N 0X2
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre): Dr. Kevin Rozwadowski, Recombination Biology
Other AAFC collaborators/Autre collaborateurs à AAC: Drs. Dwayne Hegedus & Derek Lydiate
University collaborators/Collaborateurs universitaires:
Industry partners/Partenaires industriels:
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue: Seed-based synthesis of recombinant proteins is a highly attractive system for production of
industrial proteins (e.g. enzymes, fibres, etc.) due to the ease of scalability, transport and storage. We have advanced
technologies to promote accumulation of recombinant proteins. However, in addition to high-levels of accumulation, a
fundamental requirement of seed-based expression systems is ensuring recombinant proteins retain functionality. Recently it
has been demonstrated that seed proteins are extensively modified by carbonylation, an irreversible process involving the direct
oxidation of some amino acid residues and their covalent linkage to lipids and reducing sugars. This process results in the
inactivation of proteins and their increased proteolysis. Therefore, inhibition of the protein carbonylation process is an
important consideration to ensure production of functional recombinant proteins in seed-based protein expression systems.
Objective/Objectifs: The research will investigate the biology of protein carbonylation in seeds and development of methods
to inhibit this process to enhance accumulation of non-carbonylated, functional recombinant proteins in seeds. The
Arabidopsis model system will be used in these studies to investigate the biochemical pathways regulating oxidative state in
developing seeds and evaluation of methods to suppress oxidative damage of seed proteins. This will include characterising
mutant lines of Arabidopsis defective for genes involved in oxidative processes as well as creating transgenic lines expressing
candidate genes expected to reduce oxidative potential in the seed.
Outcome expected/Résultats attendus: The research in the Arabidopsis model system will identify strategies to reduce
oxidative damage and carbonylation of proteins in seeds. These results will be applied to oilseed crucifer crop species to
develop a platform for producing recombinant proteins in seeds to meet industry needs and provide an alternate revenue stream
for producers.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
Internship program—The postdoctoral intern will work in an established plant molecular biology lab conducting plant
biology research in a work group consisting of experienced technicians and other post-doctoral researchers. The intern will
participate in ongoing aspects of the research program and be responsible for an independent research project that is integrated
with the lab’s research program. The research will involve a wide-range of molecular biology, biochemistry and genetic
techniques including: gene cloning and engineering; protein engineering; protein purification and characterisation;
characterising seed and whole plant development and growth; generation and characterisation of transgenic plants.
Candidate qualifications—A Ph.D. in plant biology, preferably with experience in molecular biology, is required. Ability to
work independently, with good oral and written communication skills in English is also necessary.
Benefits to the candidate—The intern will develop comprehensive knowledge and skills in plant molecular biology
transferable to a breadth of possible subsequent studies in applied and basic plant biology.
(Update: January 28, 2009)
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PROJECT ID/ NO DU PROJET: 2009_Saskatoon_02
Back
PROJECT TITLE / TITRE DU PROJET : DNA recombination and repair in plants
Internship location in Canada/ Saskatoon Research Centre,
Internship Duration/Durée du
Emplacement du stage
Saskatoon, Saskatchewan
stage: 12 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: RozwadowskiK@agr.gc.ca
d’AAC) Kevin Rozwadowski
Phone/Téléphone: 1-306-956-7692
Name of Research Centre/Nom du Centre de Recherche : AAFC-Saskatoon Research Centre
Mailing address/Adresse postale du Centre : 107 Science Place, Saskatoon, Saskatchewan, Canada S7N 0X2
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre): Dr. Kevin Rozwadowski, Recombination Biology
Other AAFC collaborators/Autre collaborateurs à AAC:
University collaborators/Collaborateurs universitaires:
Industry partners/Partenaires industriels:
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue: DNA recombination and repair are essential biological processes that both maintain genome
fidelity in vegetative and germ-line cells and generate genetic diversity during meiosis. Double-strand breaks (DSBs) are
critical, potentially lethal, DNA lesions that result from normal metabolism, environmental stress and programmed cellular
processes. DSBs may be repaired by a high-fidelity, homologous recombination process or an error-prone, non-homologous
end joining mechanism. The research project will focus on DSB-repair systems in plants using the model plant Arabidopsis
thaliana and will build on a foundation of DNA repair research established in the Rozwadowski laboratory. The results will
contribute to developing effective approaches for manipulating DNA recombination processes in crop species to enable highfrequency gene targeting. Gene targeting is a process enabling precision engineering of plant genomes via using homologous
recombination to precisely alter the genetic sequence of a specified genomic target locus, as opposed to the random genetic
alterations resulting from conventional transgenic approaches. In addition, the results will be applied to developing systems for
controlling recombination frequency during meiosis, a capability that will enhance the efficiency of plant breeding programs.
Objective/Objectifs: The research will involve characterising Arabidopsis plants with altered DNA recombination potential
resulting from mutation of DNA repair genes or their overexpression through development of transgenic lines. The
characterisation will apply techniques already established in the lab and involve quantifying responses to DNA damaging
agents, evaluating for defects in DNA metabolism (e.g. replication defects) and signal transduction processes, as well as
defining altered growth and development. Candidate genes with pronounced effect on DNA repair capability will be applied in
transgenic approaches to alter recombination potential in vegetative cells and during meiosis.
Outcome expected/Résultats attendus: The initial research using Arabidopsis will identify genes and define strategies for use
in manipulating recombination frequency in plants. These results will be applied to manipulate recombination frequency in
crop species, particularly oilseed Brassica species, to accelerate plant breeding and enable direct optimisation of metabolic
pathways via in vivo protein engineering.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
Internship program—The postdoctoral intern will work in an established plant molecular biology lab conducting plant
biology research in a work group consisting of experienced technicians and other post-doctoral researchers. The intern will
participate in ongoing aspects of the research program and be responsible for an independent research project that is integrated
with the lab’s research program. The research will involve a wide-range of molecular biology, biochemistry, cell biology and
genetic techniques including: gene cloning and engineering; gene expression analysis; protein engineering; protein-protein
interactions; subcellular localisation of proteins through fluorescent protein fusions; SNP analysis, development and
characterisation of transgenic plants.
Candidate qualifications—A Ph.D. in plant biology, preferably with experience in molecular biology, is required. Ability to
work independently, with good oral and written communication skills in English is also necessary.
(Update: January 28, 2009)
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Benefits to the candidate—The intern will develop comprehensive knowledge and skills in plant molecular biology
transferable to a breadth of possible subsequent studies in applied and basic plant biology.
(Update: January 28, 2009)
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PROJECT ID/ NO DU PROJET: 2009_Saskatoon_03
Back
PROJECT TITLE / TITRE DU PROJET : Seed-based production of recombinant proteins
Internship location in Canada/ Saskatoon Research Centre,
Internship Duration/Durée du
Emplacement du stage
Saskatoon, Saskatchewan
stage: 12 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: RozwadowskiK@agr.gc.ca
d’AAC) Kevin Rozwadowski
Phone/Téléphone: 1-306-956-7692
Name of Research Centre/Nom du Centre de Recherche : AAFC-Saskatoon Research Centre
Mailing address/Adresse postale du Centre : 107 Science Place, Saskatoon, Saskatchewan, Canada S7N 0X2
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre): Dr. Kevin Rozwadowski, Recombination Biology
Other AAFC collaborators/Autre collaborateurs à AAC: Drs. Dwayne Hegedus & Derek Lydiate
University collaborators/Collaborateurs universitaires:
Industry partners/Partenaires industriels:
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue: Seed-based synthesis of recombinant proteins is a highly attractive system for production of
industrial proteins (e.g. enzymes, fibres, etc.) due to the ease of scalability, transport and storage. However, attempts to
accumulate novel proteins in seeds from transgenes have resulted in disappointing yields to-date. This is due to the
evolutionary programming of seed development to channel much of metabolism in the developing embryo to accumulate native
seed storage proteins (SSPs) which act as a reserve of sulfur and nitrogen for the germinating seed: this natural metabolic
programming commits metabolic resources to produce the native SSPs instead of the desired introduced recombinant protein.
Therefore, a practical approach to promote accumulation of recombinant proteins is to suppress the accumulation of the native
SSPs. The most efficient way to achieve this in crop species with complex genomes encoding large SSP gene families is
through expression of transcriptional repressors that directly inhibit expression of SSP genes. We have used genetic and
molecular approaches to develop candidate repressors that are effective in suppressing SSP accumulation
Objective/Objectifs: The research will investigate development and analysis of transcriptional repressors of SSP genes for
application to inhibiting SSP accumulation in oilseed crucifer species. Initial research will be conducted using the Arabidopsis
model system to characterise repressor candidates. This will involve engineering DNA binding proteins with protein domains
encoding repressor motifs or chromatin-remodelling components. Gene promoters specific for the maturation stage of seed
development will be identified. Transgenic Arabidopsis lines will be created using the promoter and repressor combinations
and characterised for SSP accumulation.
Outcome expected/Résultats attendus: The research in the Arabidopsis model system will identify repressor genes,
promoters and strategies for inhibiting the accumulation of SSPs. These results will be applied to oilseed crucifer crop species
to develop a platform for producing recombinant proteins in seeds to meet industry needs and provide an alternate revenue
stream for producers.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
Internship program—The postdoctoral intern will work in an established plant molecular biology lab conducting plant
biology research in a work group consisting of experienced technicians and other post-doctoral researchers. The intern will
participate in ongoing aspects of the research program and be responsible for an independent research project that is integrated
with the lab’s research program. The research will involve a wide-range of molecular biology, biochemistry and genetic
techniques including: gene cloning and engineering; gene expression analysis; protein engineering; protein-protein interactions;
promoter characterisation; characterising embryo, seed and whole plant development and growth; generation and
characterisation of transgenic plants.
Candidate qualifications—A Ph.D. in plant biology, preferably with experience in molecular biology, is required. Ability to
work independently, with good oral and written communication skills in English is also necessary.
(Update: January 28, 2009)
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Benefits to the candidate—The intern will develop comprehensive knowledge and skills in plant molecular biology
transferable to a breadth of possible subsequent studies in applied and basic plant biology.
(Update: January 28, 2009)
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PROJECT ID/ NO DU PROJET: 2009_Saskatoon_04
Back
PROJECT TITLE / TITRE DU PROJET : Formulation development for baculovirus
Internship location in Canada/ Saskatoon Research Centre,
Internship Duration/Durée du
Emplacement du stage
Saskatoon, Saskatchewan
stage: 12 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: hynesr@agr.gc.ca
d’AAC) Russell K. Hynes
Phone/Téléphone: 1-306-956-7638
Name of Research Centre/Nom du Centre de Recherche : AAFC-Saskatoon Research Centre
Mailing address/Adresse postale du Centre : 107 Science Place, Saskatoon, SK, Canada S7N 0X2
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Drs. Russell K. Hynes and Martin Erlandson
Other AAFC collaborators/Autre collaborateurs à AAC:
University collaborators/Collaborateurs universitaires: Dr. D. Korber, Department of Food and Bioproduct Science, Univ. of
Saskatchewan
Industry partners/Partenaires industriels:
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
The cabbage looper (Trichoplusia ni) (Lepidoptera: Noctuidae) has become a serious pest of greenhouse vegetable (tomato,
sweet pepper and cucumber) production in Canada due in part to the development of populations that are resistant to Bacillus
thuringiensis (Bt) based bioinsecticides. Baculoviruses provide an attractive alternative to Bt products for cabbage looper
control as they are highly infectious and typically host specific and therefore, compatible with IPM systems based on the use of
a complex of insect biological control agents. The Baculoviridae are a diverse family of rod-shaped, occluded viruses that have
circular dsDNA genomes ranging in size from 80 to 180 kb and are divided into two genera: the Nucleopolyhedrovirus (NPVs)
and the Granulovirus (GVs). Baculoviruses, TnSNPV and TnMNPV, have been evaluated as biocontrol agents for T. ni in cole
crops and deemed to have good potential for development as viral insecticides. Research studies conducted at AAFC Saskatoon
Research Centre have indicated that strain AcMNPV may have greater utility then other baculovirus strains tested. However, a
formulation technology for AcMNPV that promotes survival and application using conventional greenhouse delivery systems
is lacking.
Formulations are composed of i) an active ingredient, i.e. microorganism, microbial metabolite or natural product, ii) carriers,
often inert materials used to support and deliver a high concentrations of the biopesticide and iii) adjuvants, compounds that
promote and sustain the function of the biopesticide, provide protection from UV radiation, ensure attachment on the target,
promote the spread and dispersal of the biopesticide and if required retain moisture or provide protection against desiccation.
The scope of formulation types that can be investigated in this study can include, for example, wettable powders and
microencapsulation technologies for these baculovirus. This project will require i) screening of formulation components for
compatibility with survival and efficacy of AcMNPV with T. ni, ii) screening of formulation processing technologies such as
extrusion, spheronization and fluidized bed drying, and iii) survival and efficacy testing of formulated AcMNPV following
application using conventional greenhouse delivery systems.
Objective/Objectifs: The objectives of this research program are to i) develop formulation and application technologies for
biopesticides for insect pest management in greenhouse vegetable production, ii) promote the transfer of this technology to the
agriculture industry sector.
Outcome expected/Résultats attendus: Postdoctoral candidate will receive training in handling baculovirus, insect rearing,
plant cultivation, and biopesticide formulation development including operating the following equipment extruder, spheronizer,
fluidization bed dryer and particle sizer (Mastersizer 2000 laser scanning system).
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The internship program is for a post doctoral candidate at Agriculture and Agri-Food Canada and with potential for
collaboration with scientists at the University of Saskatchewan. Agriculture and Agri-Food Canada, Saskatoon Research Centre
(Update: January 28, 2009)
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is located on the campus of the University of Saskatchewan (http://www.usask.ca/). The Research Centre is equipped with
state-of-the-art equipment to carry out the research project described above.
Candidates must have graduated from a recognized university with a Ph.D. or an equivalent degree with expertise in
microbiology, entomology or plant pathology. The candidate must be proficient in the English language.
Under the advice and guidance of your supervisors you will conduct research that addresses the needs of the project described
above.
(Update: January 28, 2009)
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PROJECT ID/ NO DU PROJET: 2009_Saskatoon_05
Back
PROJECT TITLE / TITRE DU PROJET : Molecular characterization of wheat adaptation genes
Internship location in Canada/ Saskatoon Research Centre,
Internship Duration/Durée du
Emplacement du stage
Saskatoon, Saskatchewan
stage: 24 months/mois
Contact: Yong-Bi Fu
Email/Courriel: fuy@agr.gc.ca
Phone/Téléphone: 1-306-956-7642
Name of Research Centre/Nom du Centre de Recherche: AAFC-Saskatoon Research Centre
Mailing address/Adresse postale du Centre: 107 Science Place, Saskatoon, SK, S7N 0X2 Canada
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherché
Supervisor/superviseur: (name and title/ nom et titre): Dr. Christiane Deslauriers, Science Director
Other AAFC collaborators/Autre collaborateurs à AAC: Dr. Ron DePauw, Semiarid Prairie Agricultural Research Centre
University collaborators/Collaborateurs universitaires:
Industry partners/Partenaires industriels:
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique: Wheat is one of the most important staple crops worldwide. Wheat genetic improvement depends largely on genetic variability available in the adapted wheat gene pool. Molecular
characterization of diverse wheat germplasm provides essential information for understanding the genetic basis of wheat
adaptation and useful guidance to utilization of wheat germplasm for further genetic improvement. Recently, a number of
wheat genes associated with adaptation to environment stresses such as drought, salinity, winter hardiness, early maturity, have
been cloned. However, there is lack of detailed characterization of these adaptation genes in improved wheat gene pools.
Research effort is warranted to characterize and categorize the unique adaptation alleles for sustainable wheat improvement to
various environment stresses.
Objective/Objectifs: The overall goal is to enhance the utilization and conservation of diverse wheat germplasm. The specific
objectives are 1) to infer the genetic basis of wheat adaptation by characterizing adaptation genes and categorizing unique
adaptation alleles and 2) to develop effective strategies for searching unique wheat germplasm of wide adaptation.
Outcome expected/Résultats attendus: Information on wheat adaptation genes, a list of genetically unique wheat germplasm,
and scientific publications.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The Internship Program: The candidate is expected to conduct molecular research supervised by the research scientist by
planting wheat seeds in greenhouse, collecting leave tissue, extracting DNAs, performing sequence analysis of various
adaptation genes, analyzing sequence data with advanced bioinformatics tools, and publishing scientific findings.
Qualifications: The candidate should have a PhD degree in molecular biology from a recognized university, is proficient in
English, and is motivated to do independent scientific research.
Benefits to Student: Saskatoon Research Centre is a state of art plant biotechnology/ genomics research facility. The candidate
will have the opportunity to gain research experience in plant genomics and bioinformatics. The candidate will also have the
opportunity to interact with other research groups within and outside the centre through joint lab meetings, collaborations,
workshops and conferences.
(Update: January 28, 2009)
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PROJECT ID/ NO DU PROJET: 2009_Sherbrooke_01
Back
PROJECT TITLE / TITRE DU PROJET : Ammonia recovery by volatilization and capture
Internship location in Canada/ Dairy and Swine Research and Development Centre,
Internship Duration/Durée du
Emplacement du stage
Sherbrooke, Canada
stage: 12 months/mois
Contact: Lucie Masse
Email/Courriel: massel@agr.gc.ca
Phone/Téléphone: 1-819-565-9171 ext. 132
Name of Research Centre/Nom du Centre de Recherche : AAFC-Dairy and Swine Research and Development Centre
Mailing address/Adresse postale du Centre : 2000 COLLEGE STREET, PO BOX 90, STN LENNOXVILLE, SHERBROOKE,
QC, CANADA J1M 1Z3
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Dr. Lucie Masse, Environmental Health
Other AAFC collaborators/Autre collaborateurs à AAC: Dr. Daniel Massé
University collaborators/Collaborateurs universitaires:
Industry partners/Partenaires industriels: Bioterre System Inc.
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
Wastes generated by large animal farms or slaughterhouses often contain excessive amounts of nutrients for the regional
cultivated land base. Solid-liquid separators and biological reactors have been developed to concentrate phosphorous in the
solid fraction. However, the liquid fraction generated by these technologies still contains most of the ammonia. Excess nitrogen
can be processed in nitrification-denitrification bioreactors, but this system eliminates a valuable nutrient that could be used in
feed and food producing regions. The wastage of nitrogen means that additional inorganic fertilizers must be produced, using
an energy-intensive and greenhouse emitting process. On the other hand, the transport of manure and sludges is often
excessively costly given the low nitrogen concentrations compared to chemically produced nitrogen fertilizers. Also, organic
wastes may contain contaminants (e.g. pathogens) of volatile compounds (e.g. methane and CO2 precursors, NH3), that could
produce undesirable emissions during transport and land applications.
Our research team, composed of two research scientists, two technicians qualified in laboratory analysis, data acquisition
systems and mechanical engineering, as well as graduate and undergraduate students, has been actively working in the area of
nitrogen recovery. The project presented here would consist in developing a technology to volatilize ammonia in organic waste
and capture it in a clean and transportable medium. An experimental set up has been installed in our laboratory and analytical
procedures have been tested. We are now establishing the optimum conditions (pretreatment, pH, initial and final
concentration, receiving solution, temperature, air velocity, air/liquid contact, etc.) for the process. The setup has been linked to
membrane systems to create these optimum conditions. The laboratory also has anaerobic digesters that can provide treated
manure and slaughterhouse sludge effluents.
Objective/Objectifs:
The ultimate objective of the project is the development of a technology to volatilize and capture ammonia from liquid
manure, slaughterhouse sludges and anaerobic effluents. The end-produce would be a clean nitrogen fertilizer that could be
sold to feed and vegetable farmers as an alternative to chemical nitrogen fertilizers.
Outcome expected/Résultats attendus:
The outcomes expected from the one-year internship would be:
 the elaboration of optimum conditions for the operation of the system
 a list of technical specifications for the design of a semi-commercial scale pilot
the draft of a scientific paper
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The work of the intern would consist in:
1. familiarising him/herself with existing literature, based on a review already written by the project leader
(Update: January 28, 2009)
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2.
3.
4.
5.
6.
7.
writing experimental protocols
if required, modifying or improving the existing experimental setup
carrying the experiments – with the help the team technicians
supervising the laboratory analyses of the samples
analysing results and suggesting modifications to the procedures, protocols and experimental setup
write up the draft for a scientific article to be published in a referee journal
Qualifications:
 be able to read scientific articles in English and write protocols in French or English
 have a basic knowledge of waste composition and treatment systems, especially in the field of nutrient recovery
 have a good chemistry background
Benefits to the intern
 Acquiring experience in the emerging field of nutrient recovery, which aim is to reduce consumption of nonrenewable resources and limit the leaching and emissions of contaminants in the environment.
 Acquiring experience in environmental research in a well equipped governmental laboratory working with laboratoryscale as well as commercial scale treatment systems.
 Developing technical knowledge of treatment systems such as membrane filtration, anaerobic digestion, and
volatilisation/capture technologies.
(Update: January 28, 2009)
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PROJECT ID/ NO DU PROJET: 2009_Sherbrooke_02
Back
PROJECT TITLE / TITRE DU PROJET : Effect of vehicle design and transport distance on stress response and carcass
and meat quality of three pig lines
Internship location in Canada Dairy and Swine Research and Development Centre,
Internship Duration/Durée du
Sherbrooke, Quebec
stage: 12 months/mois
Contact: Luigi Faucitano
Email/Courriel: faucitanol@agr.gc.ca
Phone/Téléphone: 1-819-565-9174 ext. 237
Name of Research Centre : AAFC-Dairy and Swine Research and Development Centre
Mailing address : 2000 COLLEGE STREET, PO BOX 90, STN LENNOXVILLE, SHERBROOKE, QC, CANADA J1M 1Z3
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor: Luigi Faucitano, PhD, Bioproducts and Bioprocesses
Other AAFC collaborators : Nicolas Devillers, PhD and Stephanie Torrey, PhD
University collaborators : Linda Saucier (Laval University); Anna Bassols (University of Barcelona, Spain) and Matilde
Piñeiro (University of Zaragoza, Spain)
Industry partners: Breton Food
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue:
The higher susceptibility to stress of the Piétrain breed results in increased transport mortality rate and inferior meat quality. However,
it’s not sure whether the higher stress sensitivity is due to the high frequency of the so-called Halothane (HAL) gene in this genotype
or to the breed itself. The major international pig genetic companies are selling terminal boars of 25-50% Piétrain genetics in order
to take advantage of the high growth performance and carcass yield. However, the use of pigs of P genetics is more challenging in
North America given the difficult transport conditions (vehicle design, distance and climate). The transport factor contributed by 19%
to the mortality rate variation reported in a transport survey in Canada. Poor vehicle design may explain the effects of the transporter
on these mortality losses. In Canada pigs are mostly transported to slaughter using pot-belly trailers. This trailer design is not
considered suitable for swine transportation as it has a large number of steep ramps resulting in more stress during loading and
unloading with clear consequences on the incidence of deads-on-arrival and downers. Other common vehicle for swine transportation
is the flat deck trailer. Compared to the pot-belly trailer, the flat deck model is shorter to load and unload and produces less
casualties. However, like the pot-belly trailer, its effects on response and meat quality of pigs of different genetics transported
at different travel distance were never evaluated.
Objectives :
1) Study of the effects of vehicle design and transport distance on behaviour, physiology and carcass and meat quality of pigs;
2) Study of the response to transport stress in pigs of Halothane-free Pietrain pigs and its effects on carcass and meat quality
variation
Outcome expected:
The interest of swine producers towards pigs of Piétrain genetics is based on their higher feed efficiency, faster growth rate and
better carcass traits. However, their use is limited because of the high stress-susceptibility leading to two-fold higher transport
mortality and up to four times higher incidence of PSE pork. The recommendations for the preslaughter management of
Piétrain pigs arising from this study will be useful to producers who want to take advantage of the high performance and
carcass value of this genotype and, at the same time, limit the losses caused by death in transit or PSE pork.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
A post-doc student in Animal Science would qualify for this program. The intern will participate in the sample and data
collection at the farm and slaughter plant, laboratory analysis (blood analysis, body temperature and behavioural data
handling). The intern will get acquainted with the techniques for the assessment of animal welfare before slaughter and the online assessment of carcass and meat quality traits.
(Update: January 28, 2009)
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PROJECT ID/ NO DU PROJET: 2009_Sherbrooke_03
Back
PROJECT TITLE / TITRE DU PROJET : Factors influencing variations in milk protein constituents
Internship location in Canada/ Dairy and Swine Research and Development Centre,
Internship Duration/Durée du
Emplacement du stage:
Sherbrooke, Québec
stage: 12 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: Daniel.Ouellet@agr.gc.ca
d’AAC) Daniel Ouellet
Phone/Téléphone: 1-819-565-9171 ext. 209
Name of Research Centre/Nom du Centre de Recherche : AAFC-Dairy and Swine R&D Centre
Mailing address/Adresse postale du Centre : 2000, College street P.O. Box 90 STN Lennoxville, Sherbrooke (Québec) Canada
J1M 1Z3
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) : Dr. Daniel Ouellet, Sustainable Production Systems
Other AAFC collaborators/Autre collaborateurs à AAC:
University collaborators/Collaborateurs universitaires: Kevin Wade, Ph.D. Professor, McGill University; René Lacroix, Ph.D.
Professional associate, McGill University
Industry partners/Partenaires industriels: Daniel Lefèbvre, Ph.D. Director of R&D, Valacta
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
A better control by dairy producers on milk components that are produced at the farm is imperative for the dairy industry to
continue to grow. Factors that influence the distribution of the different fractions of protein and lipids are numerous and include
climate, breed, feed, genotype, stage of lactation, parity, etc. The focus of this project will be on milk protein constituents, for
which regional and seasonal variations have been observed in past studies. In order to better understand such variations and
factors influencing it, more than 900 milk samples were collected on about 30 dairy farms in Quebec between 2005 and 2008.
The samples were collected on test day on farms that were enrolled in a Dairy Herd Improvement (DHI) program with Valacta
inc. The DHI program involved the collection of milk recording data on each cow (e.g. days in lactation, disease), feed
recommendations and feed chemical analyses, and farm characteristics. Samples were collected for individual cows and from
bulk tanks (25% of the samples). Milk samples were analyzed in details (content and profiles) for fat and protein.
Objective/Objectifs:
The goal of the present project is to analyze factors that could lead to variations in milk protein constituents especially protein,
casein, urea, and whey, using results from milk sample laboratory analyses combined to DHI production and feed data.
Outcome expected/Résultats attendus:
The first outcome from this work it the establishment of mathematical relationships as the basis of a model relating feed and
management data to milk protein profiles. The proposed approach differs from previous studies in the sense that the model will
be based on data routinely collected on farms by a DHI. This allows for the application of the model to potentially all farms
using DHI feed services. In turn, this leads to two important outcomes: 1) the extension of the study by using the model with
the data from all those farms (i.e., several thousands in the Province of Quebec), to predict and analyze variations of the protein
profiles, 2) the eventual use of the model by DHIs to help dairy producers controlling the protein profiles of the milk that they
produce through management practices, including feed ration formulation.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The results of milk sample analyses (e.g., protein profiles) and the data provided by Valacta has been organized into a central
MySQL data base. The data can be accessed with analytical tool such as SAS. Analyses of this type of data is challenging and
required an expertise that has been traditionally mastered by animal scientists in the area of quantitative geneticist, and not so
much in the area of dairy cattle nutrition. Traditionally, research by this second group of researchers has been handled mostly
through physical experimentation. In this project, it is proposed to apply a quantitative approach in an area that includes dairy
nutrition, which will be the focus of the research of the postdoctoral fellow. The postdoctoral candidate needs a strong interest
and skills in mathematics/statistics and computer literacy. At the end of the project, the candidate will have developed deep
(Update: January 28, 2009)
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skills in handling and analysis of large data sets. The candidate will benefit from the expertise in feed nutrition and milk
components at the AAC experimental station in Lennoxville, quantitative analysis from researchers at McGill University
(Macdonald Campus), and DHI data characteristics from Valacta inc (Ste-Anne-de-Bellevue). The skills that will be developed
are increasingly in demand in most research areas, for example in genomics and proteomics.
(Update: January 28, 2009)
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PROJECT ID/ NO DU PROJET: 2009_SJSR_01
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PROJECT TITLE / TITRE DU PROJET : Use phytochemical as marker to select strawberry and raspberry lines for
processing (juice & fruit wine)
Internship location in Canada/ McGill University, St. Anne de Bellevue, Quebec and
Internship Duration/Durée du
Emplacement du stage
AAFC-Horticultural Research & Development Centre, St.
stage: 12 months/mois
Jean sur Richelieu, Quebec
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: khanizadehs@agr.gc.ca
d’AAC) Shahrokh Khanizadeh
Phone/Téléphone: 1-450-515-2058
Name of Research Centre/Nom du Centre de Recherche : AAFC-Horticultural Research and Development Centre,
Mailing address/Adresse postale du Centre : 430 Boul Gouin, St Jean sur Richelieu, QC, Canada, J3B 3E6
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherché
Supervisor/superviseur: (name and title/ nom et titre) Dr. Shahrokh Khanizadeh, Sustainable Production Systems
Other AAFC collaborators/Autre collaborateurs à AAC: Dr. Marie-Thérèse Charles
University collaborators/Collaborateurs universitaires: Dr. Katrine Stewart
Industry partners/Partenaires industriels: Lareault Nurseries and Phytoclone
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique::
Strawberries and raspberries are one of the leading small fruits in Canada. The major part of the production is consumed fresh,
and a large part of it is processed. Interest in polyphenolic compounds and antioxidant activity of fruits has been very high in
recent years owing to their contribution to sensory quality of fruit, juice, dried fruits, cider, frozen fruit treat, dried fruit bar,
and fruit roll ups and their possible relationship with shelf life and disease susceptibility. For the past few years, growing
interest has been devoted to the phytochemical content of the fruits and specific attention has been given to ellagic acid and
flavonoids. These compounds not only are known to influence quality, acceptability and stability of foods by acting as
flavorants, colorants or antioxidants but also act as defence mechanisms and also play an important role in senescence and the
ageing process and shelf life.
Substantial variation has been observed in Strawberries and Raspberries for biochemical content. As underlined by several
authors, the antioxidant profile of fruits need to be considered in breeding programs, along with field performance and
responses of the selections to cultural practices as well as harvest and post-harvest storage strategies in order to bred a locally
adapted disease resistant line. The use of chemical composition as marker assisted in breeding allows plant breeders to
significantly accelerate the speed of a natural (traditional) plant breeding program, without exposure to the unpredictable health
and environmental risks associated with genetic engineering techniques. The aim of this proposal is to identify the factors
controlling fruit quality specially for processing and develop a methodology and a model in order to reduce the time from
crossing to naming to select disease resistant lines with high fruit quality.
Objective/Objectifs:
Short term
1. Study and quantify the individual phenolic compounds in selected lines from an existing population.
2. Determine the affect of phenolic content and total antioxidant capacity on fruit quality.
3. Evaluate the affect of selected environmental factors on chemical and phytochemical composition.
4. In vitro evaluation of selected antioxidant and their interaction on selected diseases progress.
Long term
5. Development of a model to use chemical composition/phytochemical as marker to select high quality disease resistant
lines for processing (juice, dried fruits, cider, Frozen Fruit Treat, dried fruit bar, and fruit roll).
Outcome expected/Résultats attendus:
1. The out come will supply breeders with a tools, such as chemical markers linked to fruit quality and disease resistance, in
order to improve selection developing distinct strawberry and raspberry lines for processing e.g. juice, fruit wine, dried
and frozen fruit treat, fruit bar and roll ups.
2. Develop a new raspberry or strawberry lines suitable for processing useful to both countries
3. World-class scientific publication
(Update: January 28, 2009)
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C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
Agriculture and AgriFood Canada and McGill University are both prestigious research and teaching institution, well known in
Canada and abroad. It offers post graduate and post doctorate training to selected Ph.D. level. This program is emphases on
chemical composition in breeding as marker to identify lines for processing. The internship not only educates the candidate
academically but also allow him/her to get familiar with research conducted at federal research center. The proposed practices
not only are useful to Canadian public and industry but also will be applicable to other countries in agriculture. The candidate
has the opportunity to work with senior scientists/academic with many years of experience and extended number of publication
in this field. More specifically the candidate will benefit by improving his experience in fruit breeding and genetics, acquiring
in-depth understanding of bio-chemical and will be involved in preparing and submitting scientific publications while working
within a research team including industry, university and research centers.
(Update: January 28, 2009)
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PROJECT ID/ NO DU PROJET: 2009_SJSR_02
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PROJECT TITLE / TITRE DU PROJET : Impact of climate change and variability on the productivity of field grown
vegetable crops: A bioclimatic modelling approach
Internship location in Canada/ Horticultural Research & Development Centre,
Internship Duration/Durée du
Emplacement du stage
St. Jean sur Richelieu, Quebec
stage: 12 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: Gaetan.Bourgeois@agr.gc.ca
d’AAC) Gaétan Bourgeois
Phone/Téléphone: 1-450-515-2017
Name of Research Centre/Nom du Centre de Recherche : AAFC-Horticultural Research and Development Centre,
Mailing address/Adresse postale du Centre : 430 Boul Gouin, St Jean sur Richelieu, QC, Canada, J3B 3E6
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherché
Supervisor/superviseur: (name and title/ nom et titre) Gaétan Bourgeois, Ph.D., Bioclimatology and Modelling
Other AAFC collaborators/Autre collaborateurs à AAC: Dominique Plouffe, B.Sc.; Danielle Choquette, B.Sc.; Nathalie
Beaudry (Computer Specialist); Élizabeth Pattey, Ph.D.
International collaborators/Collaborateurs internationaux : Marie Launay, Ph.D. and Nadine Brisson, Ph.D. (INRA, Avignon,
France)
University collaborators/Collaborateurs universitaires:
Industry partners/Partenaires industriels: Diane Chaumont (Climate change specialist, Ouranos, Montreal)
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
Many crop growth simulators have been developed for field crops such as wheat, soybean, corn, etc. They have been used
mostly to improve our understanding of crop physiology and to some extent as decision support tools at the farm. One of these
tools is the software STICS, which was developed in France to simulate the effect of climate, soil, and crop management on the
production and the environment. It was conceived as a generic model, able to adapt easily to various kinds of plant. Many
physiological processes are included in this simulator, which makes it quite mechanistic by its internal complexity. Another
crop simulator is being developed by the research team in bioclimatology and modelling of AAFC. The simulator proposed,
named Sim2Cult, will also be generic but its internal structure will be much simpler by limiting the physiological processes to
the most critical ones in the prediction of crop productivity.
The two crop simulators indicated previously were adapted mostly for field crops (i.e. wheat, maize, soybean, etc.) and limited
adaptations have been done for field vegetable crops. Since 1990, in their studies on disease and insect forecasting, the research
team in bioclimatology and modelling of AAFC has accumulated many data sets on the phenology, growth, and yield of a
number of vegetable crops, namely carrot, onion, and celery. They also have access to historical climate data and future climate
scenarios that are required inputs to crop growth simulators. All these biotic and abiotic data are key elements for the
adaptation of crop simulators to these vegetable crops.
Objective/Objectifs:
1) Adaptation of two crop growth simulators (i.e. STICS and BDGSim) to carrot, onion, and celery; 2) Using different
simulation techniques, improve our understanding of the impact of climate change and variability on vegetable crop
productivity; 3) Propositions of crop management strategies to help the agricultural sector in their adaptation to climate change
and variability.
Outcome expected/Résultats attendus:
Adaptation of two crop growth simulators (i.e. STICS and BDGSim) to a number of vegetable crops; Evaluation of the
predictions with observed field data; Simulations over many historical climate data and future climate scenarios to assess the
impact of climate change and variability on vegetable crop productivity; Generation of important information to help the
agricultural sector in their adaptation to climate change.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
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Description of internship program: The PDF intern will be in charge of 1) reviewing the litterature, 2) adapting existing
bioclimatic crop simulators (i.e. STICS and Sim2Cult) to a number of vegetable crops, 3) evaluating the predictions with
observed field data, 4) simulating future crop productivity from climate change scenarios, and 5) preparing reports and/or first
draft of scientific articles.
Expected qualifications: Good knowledge of crop physiology and productivity; Basic knowledge in crop and/or pest
bioclimatic modelling; Efficiency in using computer software and handling large data sets; Interest in impacts of climate
change and variability on agriculture; Interest in mathematics.
Benefits to the intern: Scientific experience in bioclimatology and modelling research; Training with specialized software
developed for crop and pest modelling; Active participation in meetings of the research team where many aspects of
bioclimatic modelling are discussed; International collaborations and contacts in bioclimatology, crop modelling and climate
change; Possibility of co-authorship on a number of scientific articles; Improved understanding of the expected impact of
climate change on crop productivity and associated pests.
(Update: January 28, 2009)
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PROJECT ID/NO DU PROJET: 2009_StHyacinthe_01
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PROJECT TITLE / TITRE DU PROJET : Overproduction of extremophilic bacterial enzymes (lactase and lipase) for the
industrial applications
Internship location in Canada/ Food Research and Development Centre,
Internship Duration/Durée du
Emplacement du stage
Saint-Hyacinthe, Québec
stage: 12 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: leeb@agr.gc.ca
d’AAC) Byong H. Lee
Phone/Téléphone: 1-450-773-1105
Name of Research Centre/Nom du Centre de Recherche : AAFC-Food and Research Centre
Mailing address/Adresse postale du Centre C : 3600 Blv. Casavant West, St-Hyacinthe, QC, Canada J2S 8E3
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: Dr. Byong H. Lee, Principal Research Scientist, Bioproducts and Bioprocesses
Other AAFC collaborators/Autre collaborateurs à AAC: Drs. Normand Robert and Yves Arcand
University collaborators/Collaborateurs universitaires:
Industry partners/Partenaires industriels:
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
Although the genetics and molecular tools of common bacteria exist, knowledge is lacking behind with extremophilic bacteria.
We have screened several new strong promoters to express high level of enzyme expression and thus after the molecular tools
are available and molecular mechanisms are elucidated, a more rational approach to the overproduction of industrially
important enzymes and bioactive molecules could be possible. We have successfully over-expressed more than 1,000 folds of
(1) an aminopeptidase of Lactobacillus rhamnosus which has many applications in biotechnology and foods, (2) lipase of
Rhizomucor miehei (In-house invention, 2007), (3) esterase of Lactobacillus casei (Choi et al., 2004. Appl. Env. Microbiol.
70:3213-3221), lactase of Bifidobacterium (Hung et al.2001. Appl. Env. Microbiol. 67:4256-4263) and some have scaled-up
the fed-batch process in 150 liter fermentor, very little works have been carried out with the over-expression enzymes of
extremophilic bacteria which can grow at cold temperature (below 10 oC) or above 100oC, that are very useful for the industrial
applications in detergent, food, and biotechnology. Besides the application of hydrolytic lactase for (1) reducing lactose content
in milk and lactose intolerance in dairy products, (2) producing whey syrup sweeteners from lactose, lactase can produce (3)
galacto-oligosaccharides, GOS, as bifidus factors'-promoting the growth of desirable intestinal microflora. Lipases are
endowed with a substrate specificity surpassing that of any other known enzyme. This confers on the lipases an application
potential that is literally boundless (Jaeger and Eggert, 2002. Curr Opin. Biotech., 13:390-397).
Objective/Objectifs: The goal of this work is to (1) investigate the molecular basis of enzyme expression from extremophilic
bacteria, and (2) to apply this knowledge for the production of recombinant enzymes and bioactive molecules economically
important. The long term research program is to advance our understanding of gene function and expression of extremophilic
bacterial enzymes and the effects of these activities on the production of bioactive molecules.
Outcome expected/Résultats attendus: The extremophilic bacteria derived enzymes (lactase and lipase) which are either cold
temperature active or thermostable can have many applications in bioindustries.
After the overexpression system is developed, for the application of industrial scale, we will also find a fusion system that does
not need expensive materials for the purification. One of the attractive protein that be used as fusion protein is exoglucanase
Cex (47 kDa) from Cellulomonas fimi.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
Previously Dr. Jenny Blamey (jblamey@bioscience.cl), Research Director and me. Olivier Rickmers, President
(orickmer@bioscience.cl) requested me to collaborate on the extremophilic enzymes. This non-profit industry has expertise in
the extremophilic bacteria and has the best known sources of these bacteria in the world. The expected student qualification
should be a molecular biologist and biochemistry. If possible the funding for two years will be ideal for the project, but one
year for the first trial will be fine as well.
(Update: January 28, 2009)
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PROJECT ID/ NO DU PROJET: 2009_StJohns_01
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PROJECT TITLE / TITRE DU PROJET : Bioreactor micropropagation and genetic fidelity in berry crops
Internship location in Canada/ Atlantic Cool Climate Crop Research Centre,
Internship Duration/Durée du
Emplacement du stage
St. John’s, New Foundland
stage: 12 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: debnaths@agr.gc.ca
d’AAC) Samir C. Debnath
Phone/Téléphone: 1-709-772-4788
Name of Research Centre/Nom du Centre de Recherche : AAFC-Atlantic Cool Climate Crop Research Centre
Mailing address/Adresse postale du Centre : P.O. Box 39088, 308 Brookfield Road, St. John’s, NL A1E 5Y7, Canada
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) : Dr. Samir C. Debnath, Sustainable Production Systems
Other AAFC collaborators/Autre collaborateurs à AAC:
University collaborators/Collaborateurs universitaires:
Industry partners/Partenaires industriels: Cris Lester, Lester’s Produce Inc., St. John’s, NL, Canada; Mike Rabinowitz, Organic
Farm, Portugal Cove, St. Phillips, NL, Canada.
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
An improved understanding of the important role of dietary fruit in maintaining human health has led to a dramatic increase of
the global berry crop production and berry demand in recent years. While berry fruit have long enjoyed huge popularity among
consumers, tremendous progress in plant tissue culture, resulting in great advances in micropropagation, has occurred. Of
particular significance has been the evolution of the technology permitting multiplication of berry plants through bioreactor
micropropagation. Although automation of micropropagation in bioreactors has been advanced as a possible way of reducing
propagation cost, optimal plant production depends upon better understanding of physiological and biochemical responses of
plant to the signals of culture microenvironment and an optimization of specific physical and chemical culture conditions to
control the morphogenesis of berry plants in liquid culture systems. Clonal fidelity can be a serious problem and strategies have
been developed in order to reduce the variation to manageable levels. Molecular markers such as RAPDs, RFLPs, AFLPs,
DAFs, SCARs, SSRs, and ISSRs have been introduced in tissue culture research and can potentially be used in various facets
of pertinent studies with berry crops. The current program will focus on the bioreactor systems used for in vitro culture of berry
crops (raspberry and strawberry) and employment of molecular markers in micropropagated berry plants for the assessment of
genetic fidelity, uniformity, stability, and true-to-typeness among donor plants and tissue culture regenerants.
Objective/Objectifs:
1. To develop and improve in vitro techniques for strawberry and raspberry micropropagation using bioreactors.
2. To use genetic fingerprinting protocol to monitor trueness-to-type of micropropagated berry plants and to characterize novel
somaclones in strawberry and raspberry micropropagules.
Outcome expected/Résultats attendus:
1. Best cost effective propagation method using bioreactor will be developed.
2. Protocol to monitor trueness-to-type of micropropagules and somaclones will be developed.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The internship program will consist of culturing raspberry and strawberry explants on culture media, regeneration and
proliferation of microshoots, their rooting under in vitro condition and acclimatization of in vitro-derived plants under
greenhouse and field conditions. DNA isolation, PCR analysis, gel electrophoresis and PCR data analysis will be done
following standard procedures. The expected student qualifications will be a Ph.D. degree in biology, botany, biochemistry or
related science with experience in plant tissue culture and/or molecular analysis. The student will learn new techniques on in
vitro and molecular analyses and will be a co-author of peer-reviewed journal articles.
(Update: January 28, 2009)
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PROJECT ID/ NO DU PROJET: 2009_Summerland_01
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PROJECT TITLE / TITRE DU PROJET : Diagnostic Technologies and Management Strategies for Trunk Disease of
Grapevines in British Columbia
Internship location in Canada/ Pacific Agriculture Research Centre,
Internship Duration/Durée du
Emplacement du stage
Summerland, British Columbia
stage: 24 months/mois
Contact: Dan O’Gorman
Email/Courriel: Daniel.OGorman@agr.gc.ca
Phone/Téléphone: 1-250-494-6364
Name of Research Centre/Nom du Centre de Recherche : AAFC-Pacific Agriculture Research Centre
Mailing address/Adresse postale du Centre : 4200 Hwy. 97, Box 5000, Summerland, BC, Canada V0H 1Z0
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: Daniel O’Gorman (Biologist), Environmental Health
Other AAFC collaborators/Autre collaborateurs à AAC: Peter Sholberg, Karen Bedford, Paula Haag
University collaborators/Collaborateurs universitaires: Doug Gubler (UC Davis)
Industry partners/Partenaires industriels: BC Wine Grape Council
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
Vine decline includes a number of destructive trunk and root diseases of grapevines which are commonly found throughout the
grape growing regions of the world. Some of the most important of these diseases are Esca, Botryosphaeria canker and Black
Foot. All of these diseases reduce yields and increase production costs through the removal of diseased vines, re-planting with
new vines, and any control measures (cultural and chemical) undertaken to prevent or lessen disease severity. That being said,
in Canada there are no chemicals registered for grapes that show effective control of these pathogens. In addition, each of
these diseases is caused by multiple species of fungi which complicates the ability to obtain an accurate diagnosis. The
pathogens can also effect the vines in what is known as a disease complex (more than one pathogen attacking the vine) making
it potentially difficult to identify the correct management strategies. Therefore the development of an efficient and accurate
diagnostic tool and establishment of control strategies for regional environmental conditions are required to manage these
diseases effectively.
Objective/Objectifs:
1. (a) Development and validation of molecular diagnostic DNA macro-array for rapid and accurate detection of the numerous
fungal species responsible for each of these diseases (Esca, Botryosphaeria canker and Black foot). (b) Assessment of the DNA
array as a diagnostic tool to test for infection in mature vines from vineyards, as well as nursery stock samples to ensure clean
material prior to planting.
2. Evaluate disease management strategies: potential chemical and biological controls, as well as cultural practices suited for
the unique local environmental conditions. Suitable sites have been identified for Black foot and Botyosphaeria decline disease
management trials and we will also attempt to find appropriate sites to conduct trials for the management of Esca infected
vines.
3. Continued monitoring of local vineyards to: (a) confirm the identity of the species responsible for each of these trunk
diseases in BC; (b) identify disease symptoms, severity and spread; and (c) determine if these diseases are primarily occurring,
individually or collectively as a disease complex.
Outcome expected/Résultats attendus:
This multi year project will: (a) help identify which of the species exist in BC vineyards; (b) develop a comprehensive DNA
macro-array capable of detecting one or more pathogens in a single diagnostic test in field and nursery settings; and (c) help
identify control measures (biological, chemical and cultural) which will be effective in British Columbia’s unique climate
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
During the 24 month internship the candidate will be involved in: (a) the propagation and planting of the test vineyard; (b)
(Update: January 28, 2009)
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drafting of the experimental design and conducting both greenhouse and field trials; (c) work with the PI on the design,
development and validation of probes for the DNA array; and (d) oversee the disease survey and pathogen isolation and
identification. To accomplish the goals successfully, the project will require a team effort in both lab and filed work,.
However, depending on the qualifications and abilities the candidate, he or she may assume a lead role in as many facets of the
projects as they can manage. The candidate will gain experience with diagnostics and management strategies of trunk diseases
of grapevines, an important crop in both Canada and the intern’s home country. They will also gain experience in the design of
molecular diagnostic tools which are becoming increasingly important in plant pathology.
The candidate should have: (a) a strong background and experience in plant pathology and be comfortable with both lab and
filed work. (b) a good understanding of molecular biology with practical experience with molecular lab techniques being an
asset; and (c) a positive attitude and work well as part of a team.
(Update: January 28, 2009)
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PROJECT ID/ NO DU PROJET: 2009_Summerland_02
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PROJECT TITLE / TITRE DU PROJET : Evaluation of the breadth and durability of engineered resistance to Plum pox
virus based on the induction of RNA silencing
Internship location in Canada/ Pacific Agriculture Research Centre,
Internship Duration/Durée du
Emplacement du stage
Summerland, British Columbia
stage: 24 months/mois
Contact: Helene Sanfacon
Email/Courriel: SanfaconH@agr.gc.ca
Phone/Téléphone: 1-250-494-6393
Name of Research Centre/Nom du Centre de Recherche : AAFC-Pacific Agri-Food Research Centre
Mailing address/Adresse postale du Centre : PO Box 5000, 4200 Highway 97, Summerland, BC, Canada V0H 1Z0
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: Dr. Helene Sanfacon, Bioproducts and Bioprocesses
Other AAFC collaborators/Autre collaborateurs à AAC:
This proposal is in the context of a large collaborative project aimed at engineering resistance to Plum pox virus (PPV) in
peach. AAFC collaborators on the PPV project are: Drs. Dan Brown, Lining Tian and Aiming Wang (AAFC-London), Dr.
Antonet Svircev (AAFC-Vineland) and Dr. Brian Miki (AAFC-Ottawa). The proposed research will be conducted in the
Sanfacon laboratory in Summerland.
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
Durable eradication of PV in Canada will only be possible if elimination of infected plants in the field is accompanied with
approaches to prevent future reintroduction of the virus. The generation of PPV-resistant peach germlines is necessary to
accomplish this objective. We have developed strong resistance to PPV in model herbaceous hosts and in plum lines (Zhang et
al, 2006. Can. J. Plant Pathol. 28, 263) . The resistance is based on the induction of PPV-specific RNA silencing in plants.
Because of the high level of resistance obtained, this approach is the most promising technology for delivery to the industry by
2011. Regulatory approval of transgenic PPV-resistance requires supporting research to document the stability and breadth of
the resistance
Although strong resistance to the Canadian isolate of PPV was demonstrated, further research is required to study the breadth
of the resistance to other PPV isolates. In collaboration with Dr. Ravelonandro (INRA-Bordeaux, France), we have confirmed
that transgenic lines developed in Canada are resistant to a collection of European PPV isolates. However, the strength of the
resistance varies somewhat with the isolate considered. RNA silencing is a natural antiviral resistance mechanism in plants
that directs degradation of the viral genome in a sequence-specific manner. Many (but not all) plant viruses are known to
encode proteins that can suppress RNA silencing. To evaluate the breadth and stability of the PPV resistance, it is important to
determine the relative ability of various PPV isolates to evade or suppress the engineered resistance. Because other peach
viruses are sporadically present in peach orchards in Canada, we also want to determine whether they can suppress RNA
silencing.
Objective/Objectifs:
- Compare susceptibility of European and Canadian PPV isolates to RNA silencing in transgenic lines using sensor assays
(portion of viral genome fused to fluorescent protein for visual detection of silencing and accelerated resistance assays); i.e.
determine whether European PPV isolates can transiently evade silencing.
- Evaluate silencing suppression activity in European and Canadian PPV isolates.
- Continue an in-depth study of the interaction of other peach viruses with the RNA silencing pathway (see Jovel et al, 2007.
J. Virol. 81, 12285-12297 for results obtained to date).
Outcome expected/Résultats attendus:
- Supporting documentation regarding the strength, breadth and stability of PPV-resistance for regulatory acceptance and
commercialization
- Increased understanding of the interaction between peach viruses and the plant RNA silencing pathway for eradication of
PPV and improved management of other viruses
(Update: January 28, 2009)
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C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
Funding for this research has been secured until April 2011. Dr. Sanfacon is a recognized leader in the field of molecular plant
virology and has demonstrated expertise in the proposed research as evidenced by publications in high-impact international
scientific journal. The research station is well equipped for research in molecular plant virology. Dr. Sanfacon leads a team of
technicians, post-doctoral fellows (PDF) and Ph.D. students offering a dynamic environment for post-doctoral research. The
research proposed will allow the student to develop expertise in an exciting, leading-edge field of research. Although the
proposed research is aimed at the study of plant viruses occurring in Canada, the technology and expertise developed by the
applicant will be directly applicable to the study and management of plant viruses in the home country.
The PDF applicant must have previous experience in molecular plant biology and must have a Ph.D. in molecular biology or
biochemistry from a recognized university. Previous experience with plant viruses would be an asset but is not required. The
applicant must have a good command of the English language and must be prepared to work well with a team of researchers
coming with various backgrounds and cultures.
(Update: January 28, 2009)
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PROJECT ID/ NO DU PROJET: 2009_Summerland_03
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PROJECT TITLE / TITRE DU PROJET : Biological control of orchard insect pests
Internship location in Canada/
Pacific Agriculture Research Centre,
Internship Duration/Durée du
Emplacement du stage
Summerland, British Columbia
stage: 24 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: Joan.Cossentine@agr.gc.ca
d’AAC) Joan Cossentine
Phone/Téléphone: 1-250-494-6366
Name of Research Centre/Nom du Centre de Recherche : AAFC-Pacific Agri-Food Research Centre
Mailing address/Adresse postale du Centre : 4200 Highway 97, Box 5000, Summerland, BC, Canada, V0H 1Z0
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Dr. Joan Cossentine, Research Scientist, Environmental Health
Other AAFC collaborators/Autre collaborateurs à AAC: Dr. Gary Judd
University collaborators/Collaborateurs universitaires:
Industry partners/Partenaires industriels: BC Fruit Growers Association, Okanagan-Kootenay Sterile Insect Release Program
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
Apple and pear orchards in British Columbia, Canada have benefited from the worlds largest area-wide control program for the
key apple pest, the codling moth, for the last 15 years. The program is based on the release of sterile males, however integrates
other codling moth control strategies including mating disruption and the codling moth granulovirus. Without the use of broadspectrum chemical insecticides, the introduction or use of parasitoids may be justified to supplement fruit pest suppression. The
exotic codling moth parasitoid, Mastrus ridibundus, is being considered for introduction as it shows excellent potential to find
and suppress low residual codling moth populations which are characteristic of area-wide control orchards. The program
maintains a mass codling moth rearing facility that could be used to rear parasitoids however the technology and economics
need to be developed and evaluated as well as a thorough field efficacy evaluation of parasitoid releases.
Integrating biological controls makes the possibilities for pest suppression more complex. Parasitoids not only suppress insect
pest populations by parasitizing and killing hosts, but have also been shown to enhance entomopathogenic biological control
agents, by mechanically transmitting them to host larvae. Ichneumonid parasitoids, such as Mastrus species also inject a
polydnavirus into host larvae to suppress their immune response. The suppression of the host’s immune system has been
recorded to enable baculoviruses to cause virus-induced mortality in parasitized hosts. Wild orchard codling moth populations
could experience previous exposure to sublethal concentrations of the codling moth granulovirus as an applied biopesticide or
as a sublethal or latent infection. Prior viral infection of host larvae has also been shown to suppress the development of
parasitoids. Consequently, the release of Mastrus ridibundus for the suppression of codling moth in British Columbian
orchards may have the potential to augment or be suppressed by the use of the codling moth granulovirus. Molecular tools have
been developed to identify the codling moth granulovirus.
Objective/Objectifs:
To determine if the mass-rearing and release of Mastrus ridibundus are an efficacious and economical pest management
strategy to suppress hosts within an area-wide codling moth control program.
Outcome expected/Résultats attendus:
- Development of codling moth based mass-production technology for Mastrus ridibundus
- Laboratory evaluation of the interaction of parasitoids with codling moth granulovirus
- Field evaluation of strategic parasitoid releases assessing established parasitism, impact on host population densities,
- and fruit damage suppression
- Publication of all results
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The post doctorate candidate would be expected to have knowledge in the areas of entomology, biological control, and
molecular biology and have experience working in the laboratory and field. Experience and knowledge in the area of
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invertebrate pathology and parasitology would be helpful.
The successful candidate will work in a biological control laboratory within a large, well equipped federal research facility with
a team conducting research on the suppression of pests within temperate fruit orchards. The intern will become trained in the
integrated pest management of lepidopteran apple orchard pests within the area-wide control program in British Columbia,
develop skills in the mass production of both codling moth and parasitoids, gain experience in bioassay techniques, polymerase
chain reaction skills for testing for the presence of a granulovirus, gain knowledge in the pathogenesis of the codling moth
granulovirus and gain field experience in parasitoid release and assessment trials in Canadian orchards. Access to local
commercial orchards will be arranged to carry out field trials.
The knowledge obtained on the biological control of the codling moth may be applied to codling moth management within
orchards of the intern’s home country. The knowledge obtained in all aspects of the program will potentially benefit the
rearing, release, and evaluation of orchard parasitoids and our understanding of how they interact with pathogens.
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PROJECT ID/ NO DU PROJET: 2009_Summerland_04
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PROJECT TITLE / TITRE DU PROJET : Landscape ecology and genetics of invasive pests in orchards
Internship location in Canada/ Pacific Agriculture Research Centre, Summerland, British Internship Duration/Durée du
Emplacement du stage
Columbia and either University of British Columbia,
stage: 12-24 months/mois
Okanagan at Kelowna, B.C. or University of Western
Ontario, London, Ontario
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: howard.thistlewood@agr.gc.ca
d’AAC) Howard Thistlewood
Phone/Téléphone: 1-250-494-6419
Name of Research Centre/Nom du Centre de Recherche : AAFC-Pacific Agri-Food Research Centre
Mailing address/Adresse postale du Centre : 4200 Highway 97, Box 5000, Summerland, BC, Canada, V0H 1Z0
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Dr. Howard Thistlewood, Research Scientist, Environmental Health
(Website/site Web: http://www4.agr.gc.ca/AAFC-AAC/display-afficher.do?id=1181923175739&lang=e)
Other AAFC collaborators/Autre collaborateurs à AAC: Grace Frank, Coordinator of Geomatics (GIS) Unit, PARC; Scott
Smith, Supervisor of Geomatics (GIS) Unit, PARC; Other partners in related Abase project, AAFC and JK Institute, Germany,
or a possible continued IAEA collaboration.
University collaborators/Collaborateurs universitaires: Prof. Jason Pither (Biology), or Prof. Sylvia Esterby, Paramjit Gill
(Statistics) or Prof. Rebecca Tyson (Mathematics), at University of British Columbia – Okanagan, in Kelowna, B.C.;
Prof. Nusha Keyghobadi (Biology), University of Western Ontario, in London, ON
Industry partners/Partenaires industriels: Okanagan-Kootenay Sterile Insect Release Program, B.C.; BC Fruit Growers
Association, Okanagan Tree Fruit Company, and others.
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
Of value is that PARC Summerland is the only centre in Canada with significant research on fruit flies, the only Canadian
centre for sustainable management of fruit pests in an arid area, unique in AAFC in having a state-of-the-art GIS unit for
research, and has the largest dataset in Canada on physical topography, land use, micro-climates, and associated spatiotemporal insect counts. The projects in the Thistlewood lab typically involve academic collaborators at two sites per year and
provide solutions to a variety of questions of interest to national quarantine agencies and large pest control projects, worldwide. We are bringing new analytical techniques and higher mathematics to bear on the data and have a good publishing record
with enthusiastic collaborators. Together, a synergy may be developed that enhances skills of scholars and benefits colleagues
in university or government laboratories.
Objective/Objectifs:
The project is part of a collaborative study on area-wide management of pest insects, to enable the sustainable and safe
production of horticultural crops in a region of varied land use and varied terrain. The project is measuring insect movement
and applying mathematical and statistical technology, geographic information systems and molecular microsatellite DNA tools,
on fruit flies and moths. It supports a cooperative industry-government $60 million area-wide management program that has
greatly reduced harsh insecticide use.
Outcome expected/Résultats attendus:
Understanding of movement and ecology of invasive insects in highly varied terrain and landscapes, or of micro-climates
within a mountainous region, or of new molecular or GIS technology to enhance sustainable horticulture. One or two peerreviewed papers per year. Related publications have appeared in Acta Horticulturae, Biological Control, Canadian
Entomologist, Canadian Journal of Statistics, Canadian Journal of Zoology, Ecological Modelling, Entomologia Experimentalis
et Applicata, Environmental Entomology, Experimental & Applied Acarology, Insect Molecular Biology, Journal of Applied
Ecology, Journal of Theoretical Biology, Landscape Ecology, Molecular Ecology Resources, and Pest Management Science.
The Universities of British Columbia and of Western Ontario are highly rated within Canada and in international rankings.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
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The scholar will study existing projects and methods, when planning with Thistlewood and collaborator(s). Field-work in the
Summer or Autumn at PARC Summerland, and in Winter conduct the analytical work, present it for review, constructive
criticism, and prepare for publication. Based at Summerland with travel or stay at the University of BC – Okanagan nearby, or
University of Western Ontario, depending on the project and academic interaction required. Possible interactions with fruitgrowing organizations in Canada, USA, and other international collaborators.
Expected qualifications
Proficient English. Biologist interested in molecular, analytical, or computer skills, or a mathematical person interested in
biology. Interest in one or more of: spatial ecology, landscape genetics of insects, Geographic Information Systems,
microclimatic data, modelling of movement and invasion.
Benefits to scholar
Opportunity to work with an established group of biologists, modeller, statisticians, and a molecular ecologist. To develop
skills with molecular, modelling, or GIS-based technology in the important new area of spatial and landscape ecology.
Experience working in a GIS project analysing the largest dataset in Canada of physical topography, land use, micro-climates,
and spatio-temporal insect counts; working with mark-release-recapture experiments; agent-based modelling; or molecular
probes (proteins or microsatellite DNA) of moths or flies.
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PROJECT ID/ NO DU PROJET: 2009_Swift Current_01
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PROJECT TITLE / TITRE DU PROJET: Identification of molecular markers linked to disease resistance through linakge
analysis and association mapping approaches in durum wheat
Internship location in Canada Semiarid Prairie Agricultural Research Centre,
Internship Duration/Durée du
Emplacement du stage
Swift Current, Saskatchewan
stage: 24 months/mois
Contact: Asheesh (Danny) K. Singh
Email/Courriel: singhak@agr.gc.ca
Phone/Téléphone: 1-306-778-7256
Name of Research Centre/Nom du Centre de Recherche : AAFC-Semiarid Prairie Agricultural Research Centre
Mailing address/Adresse postale du Centre : P.O. Box 1030, Swift Current, SK, Canada S9H3X2
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre): Dr. Asheesh K. Singh, Durum Breeder, Sustainable Production Systems
Other AAFC collaborators/Autre collaborateurs à AAC: Dr. Ron Knox, Dr. Myriam Fernandez, Dr. Jeannie Gilbert, Dr. Ron
DePauw, Dr. Fran Clarke, Dr. T. Fetch, Dr. B. McCallum
University collaborators/Collaborateurs universitaires: Dr. Curtis Pozniak
Industry partners/Partenaires industriels:
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Project background and rationale: Durum is an important world crop (for area, production, $ value) and diseases are major
obstacles to producing high yield and quality crop. Identification of genetic resistance in durum wheat germplasm can impact
profitability and sustainability of Canadian durum and stabilize international market because Canadian durum occupies the
largest share of the world market. The focus of this research will be stripe, leaf and stem rusts; tan spot; septoria leaf blotch;
and common root rot.
Objective: The objective of this project will be to identify new sources of resistance to these pathogens, and then utilize
existing and new molecular marker information to tag these resistance genes.
Outcome expected: Our research groups at Agriculture and Agri-Food Canada and the University of Saskatchewan has
genotyped an association mapping population consisting of diverse germplasm from around the world and several bi-parental
mapping populations using molecular markers. Evaluation of disease resistance in this diverse set of germplasm will be useful
to identify disease resistance genes and linked DNA markers. This research will characterize the complement of disease
resistance genes existing in the Canadian germplasm pool. Disease screening will be conducted in the greenhouse and field
conditions in multi-location, -replicated trials. The proposed disease evaluation will help identify sources of resistance; and
coupled with extensive molecular data already compiled, will permit association genetic studies to identify novel genes. This
will be beneficial for breeders to use as a source of disease resistance through conventional breeding and marker assisted
breeding. The outcomes of this project will be the identification of new sources of disease resistance to several pathogens that
can be used in cultivar development efforts in Canada and worldwide. The subsequent output of new cultivars with disease
resistance will be available to producers, thus reducing current inputs for disease control and lowering the impact of chemical
use on the environment.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
We have done extensive genotyping with molecular markers of the bi-parental and association mapping populations. There will
be opportunities to do further molecular work in the lab. Disease resistance screenings in the field and greenhouse are the
planned role of a post-doctoral-fellow (PDF) along with molecular marker analysis. The PDF will also be involved in the
statistical analysis, and publication writing. There is flexibility for the PDF to incorporate new ideas in the broader scope of
disease resistance breeding.
Experience/education in plant genetics and pathology is required. It will be desirable to have background in molecular markers,
breeding and statistics.
The intern will be provided the opportunity to do QTL and association mapping analysis, and to work as a part of a multidisciplinary team, and will have freedom to contribute new ideas, and write publications from their project. The PDF will have
the opportunity to be involved and learn in the wheat breeding program at SPARC-AAFC.
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PROJECT ID/ NO DU PROJET: 2009_Winnipeg_01(Morden)
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PROJECT TITLE / TITRE DU PROJET :
Genetic diversity and breeding use of dry bean (Phaseolus vulgaris L.) germplasm
Internship location in Canada/ Cereal Research Centre - Morden Research Station,
Internship Duration/Durée du
Emplacement du stage
Morden, Manitoba
stage: 12 months/mois
Contact: (name of AAFC scientist / nom du chercheur d’AAC)
Email/Courriel: houa@agr.gc.ca
Phone/Téléphone: 1-204-822-7228
Anfu Hou
Name of Research Centre/Nom du Centre de Recherche : AAFC-Cereal Research Center-Morden Research Station
Mailing address/Adresse postale du Centre : Unit 100-101 Route 100, Morden, MB, Canada R6M 1Y5
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Dr. Anfu Hou, Bean Breeder Research Scientist
Other AAFC collaborators/Autre collaborateurs à AAC: Dr. Robert Conner, Research Pathologist
University collaborators/Collaborateurs universitaires:
Industry partners/Partenaires industriels:
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique: Sustainable dry bean production relies on steady-flow
of cultivars with high yield potential, disease resistance, and marketable seed quality. Public elite genetic materials suitable for
hybridization and breeding selections are very limited and becoming restrictive factors in breeding. Genetic diversity exists in
world wide dry bean resources, and can be estimated by modern technologies such as DNA markers. Evaluation of genetic
diversity and characterization and identification of new genetic resources for adaptation to Manitoba will expand regional gene
pool, facilitate molecular marker-assisted cultivar development, and improve efficiency of germplasm conservation.
Objective/Objectifs: To evaluate genetic diversity in dry bean germplasm using molecular markers and develop diverse
breeding materials for adaptation to Manitoba.
Outcome expected/Résultats attendus: 1). Phenotyping of agronomic traits in dry bean genetic materials for use in breeding
and gene mapping; 2). Estimation of genetic diversity in worldwide dry bean germplasm collections; 3). Publication of research
results in newsletters and international refereed journals.
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The internship program is designed for a postdoctoral researcher to conduct research and gain training in modern crop breeding
and genetic practices, including technologies in molecular markers, seed quality analysis, disease resistance screening and gene
mapping, genetic diversity evaluation, and genetic enhancement of germplasm resources. The qualified candidates are expected
to have advanced knowledge and training in disciplines of plant science, especially in the areas of plant genetics and breeding,
plant pathology, and molecular markers and technology. Fluency in English language is required. Willingness to do field-work
is a prerequisite. The successful applicant should be able to work in a multi-disciplinary team, and be multi-task oriented. The
training will provide opportunities to the candidate for experience in both conventional and molecular plant breeding and
genetics, and lead to a successful career in managing a modern comprehensive breeding program.
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PROJECT ID/ NO DU PROJET: 2009_Winnipeg_02
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PROJECT TITLE / TITRE DU PROJET : Novel molecular markers for wheat improvement
Internship location in Canada: Cereal Research Centre,
Internship Duration/Durée du
Emplacement du stage
Winnipeg, Manitoba
stage: 24 months/mois
Contact: (name of AAFC scientist / nom du chercheur
Email/Courriel: Mark.Jordan@agr.gc.ca
d’AAC) Mark Jordan
Phone/Téléphone: 1-204-983-1453
Name of Research Centre/Nom du Centre de Recherche : AAFC-Cereal Research Centre
Mailing address/Adresse postale du Centre : 195 Dafoe Rd., Winnipeg, MB, Canada R3T 2M9
Website/site Web: http://www.agr.gc.ca/science
A – The Research Team / L’équipe de recherche
Supervisor/superviseur: (name and title/ nom et titre) Dr. Mark Jordan, Section Head, Molecular Genetics
Other AAFC collaborators/Autre collaborateurs à AAC: Mr. Travis Banks, Dr. Gavin Humphreys
University collaborators/Collaborateurs universitaires:
Industry partners/Partenaires industriels:
B – Project Description: rational, objectives, outcome expected /
Description du projet: rationnel, objectifs, résultats attendus
Background, Rational, Issue / Contexte, Rationnel, Problématique:
Our group are leaders in the development and application of genetical genomics tools to wheat. We were the first group to
supply proof of concept that whole genome expression quantitative trait loci (eQTL) analysis (Jordan et al., 2007) and single
feature polymorphism (SFP) analysis and mapping (Banks et al., 2008) are feasible in wheat. We found that several genome
regions contained hotspots which explained a significant amount of the variation in expression of many genes. These regions
could harbour regulatory genes important in seed development and end-use quality. What is needed is a larger population size
to validate these regions. In addition, more markers can be applied to the map using the same data used for eQTL analysis. This
relies on taking advantage of the design of the microarray chips used to identify and map SFPs. Using a single time point in
seed development we have identified and mapped over 1000 SFPs. The potential now exists to combine eQTL and SFP
analysis in a larger population over several time points in seed development. This will provide a resource that will include the
addition of thousands more potentially useful molecular markers to wheat maps, provide the physical location of thousands of
genes expressed during the course of seed development and identify genome regions responsible for regulating seed expressed
genes. These can then be associated with trait QTL data (agronomic and extensive end-use quality traits) already collected on
this population.
Banks, T.W. et al (2008). In The 11th International Wheat Genetics Symposium proceedings. http://hdl.handle.net/2123/3375
Jordan, M.C. et al. (2007). Plant Biotechnol. J. 5:442-453.
Objective/Objectifs:
Identify SFPs in several time points of seed development in the RL4452 X AC Domain population
Map the SFPs along with existing SSR data for the population
Validate the SFPs using robustness, rice synteny, PCR and 454 sequencing
Create a database of mapped sequenced based polymorphisms which will identify the physical location of genes expressed in
seed development and relate these to existing eQTL data to assist in the identification of regulatory genes
Outcome expected/Résultats attendus:
By assigning more markers to the linkage map the database will assist map based cloning efforts in wheat. Ultimately this will
allow the identification of key regulatory genes controlling seed development and end-use quality and provide molecular
markers for these genes that can be used in molecular breeding efforts to improve end-use quality (food or industrial uses
derived from grain).
C – Internship: Describe the internship program, qualifications of and the benefits to the expected intern /
Stage: Décrire le stage, les qualifications demandées et les avantages pour l’interne.
The intern will be involved in aspects of QTL and genetic linkage mapping using traditional and novel molecular markers. This
will include integrating new molecular marker data (eg. SFP) with currently available data using existing segregating
populations, association populations, QTL data, gene expression and marker data. The intern will gain experience in aspects of
wheat genomics including associating genotype to phenotype, identifying novel molecular markers, associating markers to
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traits, new sequencing technology and microarray analysis. This experience will allow the development of expertise in modern
methods in molecular breeding that can be applied to the wheat breeding programs in the intern’s home country. The intern
must have a strong background in statistical genetics including QTL analysis, creation of genetic linkage maps and knowledge
of associated software and theory. Experience in association mapping and aspects of bioinformatics such as sequence assembly
would be beneficial. The intern will collaborate with AAFC scientists involved in wheat breeding, bioinformatics, genetics and
genomics and be involved in projects to identify genes, genomic regions and molecular markers involved in traits such as
improved human nutrition, pre-harvest sprouting and insect resistance.
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