Australian Centre for Plant Functional Genomics | 2008 Annual Report
A program initiated by
The Commonwealth Government of Australia
And funded by
The Australian Research Council
The Grains Research and Development Corporation
Support also provided by
The Government of South Australia
Additional financial support from
The University of Adelaide
The University of Melbourne
The University of Queensland
Research providers
The University of Adelaide
The University of Melbourne
The University of Queensland
The University of South Australia
Department of Primary Industries, Victoria
www.acpfg.com.au
Drought
Boron
Nutrients
Cold
Salinity
Bioinformatics
‘omics
Genome Analysis
Resources
Cell Walls
Nitrogen Use Efficiency
High-Iron Rice
2008
Annual
Report
ACPFG Mission Statement
To create and commercialise cutting edge knowledge to significantly enhance grain quality and
yield in our challenging environment.
Australian Centre for Plant Functional Genomics (ACPFG) uses functional genomics to improve
the resistance of wheat and barley to hostile environmental conditions such as drought, salinity,
frost and mineral deficiencies or toxicities. These stresses, known as abiotic stresses, are a major
cause of cereal crop yield and quality loss throughout the world.
02 04 06 11
Chairman’s Report
CEO’s Report
Board Members & Executive
Management Group
Nodes
12 13 14 36
Collaborations
Visitors
Research
Communication
38 40 41 44
Education
Conferences & Meetings
Student List
Patent List
48 50 51 52
Publication List
ACPFG Structure
Summary of Contributions
Contacts & Acronyms
CHAIRMAN’S
REPORT
On behalf of my fellow directors, I am pleased to present the sixth annual report of the Australian Centre
for Plant Functional Genomics Pty Ltd (ACPFG).
Funding for the second five year period of ACPFG (“ACPFG II”) was finalised in early 2008.
On behalf of all within the ACPFG, I thank our shareholders and stakeholders for their confidence
in us based on our performance during the first five years and also on the abilities and skills of
our people to achieve our plans for the next 5 years. Following the confirmation of our funding
for ACPFG II, and subsequent approval of our business plan, we are continuing the work that
characterises ACPFG’s world-renowned research.
The number of patents filed increased to 27 during 2008 and we now have 127 scientific and
commercial agreements in place with some of the world’s most significant commercial entities
in our field. We also have many agreements with other major Australian research organisations.
Late in 2008, shareholders and stakeholders appointed Dale Baker as a Director. An experienced
grain farmer from Western Australia with extensive industry experience, he was welcomed at our
August 2008 board meeting. After welcoming the University of South Australia (UniSA) as a new
shareholder in 2007, we spent 2008 searching internationally and recruiting appropriate individuals
for the Phenomics and Mathematics node at UniSA.
State and federal politicians maintained an active interest in the activities of ACPFG and senior staff
continued to meet and brief politicians and government staff around Australia on matters of mutual
interest. ACPFG continued representations advocating the removal of the various state moratoria
prohibiting growing of genetically modified (GM) crops. Late in 2008, the Western Australian
Government followed Victoria and NSW in partially lifting its moratorium on the growing of
GM crops, reflecting the subtle changes occurring in community attitudes to GM.
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2008 ACPFG Annual Report
ACPFG continued to be a destination of choice for many international visitors, school students,
community groups and other interested parties. We maintained our close links with the Australian
grain and farming community through our regular attendance at industry briefings and events as well
as field days around Australia.
Vector magazine, continued to attract significant interest from Australia and overseas with
distribution to more than 1,000 people.
ACPFG scientists have enjoyed success with scientific work published in major journals.
Senior ACPFG management travel interstate and overseas regularly to attend conferences, present
scientific papers, represent the ACPFG, or to meet with industry and scientific partner. In addition,
ACPFG researchers at all nodes have continued to be outstandingly successful in attracting grant
funds for work within the ACPFG.
In expanding its number of international linkages, ACPFG has submitted two grant applications
to work with a partner company in India and has also held discussions with a government
in Asia.
ACPFG maintained a focus on the establishment of a National Delivery Pathway and will continue
to do so for the life of ACPFG II. We continued discussions and consultation about a delivery
pathway for GM technologies with shareholders, stakeholders, industry members and other
potential participants.
On behalf of my fellow directors, I again thank our shareholders and stakeholders for their support
for the activities of ACPFG. In addition, I thank our researchers, scientists, staff, national and
international visitors and students who have worked within the nodes of the ACPFG around Australia
on the campuses of the University of Adelaide (UA), University of Melbourne (UM), University
of Queensland (UQ) and UniSA. Their dedication and efforts are acknowledged and are very
highly valued. ACPFG has maintained one of the world’s most desirable environments in which
to undertake abiotic stress research in cereals and this is confirmed by the number of requests for
collaborative participation.
As a team, we have consolidated the respected name of the ACPFG in the global scientific and
commercial world of environmental stresses in grains.
Finally, I sincerely thank my fellow directors for their efforts, dedication and continued wise counsel.
Nicholas Begakis AM | Chairman
2008 ACPFG Annual Report
3
CEO’S
REPORT
2008 has been an exciting year with several major scientific achievements.
There have been significant advances in almost all areas of activity. In the analysis of drought
responses in adapted wheats, we were able to identify four major genomic regions that have
consistently emerged in the 20 field trials that have been run since 2006. Importantly, a region of
the genome has been identified as playing a key role in tolerance to heat stress. All target regions
are now undergoing more detailed analysis and screening of large populations to zero in on the
actual genes responsible for the drought tolerance characteristics, or “phenotype”, of these lines.
The significance of these results has been confirmed by the strong international interest in the target
chromosome regions and associated markers. Over the next few years our international linkages
should help us to validate the markers in different germplasm pools and across diverse environments.
The transgenic approach to drought tolerance was also given a large boost through the analysis
of a new set of transgenic lines. We’ve known for some time that over-expressing several of our
drought-related “transcription factors” will improve drought tolerance responses. Unfortunately,
this comes at a major cost to the plant through greatly delayed development, dwarfing and several
other negative characteristics. However, by hooking-up the “transcription factor” genes to a drought
inducible promoter (a promoter that switches on only when the plants are under drought stress), a
positive drought response can be achieved without the negative developmental phenotypes. The
results to date have all been based on glasshouse analysis, which is notoriously poor at predicting field
performance. Field evaluation of these transgenic lines will be a high priority for the coming seasons.
The genetic engineering approach for salinity tolerance has also moved forward substantially.
Transgenic rice and barley lines able to maintain biomass production under salt stress, and also
show a good level of salinity tolerance, have been generated through controlled expression of the
PpENA gene from a moss as well as a gene from Arabidopsis involved in vacuolar sequestration of salt.
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2008 ACPFG Annual Report
This year, the forward genetic approach to studying salinity tolerance in cereals made a major
leap forward through the development of a new method for assessing tissue tolerance to salt.
Most previous work was built around the analysis of plants that were able to exclude salt from
their leaves. However, sodium exclusion was clearly only one component of the salinity tolerance
mechanism. The use of the Lemnatec plant imaging and analysis platform allowed us to measure
the amount of leaf damage under saline conditions and provided a tool for screening for tissue
tolerance. This work has opened a new path for the genetic and physiological analysis of salinity
tolerance. The new Plant Accelerator, due to open at the end of 2009, will provide a platform for
large scale screening for this tolerance mechanism. Consequently we’re expecting exciting new
developments in salinity tolerance research over the next few years.
The boron tolerance project also advanced in leaps and bounds. It took us five years to isolate the
first boron tolerance gene from barley, but in 2008 the likely genes underlying the 6H and 3H loci
in barley and the 7BL locus in wheat were all isolated.
The development of skills and resources for positional cloning in wheat and barley have improved
so rapidly that we’re building confidence to tackle the really difficult traits such as those mentioned
above for drought and heat tolerance.
We have actively participated in the development of several of the key resources now available for
genome analysis in wheat and barley. Amongst the most important have been the development of
a physical map of the barley genome being led by colleagues at Leibniz Institute of Plant Genetics
and Crop Plant Research (IPK) in Germany and the evaluation of the next generation DNA
sequencing platforms where our Brisbane node has been active.
For the first time we have included reports on major projects associated with the core ACPFG
research programs. These reports cover the cell wall, nitrogen use efficiency and biofortification
work. Although these research areas receive no funding from ACPFG, the researchers involved
interact closely with ACPFG scientists and are able to make full use of facilities and resources
developed by ACPFG. This builds on the original concept that ACPFG would not only conduct its
core research projects but would also build resources and capabilities to support plant genomics
research more broadly. We hope to see an expansion of these types of linkages over the next few years.
Over the past year there have also been several significant organisational changes in aspects of
ACPFG activities. The processes for recruiting, assessing and supporting honours, masters and
PhD students have been completely overhauled by Monica Ogierman. The new structure has
already improved operations considerably and will ensure we’re well placed to expand the
student programs. We have also been working hard to address issues of technology delivery
and have been developing linkages to help develop an effective delivery pathway for both
conventional and genetically engineered germplasm. The new node at the UniSA was initiated
in 2008 through the appointment of Desmond Lun. The development of this node into an
internationally recognised group in plant phenomics and bioinformatics will be a significant
undertaking over the next few years.
The research advances in 2008 have opened a wide range of new options for ACPFG over the
next few years including opportunities arising from important fundamental scientific discoveries.
Importantly, we have now developed several technologies that have the potential to significantly
improve stress tolerance in cereals. The translation of these findings into practical outcomes
remains a challenge given that many of the processes and structures needed for delivery are poorly
developed. However, we are now in a position to demonstrate the practicality of many of the
research outcomes and this will help build the necessary delivery pathways.
Peter Langridge | CEO
2008 ACPFG Annual Report
5
BOARD MEMBERS
Mr Simon Drilling | Professor Geoff Fincher (Deputy CEO) | Mr Nicholas Begakis (Chair) | Dale Baker
Professor Viki Sara | Professor Peter Langridge (CEO) | Ms Maggie Dowling | Michael Gilbert (Company Secretary)
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2008 ACPFG Annual Report
Executive Management Group
Professor Kaye Basford | Mr Michael Gilbert | Professor Mark Tester | Professor Tony Bacic | Professor Geoff Fincher (Chair)
2008 ACPFG Annual Report
7
Board and Executive Management Group
Tony Bacic
Professor Tony Bacic leads the
ACPFG team at the University of
Melbourne and is a member of
the Executive Management Group
(EMG). He holds a Personal Chair
in the School of Botany and is a
Fellow of the Australian Academy
of Sciences (FAA). He is Director
of the Plant Cell Biology Research
Centre, Platform Convenor of the
National Collaborative Research
Infrastructure Strategy (NCRIS)funded Metabolomics Australia
(MA), and Interim Director of
the Bio21 Molecular Science
and Biotechnology Institute.
He is on the Management
Committees of Bioplatforms
Australia Ltd., the Australian
Proteomics Computational Facility,
the Integrative Neuroscience
Facility Platform and the Maud
Gibson Trust of the Royal Botanic
Gardens in Cranbourne. He is a
monitoring editor for the journal
Plant Physiology, associate editor
for Glycobiology and is on the
editorial boards of Planta and
Plant and Cell Physiology. He
is a member of the organising
committee for the 18th
International Botanical Congress to
be held in 2011 and the program
committee for OzBio 2010 – an
international conference on
“Molecules of life: from discovery
to biotechnology”. In 2008 he
was an invited speaker at the Third
Conference on the Biosynthesis
of Plant Cell Walls, Asilomar,
United States of America (USA),
and the International Symposium
on Bioenergy and Biotechnology,
Wuhan, China. His research is
focused on the structure, function
and biosynthesis of plant cell
walls and their biotechnological
application, as well as the
application of functional
genomics tools to abiotic stress
and productivity in cereals. 8
2008 ACPFG Annual Report
Nick Begakis
Kaye Basford
Dale Baker
ACPFG Director Dale Baker has
been a grain grower in Western
Australia’s southeast for more
than 40 years. He has had a long
and close association with grains
research and development, starting
with the Kondinin Group and
11 years as a Grains Research
and Development Corporation
(GRDC) panel member, with five
years as Western Panel Chairman.
Dale has also been a Director of
the Cooperative Research Centre
(CRC) for Weed Management
Systems and Chairman of the
Australian Government’s Managing
Climate Variability Program. He
has also spent time in the US,
Canada, Argentina and South
Africa studying their production
systems. His current roles include
Chairman of InterGrain Pty Ltd
and member of the University
of Western Australia (UWA)
Albany Foundation. Dale is also
a graduate of the Australian
Institute of Company Directors.
Professor Kaye Basford is a
member of the EMG. She leads the
ACPFG bioinformatics program
and oversees the University of
Queensland (UQ) node. Kaye
is Deputy President of the UQ
Academic Board and Head
of the School of Land, Crop and
Food Sciences. Her teaching and
research is at the forefront of
statistics and quantitative genetics,
through the development and
dissemination of methodology for
the analysis and interpretation of
genotypic adaptation in largescale plant breeding trials. She
has published widely in this
area, including two monographs.
Kaye is a Fellow of the Australian
Academy of Technological
Sciences and Engineering (ATSE),
the Australian Institute of Company
Directors, the Royal Statistical
Society and the Australian Institute
of Agricultural Science and
Technology. She is also PresidentElect of the International Biometric
Society. Her awards include the
1998 Medal of Agriculture from the
Australian Institute of Agricultural
Science and Technology and
a 1986 Fulbright Postdoctoral
Fellowship to Cornell University.
Chair of the Board, Nick Begakis
AM, has an electronic engineering
degree and more than 30 years’
experience in senior management
roles in manufacturing industries;
as an entrepreneur creating
his own enterprises; in venture
capital, investment and merchant
banking; in corporate recovery
roles; and as an independent,
non-executive chairman and
company director. Nick is involved
in creating intellectual property
and capturing value as Chairman
of ACPFG. He also assists in
the establishment of enterprises
and encourages entrepreneurial
activities as Chairman of Enterprise
Development Inc; prudently
manages invested funds and
creates wealth as a Director
of Statewide Superannuation
Trust (SA); and encourages trade
and exports as Chairman of the
Council for International Trade and
Commerce SA Inc. Nick represents
business and industry interests
at the state and national level as
a member of the Premier’s Food
Council (SA), as a Director of
Business SA and of the Canberrabased Australian Chamber of
Commerce and Industry. He
supports the non-profit sector as
a Member of Flinders University
Council and as Chairman of the
Women’s and Children’s Hospital
Foundation (SA). Nick co-owns
and is Chairman of a leading
Australian supermarket food brand
with interests in Asia and which
exports to the European Union,
USA and New Zealand. He is a
Fellow and past Deputy Chair (SA
and NT) of the Australian Institute
of Company Directors and a
past member of the Environment
Protection Authority (SA).
Board and Executive Management Group
Geoff Fincher
Maggie Dowling
Maggie Dowling, ACPFG Director,
has more than 20 years’ experience
in the grains industry. She has
been a Manager at AusBulk and
ABB Grain, as well as Director of
Grains Industry Development for
the South Australian Government.
Maggie has been on advisory
committees; nationally for
molecular plant breeding, and for
the SA Government on GM crops.
She has been on national steering
committees for the implementation
of intellectual property royalty
systems in agriculture and
GRDC’s Partners in Grain project.
She has also been on the SA
Premier’s Science and Research
Fund Selection Panel. Maggie
has qualifications in business,
management and company
directorship, and has been chair or
director of several grains-focused
companies. She is currently
General Manager at the CRC for
Contamination Assessment and
Remediation of the Environment. Simon Drilling
ACPFG Director Simon Drilling is
trained as a chartered accountant
and an investment research
analyst with Thornton Group. He
has previously been Director of
Kirribilli Wines, Director of the
Deloitte Touche Tohmatsu Policy
Board, member of the Deloitte
Consulting Asia Pacific Africa
Management Committee and
member of the Deloitte Consulting
Worldwide Board. His previous
roles include Project Director for
BioInnovation SA, CEO for Deloitte
Consulting Australasia and leader
of Deloitte Consulting Utility
Industry Group in Australasia. Professor Geoff Fincher is Deputy
Chief Executive Officer of ACPFG,
where he chairs the EMG and
takes specific responsibility for
new projects and initiatives.
Geoff’s research interests are
in the enzymology, molecular
biology, structural biology, genetics
and biochemistry of plant cell
wall metabolism. Geoff is also
Director of UA’s Waite Campus.
He is an editor for the Journal of
Cereal Science and BioEnergy
Research, and is a long-serving
member of the editorial board of
Planta. He chairs the Scientific
Advisory Committee of Biomime,
the Swedish centre for wood
functional genomics. In 2008,
Geoff was a plenary speaker at the
10th International Barley Genetics
Symposium in Alexandria, Egypt,
and at the Plant Polysaccharide
Workshop in Sweden. Also in
2008, he was an invited speaker
at the Plant Cell Wall Meeting in
the US, the European Agronomy
Society meeting in Italy, the Plant
Genomics European Meeting in
Bulgaria, the Royal Australian
Chemical Institute Cereal
Chemistry Division’s annual
meeting in Surfers Paradise, and
the BioForum meeting in Italy. With
Mark Tester, he secured $26 million
to construct the Plant Accelerator
at the Waite Campus, as part of the
Australian Plant Phenomics Facility.
Michael Gilbert
ACPFG General Manager,
Company Secretary and EMG
member Michael Gilbert is on the
Board of Ausbiotech and is Chair
of its Risk and Audit Committee. In
2006, Michael was also appointed
to the Federal Government’s
Advisory Council on Intellectual
Property (ACIP), which advises the
Federal Minister for Innovation,
Industry, Science and Research on
intellectual property matters and
the strategic administration of IP
Australia. Michael graduated as a
mechanical engineer then worked
in research and development
for lens manufacturer SOLA
International both in Australia
and overseas. He became
General Manager of a South
Australian group of manufacturing
companies, then began working for
himself in 1998 after completing
an MBA at the University of
Adelaide. His company, Adelaide
Consulting, included clients
such as Haigh’s Chocolates and
Laubman and Pank as well as
professional firms seeking to
restructure underperforming
businesses. Michael worked
increasingly with the University
sector and was the project manager
for the start-up of ACPFG in 2002.
In 2003 Michael officially joined
ACPFG, where his responsibilities
include finance, reporting and
intellectual property management
as well as board secretarial matters. 2008 ACPFG Annual Report
9
Board and Executive Management Group
Peter Langridge
ACPFG CEO, Professor Peter
Langridge, is on the advisory
boards of the European Union
BioExploit and TriticeaeGenome
Programs, the Australian Research
Council Centre for Integrative
Legume Research and the
National Science Foundation
Wheat D-Genome Program in
the USA. He was also on the
Research Advisory Committee
of the Consultative Group
on International Agricultural
Research’s Generation Challenge
Programme (GCP). In 2008 Peter
was invited to join the Science
and Impact Advisory Board
at the Institute of Biological,
Environmental and Rural Sciences
in Aberystwth, United Kingdom
(UK). He is currently a Director
of LifePrint Australia Pty Ltd, a
plant DNA diagnostic company,
and a member of the management
committee of the International
Triticeae Mapping Initiative (ITMI).
Peter is an Honorary Fellow of the
Scottish Crop Research Institute
and in 2007 was appointed Fellow
of Food Standards Australia and
New Zealand. Peter is often
approached by the media to
talk about scientific advances
for agricultural development. In
2008, he published nine papers
in international journals and coedited the book Methods in Plant
Molecular Biology. He was an
invited speaker at the European
Plant Science Organisation
Conference in France, the
International Durum Symposium
in Italy and the Australian
Agronomy Conference. Peter
also co-chaired the organising
committee for the International
Wheat Genetics Symposium which
was held in Brisbane in August.
Peter co-supervises six PhD
students and is on three journal
editorial boards: Theoretical and
Applied Genetics, Plant Methods
and International Journal of
Plant Genomics. His research
has focused on the development
and application of molecular
biology to crop improvement. 10 2008 ACPFG Annual Report
Mark Tester
Vicki Sara
ACPFG Director Professor Vicki
Sara is Chancellor of the University
of Technology Sydney. She was
Vice-Chair of the Organisation
for Economic Co-operation and
Development’s (OECD) Global
Science Forum in 1999, a member
of the Advisory Board of the AsiaPacific Economic Cooperation
(APEC) Research and Development
Leaders’ Forum in 2002, and
Consul General for Sweden in
Sydney in 2006. She has been
Chair and CEO of the Australian
Research Council, on the CSIRO
Board, member of the Prime
Minister’s Science Engineering
and Innovation Council (PMSEIC),
Dean of Science at the Queensland
University of Technology (QUT)
and Director of the CRC for
Diagnostic Technologies. Before
moving into management, Vicki
held various research positions at
the Karolinska Institute, Stockholm,
which she joined on a United
Nations Educational, Scientific and
Cultural Organization (UNESCO)
postdoctoral fellowship. There
she led the Endocrine Pathology
Research Laboratory and received
awards for isolating a growth
factor responsible for regulating
foetal brain development. In
Australia she has been awarded
the Centenary Medal, an
Honorary Doctor of Science from
both the University of Southern
Queensland and the Victoria
University, and an Honorary
Doctorate from QUT. Vicki is a
Fellow of the Australian Academy
of Science and the Australian
Academy of Technological
Sciences and Engineering.
Professor Mark Tester is a member
of the EMG. He completed a PhD
in biophysics at the University
of Cambridge in 1988, where
he was a lecturer for 11 years
before moving back to South
Australia as a Federation Fellow
at the University of Adelaide.
Mark oversees ACPFG’s salinity
tolerance research, using both
forward and reverse genetics
approaches. In 2008, besides
continuing work to understand and
manipulate sodium transport and
accumulation in plants, this team
developed techniques to dissect
salinity tolerance into a series of
components using image capture
and processing. These techniques
will enable forward genetic
studies into previously intractable
components of salinity tolerance.
Mark co-supervises twelve PhD
students and is an enthusiastic
science communicator who is
regularly involved in ACPFG media
coverage. He is the Director of
the Australian Plant Phenomics
Facility, including The Plant
Accelerator, which commenced
construction in 2008. In 2008,
Mark published several papers in
international journals, including a
seminal review with Rana Munns
in Annual Reviews of Plant Biology
and gave several presentations,
notably at the University of
Oxford. Mark is on seven journal
editorial boards, including Plant,
Cell and Environment, Journal of
Experimental Botany and Molecular
Plant. He was co-chair of the
Gordon Research Conference
on drought and salinity, held
in Montana, USA in September
2008, and is on the steering
committee for both Interdrought
III in Shanghai in 2009 and the
15th International Workshop for
Plant Membrane Biology, which
will be held in Adelaide in 2010.
NODES
NT
Qld
WA
SA
NSW
Vic
Tas
University of Adelaide
ACPFG is headquartered at the Waite Campus, Australia’s largest
crop research centre, with extensive teaching, research and plant
breeding activities. Links to plant breeding programs provide
access to germplasm and delivery pathways for research outcomes.
Activities in Adelaide include the transformation of cereals and
model plants, germplasm screening and evaluation, genetic
analysis, positional cloning, protein expression and structural
analysis, antibody production, and the construction and screening
of large insert libraries.
University of Queensland
Construction of the Plant Accelerator commenced this year. It
will be a world-leading plant growth and analysis facility, offering
more than 1km of conveyor systems and state-of-the-art imaging,
robotic and computing equipment for the automatic and nondestructive measurements of plant phenotypes. The $25 million
project is funded by the Commonwealth Government’s NCRIS,
South Australia’s Department of Further Education, Employment,
Science and Technology (DFEEST), and the University of
Adelaide. The facility is expected to open in November 2009.
In the future, there will be an increasing emphasis on integrating
advanced bioinformatics strategies with the abundant data being
produced. Bioinformatics and genomics capability at the UQ
node is expanding rapidly, supported by more than $4.7 million
in competitive funds.
University of Melbourne
The UM node is focused on functional genomics technologies
including proteomics, metabolomics, glycomics and
bioinformatics, which are needed to support high throughput
analysis. This node draws on the strengths of the Victorian Centre
for Plant Functional Genomics and MA, an NCRIS-funded
organisation launched in Melbourne in 2008 and managed
through Bioplatforms Australia.
In collaboration with MA, the University of Melbourne’s
Faculty of Science and the Department of Information Services,
information technology (IT) infrastructure was extensively
upgraded in 2008. This will lay the foundation for several years
of growth, essential to the ongoing operation of the Melbourne
node. The 2008 upgrade programme was funded by MA, with
equipment purchases totalling $100,000 and a new IT support
person for an additional $70,000.
The UQ node has developed a high quality bioinformatics
capability for ACPFG and provides bioinformatics support for
research projects across the organisation. ACPFG in Queensland
is developing internal biological databases and is working
with national and international partners to develop large-scale
database infrastructure.
University of South Australia
The UniSA node houses the new Phenomics and Bioinformatics
Research Centre (PBRC), which is developing capabilities in
phenomics and bioinformatics to complement and support the
ACPFG’s activities in all areas, particularly research anticipated
from The Plant Accelerator.
The PBRC appointed its first three core members in 2008:
Desmond Lun, Bao-Lam Huynh and Zahra Shoaei. Desmond
obtained his PhD in electrical engineering and computer science
from the Massachusetts Institute of Technology (MIT) in 2006
and, prior to joining UniSA and ACPFG, was a Computational
Biologist at the Broad Institute of MIT and Harvard and a
Research Fellow in genetics at Harvard Medical School, where his
work was focused on modelling and engineering microorganisms.
Bao-Lam joins the PBRC as a Research Associate after completing
his PhD at ACPFG with the University of Adelaide in 2008,
where he investigated a new strategy of genetic biofortification
of wheat with increased fructan content. Zahra joins the PBRC
as a Research Assistant. The PBRC is currently expanding its
capabilities by enrolling students and recruiting staff.
2008 ACPFG Annual Report 11
COLLABORATIONS
This year, ACPFG continued to grow the number
of relationships with both private and public
sector organisations.
In 2008, the first year of ACPFG II, activities were focussed on
field testing of technologies. Unfortunately, while we successfully
obtained the necessary Federal and State Government approvals,
the field planting was too late and the trials were abandoned.
They will be re-run in 2009. Non-GM field trials were also run
in 2008 at four sites in South Australia as well as at International
Maize and Wheat Improvement Centre (CIMMYT). These were
in collaboration with Australian Grain Technologies (AGT),
Barley Breeding Australia and others. A large amount of data has
been generated during a year that was characterised by a terrible
drought. Importantly the first heat stress trial was conducted in
Obregon, Mexico. This trial involved the late sowing of the wheat
mapping populations under irrigation. This meant that the plants
were exposed to high temperature during grain filling but were not
limited for water. The wheat populations have also been multiplied
in Syria and India and will enter field trials in the next season.
the area of marker development for canola will link to the UQ
node of ACPFG.
The international collaborations on genome analysis of wheat
and barley were further expanded during 2008. ACPFG has been
closely linked to the barley physical mapping project being led
by the group at IPK in Germany. A new European Commission
Seventh Framework Programme (FP7), TriticeaeGenome, also
commenced in 2008 and ACPFG is linked in through a grant from
the Federal Government under the International Scientific Linkage
Scheme. The CEO of ACPFG was also invited to join the Advisory
Board of a new US research program on physical mapping of the
D genome of wheat.
ACPFG has had a strong collaboration with colleagues in Italy
for some time. In 2008 Professor Geoff Fincher spent several
months working with Professor Roberto Tuberosa at the University
of Bologna. ACPFG also entered into an agreement with the
University of Bologna and several Italian research institutes to
explore genetic diversity in durum wheat. This collaboration will
be partially supported by the South Australian Government.
In 2009 a new collaborative project will commence with
colleagues at the Chinese Academy of Agricultural Sciences,
Beijing, on the investigation of natural variation in drought
response genes. This project will be part of the GCP and builds
on previous GCP projects.
In terms of technology commercialisation, an agreement has been
signed with Neubody Pty Ltd to commercialise antibodies arising
from the ACPFG research programs. In addition, a number of
promoters were licensed to a large multinational company who
also commissioned ACPFG to conduct a small discovery project.
As part of effort to work toward delivering technologies, a license
was negotiated with Japan Tobacco for agrobacterium wheat and
barley transformation.
As a shareholder in LifePrint Pty Ltd, ACPFG maintained an active
interest in their activities this year. LifePrint was awarded one of the
last Commercial Ready (Plus) grants and continues to be financially
assisted by Mr Helmut Miller, a German investor in the company.
ACPFG staff were again able to strengthen the relationship with
Pioneer Hi-Bred International Inc., using its funding to leverage,
through the University of Adelaide, a further million dollars
was awarded from the Australian Research Council (ARC) in the
area of cellulose biosynthesis. Evidence of the strength of this
relationship is that ACPFG have now been offered, for wheat and
barley, access to a large gene set from a previous Pioneer project.
The Harvest Plus project continued this year under the guidance
of Alex Johnson, who received additional support to collaborate with
Flinders University on a project on iron biofortification of grains.
An ARC Linkage Grant for this work was also successful.
ACPFG now boasts numberous scientific collaborations,
including:
A new collaborative relationship has developed with ABB Grain
Ltd. An application has been submitted to the ARC under the
Linkage Grant Scheme to support this work.
1.
ACPFG’s links with MA are very strong to the extent that
a key ACPFG scientist, Ute Roessner, is now employed
50% there.
The Nitrogen Use Efficiency project with Arcadia Biosciences and
CSIRO Plant Industry is progressing well with transgenic wheat
and barley now growing in glasshouses. An application has been
lodged to run the first field trials of transgenic lines in 2009.
2.
Bu-Jun Shi constructed a lupin bacterial artificial
chromosome (BAC) library for CSIRO Plant Industry in Perth.
3.
ACPFG staff have been involved in two projects proposals
under the European Commission FP7.
4.
Various projects with CSIRO Plant Industry including the
Australian Plant Phenomics Facility.
ACPFG now has a formal collaboration with the New South
Wales Department of Primary Industries (NSW DPI). The
collaborative work will investigate the link between drought
and heat stress and grain quality. This builds on the expertise in
NSW DPI in assessing wheat quality and the genetic materials
developed by ACPFG. A further collaboration with NSW DPI in
12 2008 ACPFG Annual Report
Finally, a Benefit Sharing policy for inventors was finalised this
year, providing a mechanism for sharing commercialisation
benefits with inventors.
VISITORS
January 7
January 9
January 21
January 22
February 15
February 13
February 21
February 25–26
February 27–20
March 20
April 3
April 10
April 17
May 8
May 22
May 29
June 12
June 19
July 3
July 8
July 10
July 25
July 30
August 7–8
August 15
August 18
August 21
August 21
August 21
August 28
September 1
September 11
September 15–16
September 18
September 24
October 2
October 7
October 16
October 22
October 28
October 29
November 4
November 7
November 11
November 14
November 21
November 27
November 28
December 1
December 5
December 11
December 11
December 12
December 18
January 29
Jim Fortune, Executive Director, Grape and Wine Research and Development Corporation
Jim Peacock, Australia’s Chief Scientist
Geoff Rayson, SQC Pty Ltd
Dean Brown, Ex-premier of South Australia
Puglia Delegation, Puglia, Italy
Tracey Dodd, SA Department of Further Education, Employment, Science and Technology
Jerome Konescsni, President and CEO of Genome Prairie, Canada
Alberta Crop Industry Development Fund visitors, Canada
Jinnie Kim, Senior Editor, Elsevier, New York, USA
Matt Humphry, The Max Planck Institute, Cologne, Germany
John Passioura, CSIRO Plant Industry, Canberra
Sharon Regan, Queen’s University, Kingston, Canada
Jean Finnegan, CSIRO Plant Industry Canberra
Hans Lambers, UWA
Evans Lagudah, CSIRO Plant Industry Canberra
Falk Schreiber, Leibniz Institute of Plant Genetics and Crop Plant Research, Germany
John Forster, Victorian Department of Primary Industries, La Trobe
Michael Djordjevic, Australian National University, Canberra
Rebecca Keough, ARC Centre for the Molecular Genetics of Development, University of Adelaide
David Shelmerdine and Eric Dunlop, Pan Pacific Technologies
Matthew Bellgard, Centre for Comparative Genomics, Murdoch University
Eric Dunlop, Pan Pacific Technologies
Daryl Mares, University of Adelaide
Jacqueline Heard, Monsanto, USA
C Ramasamy and Chandra Babu, Tamil Nadu Agricultural University, India
Ray Shaw, Rio Tinto
Suzanne Dreisigecker, CIMMYT, Mexico
Alain Murigneux, Limagrain, France
Rudy Dolferus, CSIRO Plant Industry, Canberra
Greg Constable, CSIRO Plant Industry, NSW
Nora Lapitan, Department of Soil and Crop Science, Colorado State University, USA
Trevor Lithgow, University of Melbourne
Brian Fowler, University of Saskatoon, Canada
Grant Booker, University of Adelaide
Robert Park, University of Sydney
Laurence Jassogne, University of Adelaide
Chris Kirk, Deputy Vice-Chancellor, Lincoln University, New Zealand
Andreas Meyer, Heidelberg Institute of Plant Sciences, Germany
Robert Reid, University of Adelaide
Reno Pontarollo, Chief Scientific Officer, Genome Prairie, Canada
Professor Mike McLaughlin, University of Adelaide
Dirk Vandehirtz, Lemnatec, Germany
Richard Trethowan, University of Sydney
Daniel Cheron, Michel DeBran, Georges Freyssinet, Valerie Mazza, Pierre Pagesse, Thierry Ronsin and Emmanuel Rogier, Limagrain, France
Professor William Erskine, University of Western Australia
Peter Sharp, University of Sydney
Ron Herring, Cornell University, USA
Harvey Millar, UWA
Serge Delrot, Université de Bordeaux, France
Grant Kramer, University of Nevada, USA
Frank Gubler, CSIRO Plant Industry, Canberra
Ian Chessell, Chief Scientist, South Australia
Dyno Keatinge, Director General, World Vegetable Center, Taiwan
Matthew Gilliham, University of Adelaide
David Smyth, Monash University
2008 ACPFG Annual Report 13
RESEARCH
15
18
20
22
23
26
28
29
30
Drought
Boron
Nutrients
Cold
Salinity
Bioinformatics
‘omics
Genome Analysis
Resources
Aligned Programs
32
34
35
14
Cell Walls
Nitrogen Use Efficiency
High-Iron Rice
Drought
DROUGHT
Peter Langridge
Peter is the interim
Drought Group leader.
See Board profile
on page 10.
Drought tolerance in cereals is a key trait
considering predicted increases in world population
and the accompanying demand for land, food and
water. Recently there has been increasing pressure
on irrigation water with significant shortages
occurring in many parts of the world.
In Australia drought stress has continued to plague
grain production, with several states showing
below average yields. In 2007 there were serious
heat waves that led to significant crop damage.
The combined impacts of low water availability
and heat pose a particularly severe stress for plants
and predictions for climate change point to a
continuation of the difficult years being experienced
by Australian grain producers.
ACPFG has been working on unravelling the
genetic control of drought responses using three
approaches. The first has been to analyse the
genetic basis for differences in drought response
in adapted Australian cultivar, the forward genetic
approach; the second approach aims to build a
descriptive database of drought responses in wheat
and barley to support gene discovery and analysis
projects. This has involved analysing transcript,
metabolite and protein profiles of plants exposed
to drought stress and building reference databases
of these responses. The third approach builds on
data developed in other species to directly target
genes involved in regulating the drought response
– transcription factors and protein kinases.
2008 ACPFG Annual Report 15
Drought
Forward genetics
The forward genetics program has been built
around two segregating populations; Kukri x
RAC875 and Kukri x Excalibur. In both cases Kukri
is the drought sensitive parent, while RAC875 and
Excalibur represent two different mechanisms for
drought response. Doubled haploid populations
of around 350 and 250 lines, respectively, have
been used as the starting material and these lines
have now been evaluated in 20 environments to
provide an extensive database covering a range of
developmental and yield traits related to drought.
In collaboration with Matthew Reynolds and Dan
Mullan at CIMMYT, one 2008 heat stress trial
involved planting the lines late so they would be
exposed to the summer heat of northern Mexico
during grain development. All of these trials have
allowed us to identify several loci that appear to
be associated with the maintenance of yield or
components of yield under drought stress. These
loci have now become the focus of detailed work
to accurately define the genetic regions and to
validate the significance of the underlying genes.
Two approaches are being used for the detailed
analysis of the target loci. The first approach aims
to validate the loci and assess the suitability of the
associated markers for wheat breeding. This has
been based around a third population, Gladius x
Drysdale. For this cross, around 4,000 recombinant
inbred lines (RILs) were developed. The first series
of 250 lines was used to construct a detailed
linkage map; these lines will move into field trials
in 2009. In the second approach, fine mapping
of loci on chromosomes 7A, 6A, 3B and 1B uses
the large RIL populations produced for the two
Kukri populations. Lines showing recombination
in the target regions have been identified for seed
multiplication and field evaluation.
In partnership with CIMMYT, ACPFG has started
to investigate drought tolerance in durum wheat.
A population developed by CIMMYT has been used
to identify and map major quantitative trait loci
(QTL) based on field trials conducted by CIMMYT.
ACPFG has also imported a durum germplasm
collection assembled by Roberto Tuberosa from the
University of Bologna in Italy, under a European
Union program aimed at investigating yield under
drought stress. This collection will be evaluated in
Australia as part of a collaborative research program
between ACPFG and Italy, supported by the South
Australian Government.
In addition to the new work on durum wheat, two
other research programs were initiated during 2008.
The first was a joint project with the NSW DPI to
investigate the relationship between the genetic
control of drought tolerance and grain quality.
Initially, this project will focus on the Gladius x
Drysdale population but new populations will
16 2008 ACPFG Annual Report
be developed in NSW. The second project is in
collaboration with the group of Jizeng Jia at the
Chinese Academy of Agricultural Sciences, Beijing,
and has been funded by the GCP. This project
links the transcription factor work with the forward
genetics approach. This work builds on
the observation that variation in expression of
drought related transcription factors, seen in the
transgenic work, is strongly correlated with the
strength of the drought tolerance phenotype in
transgenic lines. Therefore, our colleagues in China
will screen germplasm collections for natural
variation in expression levels of target transcription
factors and investigate correlations with yield under
drought stress.
Thorsten Schnurbusch left ACPFG in early 2008
to take up a group leader position at IPK in
Germany. Ali Izanloo completed his PhD in 2008
and James Edwards completed the experimental
work for his PhD and accepted a plant breeding
position with AGT.
Transcript profiling of wheat cultivars
under drought stress
In late 2007 we began a large scale microarray
experiment as part of a multinational effort funded
partially by the GCP. The aim of this project is to
investigate and compare responses to drought in
three different grasses, namely rice, maize and
wheat. Our contribution to this project was the
study of gene expression in the three wheat cultivars
used in the Forward Genetics Program, the drought
tolerant Excalibur and RAC875 and the drought
sensitive Kukri. Gene expression is being profiled in
leaf, stem and heads of plants grown under cyclic
drought condition that mimic field conditions in
southern Australia. The microarray technology
that we employ to carry out this experiment is the
Wheat Long Oligo Chip, which was designed by
an international consortium between ACPFG and
colleagues in Canada and USA.
In 2008 we performed microarray hybridizations
for RNA collected from the leaf material of these
cultivars. Altogether we examined samples from
150 individual plants and performed over 270
individual hybridizations. A software tool – the
Drought Comparator – has been written and
provides convenient access and visualisation of
the resulting datasets. A range of drought responsive
genes have been identified. Among these are
transcription factors, heat shock proteins, ABA
regulated genes and proteins involved in proline
biosynthesis. The same tissue samples were also
used to develop metabolite profiles and we have
started to compare the gene expression datasets
with metabolite concentrations measured in the
leaf samples and are moving on to profiling the
RNA from the head tissue samples.
Drought
Transcriptional regulation of drought
responses
Transcription factors have been shown to control
the activity of multiple stress response genes in
a coordinated manner. Therefore they represent
attractive targets for application in molecular plant
breeding. Genes encoding over 25 transcription
factors and several transcription-related proteins
have been isolated in ACPFG from reproductive
tissues of wheat, barley and maize subjected to
drought, heat and cold stresses.
During 2008 we focused on:
1. Generating and confirming transgenic wheat
and barley lines with constitutive and stressinducible up-regulation for most of the selected
candidate genes.
2. Characterising a drought tolerance phenotype
of transgenic plants.
3. Isolating and characterising stress inducible
promoters from wheat and barley, to
identify new cis-elements and respective
transcription factors.
We isolated three wheat promoters of genes
encoding drought inducible transcription factors,
and one for a cold inducible transcription factor,
which are under evaluation as alternatives to a
currently used maize promoter. The isolated genes
are also a good source of 3’ regulatory sequences
for cisgenic wheat (wheat transformed with wheat
DNA only).
Activity of two earlier cloned drought/cold/salt
inducible wheat promoters of LEA/COR/DHN
genes was confirmed in a transient assay. Two
cis-elements were mapped in one of the promoters
and six transcription factors (four novel) were
isolated using one of these elements. One of the
novel transcription factors can strongly activate
expression from a stress-inducible promoter in a
transient assay. This factor has been selected as a
new candidate for further characterisation.
Two PhD students, Sarah Morran and Kat Pillman,
finished their experimental work in 2008 and
are currently writing their theses. Nannan Yang
successfully finished his Masters studies and was
awarded a PhD fellowship in the US.
4. Characterising flower/early grain specific
promoters to identify promoters suitable for the
prevention of male sterility caused by drought.
We have generated 90% of the planned transgenic
plants . Expression analysis has been completed
for 70% of the transgenics with constitutive
expression and 15% of the transgenics with stress
inducible expression. Successful expression of
transgenes at the protein level was confirmed
in many of the lines by observation of altered
development in T0 plants. Preliminary experiments
for drought tolerance assessment were performed
for seven transcription factors and two protein
kinases. From these transgenic plants, clear
improvement of drought tolerance in two
consecutive experiments was demonstrated
for plants with protein kinase over-expression.
Promising results were obtained for three
transcription factors and one more protein kinase.
Analysis of these plants will continue in 2009.
During her PhD program, Sarah Morran showed
that constitutive expression of two drought
responsive element binding (DREB) factors led to
improved drought and frost tolerance. However,
transgenic plants were stunted and showed
delayed flowering. Analysis of new transgenic
plants with drought inducible expression of the
same DREB factors demonstrated a substantial
decrease of the undesired phenotype in barley
and total absence of stunting or flowering delay
in wheat. Both transgenics showed near 100%
recovery (versus 5–10% recovery of control
plants) after 14 days of drought.
2008 ACPFG Annual Report 17
BORON
Boron
Boron is essential for healthy plant growth and reproduction. Of all plant nutrient elements, boron has
the narrowest range between deficient and toxic soil concentration, and both boron toxicity and deficiency
severely limit crop production worldwide. While deficiency may be addressed easily through the application
of boron rich fertilisers, boron toxicity is more difficult to manage agronomically.
Boron levels are generally higher in subsoils than in the surface root zone, so it is difficult to address the
problem simply through soil management. In southern Australia, 30% of soils in grain growing regions
have levels of boron considered toxic to plant growth. Yield penalties of up to 17% between adjacent areas
of barley have been attributed to differences in shoot boron concentration, and similar figures have been
reported for wheat.
Tim Sutton
Tim Sutton has a Bachelor
of Agricultural Science
with Honours from the
University of Adelaide.
He obtained a PhD in
molecular genetics working
with Peter Langridge at
the Waite Campus of the
University of Adelaide,
focusing on the molecular
aspects of chromosome
pairing in polyploid wheat. He joined ACPFG as a
Research Fellow in 2003,
working on the positional
cloning of boron tolerance
genes from barley and
wheat. He is leader of the
Boron Focus Group and
a member of the MapBased Cloning Group. 18 2008 ACPFG Annual Report
BORON
Wheat boron tolerance gene on
chromosome 7BL
In wheat, we made exciting progress in the search
for the major boron tolerance gene located on
chromosome 7BL. The continuation of high
resolution mapping and marker development,
combined with a candidate gene strategy enabled
the identification of the wheat tolerance gene. This
approach has benefited greatly from the availability
of large genome BAC libraries from tetraploid
and hexaploid wheats, and collaboration with
international programs to physically map the wheat
and barley genomes. So far we have obtained full
length sequences of the gene, and these have been
genetically mapped to the critical tolerance region
(named Bo1) using the Halberd x Warrigal*MMC
doubled haploid mapping population, and the
Cranbrook x Halberd fine resolution mapping
population. At least three alleles of the gene have
been identified in wheat, and there appears to be
association between the presence and absence
of the gene, and boron tolerance. Preliminary
characterisation using heterologous expression
in yeast shows that the protein is a functional
efflux transporter of boron. This has been a major
breakthrough given the technical difficulty associated
with QTL cloning in large genome species,
particularly wheat. The characterisation of the gene,
to enable understanding of its mechanism of action,
is now a priority so that we can implement the
findings into breeding programs in Australia.
The barley 4H Boron tolerance gene Bot1
The chromosome 4H boron tolerance gene Bot1 was
identified from the highly boron tolerant Algerian
landrace barley Sahara 3771. A search of more than
100 wild barleys of diverse geographical origin
has not detected the Sahara haplotype, suggesting
it may have originated in this landrace barley. This
is presumably due to selection pressures of high
boron soils in the dry areas of Northern Africa. We
are collaborating with Barley Breeding Australia to
incorporate genetic material with recombination
close to Bot1 from this project into a breeding
strategy for cultivar improvement. A focus of this
work is to determine the agromonic impact of the
Bot1 gene in the southern Australian environment.
Boron tolerance gene on barley
chromosome 6H
We have also made good progress identifying and
characterising the gene underlying the chromosome
6H boron tolerance QTL in barley. The tolerance
allele of this gene accounts for approximately 35%
of the reduction in boron accumulation in leaves
of tolerantgenotypes, compared with intolerant
genotypes. In combination with the 4H tolerance
gene Bot1, a net effect is the reduction of leaf boron
content by up to 80%. With the goal of identifying
boron tolerant material for variety improvement,
we commenced a screen of two induced mutation
populations. In collaboration with IPK in Germany,
15 lines derived from screening a targeting induced
local lesion in genomes (TILLING) population will
be phenotypically tested for boron tolerance and
segregation analysed in relation to the mutation.
A TILLING population developed at ACPFG in
the elite malting variety Flagship has been
screened phenotypically and the selected plants
will be characterised with respect to mutations
in the 6H tolerance gene. This material could
be useful for breeding programs as a source of
boron tolerant germplasm in an otherwise highly
adapted background.
2008 ACPFG Annual Report 19
Nutrients
NUTRIENTS
Most soils in Australia are poor in almost all
plant nutrients. Farmers are heavily dependent on
fertilisers to maintain yields of our major crops.
For example, over 70% of Australian cropping
land is low in phosphate (P). For wheat and barley
production alone, P fertilisers cost Australian
farmers $400 million annually and, in the absence
of preventative measures, P deficiency would
cause yield losses worth $1 billion per annum.
The availability of P and other nutrients such as
zinc (Zn) in soil is further reduced by drought.
Aluminium (Al) toxicity also causes significant crop
losses in acid soils, before which constitute 40%
of the world’s arable land. In Australia, Al toxicity
affects 1.5 million hectares of cropping land and
causes annual yield losses of $180 million.
Transporter genes of plants play significant roles in
adaptation to low nutrient soil and in avoidance of
metal toxicity. An improved transporter capacity of
crops would not only reduce fertiliser inputs, but
also increase crop adaptation to nutrient-poor and
acid soils and nutritional values of grains. Roots are
the most important organ in nutrient acquisition
and drought tolerance. Understanding of root
functions and genetic variation in root traits is
essential for the improvement of crop yields in low
rainfall environments.
ACPFG’s nutrient research aims to determine the
physiological and biochemical mechanisms of
transporters of P and Zn; understand the molecular
regulation of the genes that alleviate P; Zn and Al
stress; develop crop plants with improved tolerance
to these stresses, and identify genetic variation in
root traits.
Chunyuan Huang
Chunyuan Huang
specialises in plant
physiology, molecular
biology and genetics.
His main research interests
are molecular mechanisms
of plant responses to
nutrient stresses, particularly
phosphate and zinc,
genetic variations in plant
tolerance to nutrient
stresses and improvement
of nutrient stresses through
genetic manipulation.
Other research interests
include root traits related to
nutrient acquisition
and drought tolerance.
At ACPFG he is improving
phosphate efficiency
and zinc deficiency
tolerance in cereal crops.
Barley roots of Sahara in deep soil (45–60 cm) 10 days
after anthesis. Root branches are fewer and shorter than
those in the top soil.
20 2008 ACPFG Annual Report
Barley roots of Sahara in top soil (0–15 cm) 10 days after
anthesis.
Nutrients
Transgenic barley lines containing a Zn transporter
were tested for improvement of Zn nutrition.
The introduced transgene increased grain Zn
concentration threefold. Potential applications in
improvement of crop and human Zn nutrition are
being explored.
Research Highlights in 2008
Two barley Pht1 transporters have been
characterised. Results reveal that one is a low
affinity P transporter which co-transports P ions
with hydrogen ions. Surprisingly, this transporter
can also transport sulphate and nitrate ions,
whereas the other Pht1 transporter does not
transport sulphate and nitrate ions. These results
provide new insights into transport mechanisms,
suggesting these two Pht1 transporters may operate
in P uptake and translocation.
BAC clones containing four closely related
paralogues of barley Pht1 transporter genes were
isolated. Promoter sequences and transcript
analyses reveal regulatory divergence of these
four paralogues, implicating their importance in
improvement of P acquisition.
Nine parental lines of double haploid wheat
mapping populations were grown in four field sites
to test P use efficiency and the association with
drought tolerance. Preliminary results showed that
considerable genetic variation in P use efficiency
existed among these parental lines. These wheat
parental lines will be grown in a P-deficient site
in Syria to examine genetic variation in P use
efficiency in a different environment.
The rye Alt4 locus was found to control the
release of malate, citrate and oxalate from the
root tips, whereas the homologous locus in wheat
facilitates release of malate only. These wheat and
rye Al tolerance loci encode ALMT1 organic acid
transporters, which are being characterized using
transgenic plant and gene expression in frog eggs,
in collaboration with colleagues at the University
of Adelaide. Large-insert (BAC) clones spanning the
rye ALMT1 gene cluster were recovered using our
rye cultivar Blanco BAC library and are being used
for sequencing.
In collaboration with Alan McKay from the South
Australian Research and Development Institute,
soil DNA analysis of roots of field-grown crops was
conducted and revealed some genetic variation.
Single-copy TaqMan probes were compared with
multiple-copy probes to quantify wheat and barley
root DNA content and estimate living cell numbers.
Field root samples were used to calibrate root
length with DNA content.
2008 ACPFG Annual Report 21
COLD
COLD
The reproductive structures (flower spikes) are
the most cold-sensitive parts of wheat and barley,
and sporadic frost events in the order of -2oC to
-5oC during flowering can damage the grain or
cause floret sterility and complete loss of grain set.
Vegetative tolerance is also a concern in parts of
the world where cereal crops need to overwinter
at the vegetative stage under severe conditions
(e.g. -20oC) before flowering in the spring/summer.
Nick Collins
After a Bachelor of
Science from Monash
University, Nick moved
to Adelaide to do his PhD
in the laboratory of Bob
Symons, working on the
genetics of barley yellow
dwarf virus resistance in
barley and rice. He then
Cold tolerance research in 2008 focussed on two
areas. These were the genes on chromosomes
5H and 2H that determine natural variation in
frost tolerance between barley varieties as well as
transcription factors involved in cold responses.
In 2008, all PhD students working on cold were
writing their theses.
Transcription factors were selected for study
because they were expressed in heads of a frost
tolerant barley variety and bound to promoter
elements of drought or cold responsive genes,
namely drought responsive elements (DREs) or
ACGT-containing ABA response elements (ABREs).
A reporter system, involving co-bombardment of
gene constructs into wheat culture cells, has been
used to confirm activation of a cold responsive
promoter by two of the transcription factors, and
to locate promoter elements by deletion and
point-mutant analysis. A gene for one dehydrationresponsive element binding factor was mapped
in the vicinity of the Fr2 vegetative cold tolerance
locus on chromosome 5H of barley. Several
transcription factor genes were shown to exhibit
cold-inducible expression, while initial efforts to
22 2008 ACPFG Annual Report
joined Tony Pryor at the
CSIRO Division of Plant
Industry in Canberra to
isolate rust resistance genes
from maize. His second
postdoctoral position
was in the group of Paul
Schulze-Lefert in the
Sainsbury Laboratory (UK)
researching mechanisms
of cell-wall penetration
resistance to powdery
mildews in barley. Nick
then returned to Adelaide
engineer cold tolerance in transgenic barley plants
by over-expressing two such factors have given
encouraging results. Transgenic plants will be more
thoroughly evaluated in a newly acquired growth
cabinet which has been especially engineered to
provide long-term cold treatments.
Study of the 5H and 2H tolerance genes was
carried out using the frost simulation chamber at
AGRF, using previously established overnight frost
simulation protocols. An approach was developed
which enabled the inheritance of these genes to
be followed accurately, despite their relatively
subtle tolerance effects. These procedures will
be employed in work to fine map and eventually
clone the tolerance genes. The tolerance gene
on chromosome 2H was shown to be genetically
separable from a nearby gene (Flt-2L) controlling
plant height, flowering time and rachis internode
length. Experiments involving ice nucleator spray
and direct measurements of ice-induced tissue
damage suggested that the 2H tolerance effect
was dependent on freezing and was not caused by
chilling damage.
to join ACPFG and lead the
positional cloning group.
Salinity
SALINITY
Stuart Roy
Stuart Roy has a Bachelor
of Science with Honours
in Plant and Environmental
Biology from the University
of St Andrews, Scotland.
He obtained a PhD at the
University of Cambridge,
where he designed
quantitative assays to
measure enzyme activities
in sap extracted from
single plant cells. In 2001
he received a Broodbank
Research Fellowship to
continue his work in
Cambridge, developing
techniques for carrying
out microarray analysis on
mRNA extracted from single
plant cells. Stuart arrived
Salinity is a global problem affecting agricultural
land. In Australia, it is estimated that currently
4.6 million hectares (ha) of Australian farmland
are affected to some extent by salt. The situation is
particularly severe in Western Australia and South
Australia, with one in two and one in five farms,
respectively, affected by salt. Due to poor land
management practices, the area of saline-affected
agricultural land is expected to increase to 13.6
million hectares by 2050.
The main toxic component of salt is the sodium
ion (Na+). High cellular concentrations of Na+,
particularly in cells in the leaf, interfere with
critical metabolic functions such as enzyme activity
and protein synthesis. In addition, high Na+
concentrations can also cause osmotic damage.
Plants can be considered to have three main
mechanisms for tolerating Na+ stress.
1.
Osmotic tolerance, which is the plant’s ability
to maintain water relations and to continue to
grow while stressed.
2.
Na+ exclusion, whereby the amount of Na+
transported to the shoots from the roots is
minimised through alteration of the movement
of Na+ throughout the plant.
3.
Na+ tissue tolerance, through
compartmentation of Na+ in tissues and
cellular organelles, such as the vacuole, away
from areas where the Na+ can do damage.
at the ACPFG in 2004
and leads the Salt Focus
Group. His current research
involves identifying QTLs
and genes for sodium
exclusion in Arabidopsis.
The aim of research in the Salt Group is to improve
the salinity tolerance of Australian cereal crops
by generating plants that can survive and produce
viable yields on saline soils. Generally, the best
yielding crop plants in saline soils are those which
accumulate the lowest concentrations of Na+ in
the shoot. Thus, if we understand the mechanisms
of Na+ movement within a plant, we can alter
Na+ transport and hence increase crop salinity
tolerance. Wild relatives of crop plants, however,
can make use of all three mechanisms of salinity
tolerance and can accumulate higher levels of Na+
in their shoots before symptoms of damage are
observed. An understanding of the mechanisms of
tolerance in these wild relatives would undoubtedly
present opportunities to enhance salinity tolerance
in commercially important cereals.
2008 ACPFG Annual Report 23
Salinity
Identification of novel genes involved
in salinity tolerance
We are using lines of interest to generate
mapping populations which allows us to identify
chromosomal regions which are linked to salinity
tolerance QTLs. Once these regions have been
located, candidate genes can be identified.
A highlight of 2008 was the use of the LemnaTec
Scanalyzer to non-destructively measure the
growth rates of lines of wheat, barley and Triticum
monococcum and quantify through time the
effects of salinity on growth and senescence.
In combination with measurements of shoot Na+
concentrations, this has allowed us for the first time
to calculate a plant’s osmotic tolerance and Na+
tissue tolerance, in addition to measuring shoot Na+
exclusion. We discovered that those plants which
were very salt tolerant used a combination of either
osmotic tolerance and Na+ exclusion, or osmotic
tolerance and Na+ tissue tolerance. The Scanalyzer
is now being used to map for QTLs linked to all
three tolerance mechanisms in wheat, barley
and T. monococcum.
A candidate gene for salinity tolerance has been
identified from a strong QTL discovered in a barley
mapping population. There was a two-fold difference
in expression of the gene between the parents during
salt stress.
24 2008 ACPFG Annual Report
In another barley mapping population, a Na+
exclusion QTL has been narrowed down to a
candidate gene which is more highly expressed in
the tolerant Clipper variety than in the intolerant
Sahara. In Arabidopsis, the gene is responsible for
controlling the activation of Na+ transporters.
Analysis of wild relatives of cultivated cereals
continues to provide exciting results. Accessions of
T. monococcum, show significant variation in growth
rates, Na+ exclusion and salinity tolerance when
compared with cultivated wheat. Similar results were
also observed with Triticum dicoccoides, wild emmer
wheat. A number of QTLs for Na+ exclusion have
been identified in T. monococcum, while several
accessions of T. dicoccoides have been shown to
possess traits which may prove useful if bred into
durum wheat.
Work with Arabidopsis thaliana, a model plant,
resulted in seven significant QTLs for Na+ exclusion
being discovered. Two are being pursued further.
A strong QTL on chromosome 2 has been narrowed
down to 35 genes and a candidate gene, with
suspected involvement in regulating the plant
cellular response to Na+, has been identified.
Expression profiling of different Arabidopsis ecotypes
shows that this gene is upregulated two to threefold
in wild type plants, and preliminary data from gene
knockout plants show that the mutants accumulate
almost double the concentration of salt in their
leaves. To characterise this candidate gene further,
transgenic plants which under or overexpress the
gene have been created.
Salinity
Characterisation of candidate genes
for salinity tolerance
A number of genes have been identified as having
an important role in salinity tolerance, the two most
notable being PpENA1 and members of the HKT
gene family. When grown under saline conditions,
we have discovered that rice expressing PpENA1 not
only has lower shoot Na+ concentrations than wild
type plants, but also has substantially more biomass.
The HKT gene family is important in regulating
the transport of Na+ throughout a plant. Rice has
nine HKT genes split between the two subgroups.
Expression profiling of these genes in salt stressed
rice indicated that only a few HKT genes are
important in salinity tolerance. One of these genes
has been shown to upregulate its expression in
the shoot during salt stress; transgenic plants are
being created to knock out this gene. Further
characterisation of the gene OsHKT1;5, the rice
equivalent of the Arabidopsis AtHKT1;1, is also
being undertaken.
While the primary focus of research in the last few
years has been on PpENA1 and the HKT gene family,
new candidate genes and gene families are also
being identified as important in Na+ tolerance.
One such gene family has been discovered in
yeast and found to be involved in the initial Na+
influx into a cell. This is a crucial discovery as the
mechanisms for the initial entry of Na+ from saline
soils into plant root cells are still unknown.
Another candidate gene from Arabidopsis that is
involved in vacuolar sequestration of Na+, has been
constitutively overexpressed in barley. It has been
shown that this gene plays an important role in plant
salinity tolerance. When grown in saline conditions,
barley plants which have been transformed with this
gene, or with a gene from yeast involved in Na+
transport, show increased biomass and fewer toxicity
symptoms than wild type plants. These transformed
barley plants will be tested in field conditions to
investigate whether yield is also increased.
Other candidate genes have been identified through
a series of microarrays conducted on salt stressed
rice plants.
Regulation of expression of salt
tolerance genes
We demonstrated, in Arabidopsis, that when
AtHKT1;1 was expressed only in the vascular
bundle of the root, the amount of Na+
accumulating in the shoot could be reduced by up
to 60%. These results have been mirrored in rice.
Experiments are now in progress to further refine
the control of gene expression by identifying the
transcription factors that are active during salt stress.
Transcription factors are elements which bind to
the promoters of genes and control the spatial and
temporal initiation of gene expression.
With spatial control of gene expression revealing
promising results in model species, introduction
of a similar system in Australian cereals is being
attempted. Promoters that activate genes in specific
cell types are being identified in barley and will
be used to control the expression of various genes
involved in ion transport and salinity tolerance.
2008 ACPFG Annual Report 25
Bioinformatics
BIOINFORMATICS
Biological research is becoming increasingly data intensive. DNA sequencers are now capable of reading
thousands of millions of bases in a single run, microarrays can measure the expression of tens of thousands
of genes, marker systems can interrogate tens of thousands of polymorphisms, and the latest automated
phenotyping systems can screen thousands of plants with little human intervention. Combined with the
internet, which enables the open sharing of this data between international groups, data overload can
generate significant headaches for researchers. While bioinformatics cannot provide an easy answer to this
problem, it can promote quality research by making data accessible for integration and interrogation.
Dave Edwards
Following his PhD studies
at the University of
Cambridge, Dave worked in
the Genetics Department of
the University of Cambridge
on rice genome structure,
before joining Long Ashton
Research Station, Bristol,
Software Development
In 2008 we have continued to write and improve
software tools as required by ACPFG researchers
UK. During his time in
Bristol, he developed cereal
QPCR integrated network suite (qINS); this is
microarrays for both high
throughput transposon
and software tool for clustering and visualising
homologous relationships of genes and associated
expression data.
a software application which will help organize and
analyze the vast amount of QPCR data generated
at the ACPFG. In 2008, improved semi-automated
primer and cDNA submission interfaces were
added and an updated Windows client for the
curator was developed and is being deployed.
Phylogenomics; as part of the GrassKin project, we
WebComparator; this is a comparative tool for
to the Victorian Department
GrassKin; a web interface for this database
have been developing algorithms for clustering genes
based on the similarity of their sequences. These
algorithms have proved useful outside their intended
application: they helped with the identification of
individual homoeologues on chromosome 7 of
wheat and, when combined with simultaneous
clustering of gene expression data, have helped with
the identification of genes potentially involved in the
biosynthesis of the (1,3;1,4)-b-D-glucan enzyme
found in plant cell walls.
FormatFasta; a tool that performs common
manipulations of files containing gene sequences.
Microarray normalization project; technical
issues with the microarrays used in a Generation
Challenge wheat drought project compelled us to
develop a new, improved normalisation technique.
We will write software that will allow us to make
use of these improvements in the analysis of future
microarray experiments.
visualising the wheat and barley gene expression
atlases. It has now been made publically available
at http://contigcomp.acpfg.com.au as part of a
submitted publication.
expression profiling, along
with computer based tools
for sequence data analysis
and molecular marker
discovery. He then moved
of Primary Industries in
Melbourne, establishing
a new bioinformatics
research team. During this
XRMAplot; we have added features to this tool,
time, he managed groups
which helps to analyse data obtained with XRMA
microscopy. It has also been made available for use
outside ACPFG.
sequencing genomes and
researching molecular
Australian Wheat Pedigrees Database; the
transcriptomics research
database system at http://gwis.lafs.uq.edu.au
has been maintained and updated with historical
information on Australian Triticale and durum
wheat pedigrees obtained from the CIMMYT library
in Mexico.
markers in Brassica and
Strawberry, as well as a
group. He recently moved
to ACPFG’s University of
Queensland node where he
is establishing a new team
to support bioinformatics
BAC and Gene Annotator; a web-based BAC and
within ACPFG, as well
genome annotator tool has been developed. The
tool is available at http://flora.acpfg.com.au/bga.
as developing systems
for genetic and genomic
Wheat phenome atlas; analysis techniques are
of crop systems.
being applied to phenotypic, marker and pedigree
data, generated for part of the CIMMYT spring
wheat breeding program for the detection of
marker-trait associations.
26 2008 ACPFG Annual Report
mutagenesis and gene
analysis for a number
bioinformatics hardware
We have pioneered methods for single sequence
repeat (SSR) and single nucleotide polymorphism
discovery from sequence data and continue with
development of pipelines, databases and web
interfaces for the discovery and annotation of
markers from the latest high throughput sequence
data. An initial database of annotated barley SNPs
has been produced and additional databases have
been produced for Brassica and rice, while a wheat
database is in preparation. Software has also been
developed for the identification of polymorphic SSR
markers and this has been assessed and validated
in barley. An SSR discovery tool (SSRPrimerII) has
been developed and is available at http://flora.
acpfg.com.au/ssrprimer2.
Four high performance computers were recently
purchased using a combination of ACPFG and
ARC funds to support bioinformatics activities at
UA and UQ. Two machines have been installed
at UA and initial web services have been
implemented (SSRPrimerII and BAC and Gene
Annotator). Further tools and applications are
under development and will be mirrored once
the UQ machines have been installed.
IT Infrastructure
Three new servers, purchased at UM, were installed
and maintained to provide additional capability:
database, website and remote desktops. Storage
has doubled with the acquisition of an additional
eight terabyte storage array. New firewalls have
been installed to provide seamless remote access
to network resources at the UM node. Dedicated
computer rooms have been refurbished and reinstalled with support for double the amount of
equipment. Network switches and the link
between buildings have been upgraded, with an
up to tenfold performance improvement over
previous technology.
Genome sequencing technology
Through other activities at UQ, ACPFG has
access to all three next generation sequencing
technologies, the Illumina Solexa, Roche 454
and Applied Biosystems SOLiD. We are applying
this sequencing technology for gene discovery,
expression analysis, physical genome mapping and
miRNA discovery. This research will support several
ACPFG projects.
Dozens of new software applications were installed
in 2008 along with a standard Windows-XP desktop
to ensure high availability of software regardless
of physical location or computer being used. The
standard desktop can roll out a new computer
within several hours and is almost completely
automated using Microsoft Remote Installation
Service. This approach permits:
acpfg.com.au
PLANT STRESS RESPONSE: ANALYSIS AND INNOVATION FOR FOOD SECURITY
# p for platform
my $parameterFile =
name=value and it will be picked up
&get_parameters();
#s for singletons
my $CONTIG = 1
»» Targeted desktops for specific requirements,
such as proteomics or metabolomics data
analysis.
# o for organism
# will get parameters and any input
files from the <organism> subdirectory
# assuming this scripts is in /scripts, the
organism subdirectory will be at
/<organism>
»» A standard suite of bioinformatics tools to
be widely deployed across the node, such
as BioEdit, Sequencher and TreeView.
# r for restrict to a number
my $numToProcess= 1000000:
if ($args {r}) {
$numToProcess = $args{r};
}
#files
my $fileToRead = ””;
my $fileOut = ““,
my $cap_infile = ““;
my $cap_outfile = ““;
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0
A new Google-like website has been added for
proteomics and metabolomics papers, enabling
researchers to share papers and locate them more
easily, regardless of who found a given paper.
We have made more websites available to
support various types of collaboration, such as
wikis, instant messaging and internet telephony.
Proteomics has received a significant boost through
four new instruments to improve the quality and
throughput of results obtained.
Metabolomics data analysis has been augmented
with multi-variate statistical analysis techniques
using software such as Unscrambler, AnalyzerPro
and Agilent Genespring to aid in interpretation of
experimental results.
2008 ACPFG Annual Report 27
Bioinformatics
Molecular marker discovery
‘Omics
‘OMICS
Proteomics and protein analysis
Metabolomics
The proteomics capabilities of the ACPFG
increased significantly during 2008. Two new
mass spectrometers were commissioned, a Qstar
Elite, used for isobaric tag for relative and absolute
quantitation (iTRAQ) profiling experiments, and
a Qtrap 4000, used for targeted analyses. Each
machine represents next generation developments
and improvements in instrumentation, each having
faster scanning rates and significant improvements in
sensitivity compared with the machines they replaced.
The metabolomics platform at UM Has been
strengthenedby the formation of a new NCRIS
project, Metabolomics Australia (MA). A number
of new gas chromatography-mass spectrometry
(GC-MS) and liquid chromatography-mass
spectrometry (LC-MS) instruments were installed
and commissioned in 2008 and are now running
at full capacity. Several new staff have been
employed and trained on those instruments
and in metabolomics. Existing metabolomics
methods have been established successfully on
the new instruments, however, a number of novel
methodologies for both targeted quantitative
metabolite profiling and metabolite mass
fingerprinting are currently under development
and validation. In addition, through the Australian
Bioinformatics Facility, we have employed four
new informaticians and IT support people. They
will support metabolomics through faster and more
reliable software for data extraction from analytical
instrumentation, and through sophisticated
statistical and multivariant analysis workflows
for data interpretation.
The Qstar Elite instrument was used in combination
with 8-plex iTRAQ peptide tagging reagents, and
was applied to the analysis of proteins isolated from
the leaves of wheat plants collected during drought
experiments. The relative abundance of close to
4,000 peptides in 24 different time points has
been identified from three different wheat cultivars
and a website has been developedto allow the
dissemination of these results.
The Qtrap 4000 instrument has been used for
quantitative, targeted analyses of selected peptides.
This machine was used to independently verify
the abundance data collected from the iTRAQ
experiments. The results of this comparison
indicated that the iTRAQ data had a high degree
of accuracy. A drought comparator website
was constructed to display iTRAQ data across
experiment runs and provide full search engine
capabilities over the identified peptides.
Proteomics studies on rice suspension cultures
under abscisic acid and salt stress treatments are
nearing completion.
Support provided to ACPFG projects included:
»» Completion of an analysis of metabolites
of three wheat cultivars exhibiting different
tolerance levels to drought.
»» Commencement of an analysis of rice pPEna
transgenic plants.
»» Comparison of organic acid profiles of exudates
of aluminum treated rye and barley roots.
»» Completion of a large study comparing the
metabolite profile of Arabidopsis mutants treated
with different salt levels.
28 2008 ACPFG Annual Report
Ute Roessner
Ute Roessner obtained her
PhD in Biochemistry at
the Max-Planck Institute
for Molecular Plant
Physiology in Germany,
where she developed
novel GC-MS methods
to analyse metabolites in
plants. Together with the
application of sophisticated
data mining, the field of
metabolomics was born
and is today an important
tool in biological sciences,
systems biology and
biomarker discovery.
In 2003 she moved to
Australia where she
established a metabolomics
platform as part of ACPFG.
Since 2007 she has been
involved in the setup of
Metabolomics Australia
(MA) and now leads the
MA node at the School of
Botany in the University of
Melbourne, complementing
her ACPFG work.
Genome Analysis
GENOME ANALYSIS
Delphine Fleury
Delphine Fleury obtained
a Master in Chemistry
and Plant Biology at the
University of Rennes
in France in 1996, for
which she studied the
genetic diversity of natural
populations of Agropyron,
a wild relative of wheat.
In 1997 she received
Honours in Genetics and
Plant Production, working
in the plant pathogenesis
group of the French
National Institute for
Agricultural Research, on
mutant analysis of the soil
bacterium Pseudomonas.
In 1998, she moved to
the Plant Biotechnology
Institute of Toulouse,
there she constructed a
genetic map of sunflower
and identified QTLs for
resistance to a pathogen
and for photosynthesis.
After completing her PhD
in 2001, she moved to
the University of Ghent in
Belgium as a postdoctoral
fellow. She cloned and
analyzed the function of
several genes involved
in leaf development
A project of physical mapping and genome
sequencing was initiated in 2008 between Europe
and the ACPFG, through an International Linkage
Project formally named ‘Genomics for Triticeae
improvement for food, feed and non-food uses’.
We are evaluating the physical distance between
markers along a chromosome, the gene content,
and the recombination in wheat and barley.
This collaborative project with the European
Commission Seventh Framework Programme aims
to a generate physical map and genome sequences
by focusing on chromosome arm 3S and group
7 chromosomes.
One of the interests of physical mapping is to allow
comparative studies, especially between wheat,
barley and rice. We identified two inversions
between the Aegilops tauschii Ph2 map and the
orthologous region on rice chromosome 1. Using
the barley genetic map data generated by Tim Close
from the University of California at Riverside in the
USA and Robbie Waugh from the Scottish Crop
Research Institute, we observed one distal inversion
between Ae. tauschii and barley, which was not
previously known. The same markers are now being
mapped on barley physical contigs and to date 40
were anchored successfully onto a BAC of barley
cultivar Morex, in collaboration with Nils Stein’s lab
at IPK in Germany. We have also sent the primers of
193 SSR and expressed sequence tag (EST) markers
on the 3DS chromosome arm to Jaroslav Dolezel
in the Czech Republic for screening of the 3DSspecific BAC library. The data will allow comparison
of the physical maps of the Ae. tauschii, barley H
and wheat D genomes.
Physical mapping generates crucial data for
map-based cloning of particular genes and is the
preliminary step to the sequencing of large and
repetitive genomes such as wheat and barley.
Our second target is the group 7 chromosomes.
The chromosome 7H of barley carries important
loci controlling traits such as malting quality,
disease resistance and salt and drought tolerance.
Our ACPFG colleagues identified four QTLs
related to yield and salt tolerance on chromosome
7A of wheat. Our goal is to assemble a physical
map across 7H and identify the full gene content
through shotgun sequencing of chromosome 7AS.
Postdoctoral fellow Bao-Lam Huynh was recruited
in December 2008 by UniSA to work on this project.
of Arabidopsis, in
collaboration with
European labs. Despite
the success of the project,
which led to several
international publications,
she decided to return to
crop genetics and chose
ACPFG. She moved to
Adelaide in 2006 to start the
Genome Analysis Group.
2008 ACPFG Annual Report 29
Resources
RESOURCES
Plant growth resources
Transformation systems
A research infrastructure block grant was awarded to
Andrew Jacobs and Sergiy Lopato for the purchase
of a new growth cabinet capable of producing
temperatures below zero. This will enable ACPFG
researchers and others within the University of
Adelaide to routinely undertake experiments
involving low temperature stress or screening.
Barley
Agrobacterium tumefaciens was used to transform
21085 immature barley scutella with 50 different
gene constructs in 2008. Approximately 810
putative transformants were transferred to soil.
Wider application of the Agrobacterium-mediated
barley transformation procedure was demonstrated
in two advanced breeding lines.
LemnaTec Scanalyser software was upgraded with
an improved database and user interface, and better
image analysis software.
Wheat
36 gene constructs were tested in stable
transformation experiments in 2008, with over
750 independent transgenics of cultivars Gladius,
Drysdale, Rees, Frame and Bobwhite produced
and analysed.
Transient transformations with the betaglucuronidase (GUS) and green fluorescent protein
(GFP) marker genes were performed for fine
mapping of the cis-regulatory domains of the new
wheat-derived stress-inducible promoters.
A mutant Cytidine deaminase gene was cloned to
check negative selection in marker gene removal
in transgenic wheat.
Experiments in Agrobacterium-mediated stable
transformation of wheat began in 2008.
Arabidopsis
21 transformations relating to cell walls, boron and
salt were conducted in 2008 using the floral dip
protocol, with an average of 15 transformants per
transformation. Protoplast transformation protocol
optimisation continued during 2008. Arabidopsis
growth rooms were shut down and decontaminated
in December.
Physcomitrella patens
Of 34 moss transformations in 2008, only two
stable transformants were produced, even though
a number of unstable transformants were obtained
during this period. The use of a new vector has
dramatically increased the efficiency of the
protocol, with 16 stable transformants coming
through the first control transformation using the
new vector.
30 2008 ACPFG Annual Report
Andrew Jacobs
Andrew Jacobs has a
Bachelor of Science with
Honours from Flinders
University and a PhD from
the University of Adelaide.
He has worked for CSIRO
Plant Industry and the
Max Planck Institute for
plant breeding research
in Cologne, Germany,
where he isolated the
gene responsible for the
formation of callose at
sites of fungal infection
in Arabidopsis leaves and
characterized the effects
of mutations in this gene.
Andrew joined ACPFG
in 2003 and leads the
Technology Platforms
Program. His current
research projects focus on
abiotic stress tolerance with
an emphasis on salinity
tolerance and developing
improved tools and greater
resources for the analysis
of relevant genes.
Resources
Mutant populations
The barley Flagship mutant population compiled
of around 5,000 families was completed. DNA has
been extracted from the bulk of these families and
the population is ready for screening. Negotiations
have been initiated with AGRF to provide a TILLING
service based on this mutant population.
Approximately 200 flanking sequence tags (FSTs)
have been isolated from F1 lines of a barley
transposon tagged mutant Ds x Ac2 population.
These crosses should further demonstrate that our
Flagship back-crossed Ds elements are able to
transpose. In 2008 we began isolating these FSTs
using an improved TAIL-PCR protocol.
Genome structure resources
Production of BAC libraries was halted in 2008
after it was decided the range of libraries already
generated were sufficient for ACPFG needs. A
number of quality assurance screens were conducted
on the BAC library stocks and a several extra
membranes for screening were produced as needed.
The BAC libraries held at the ACPFG for various
rye, barley, Phalaris and wheat varieties were
extensively screened this year for abiotic stress
tolerance genes, including boron and aluminium
tolerance genes.
Promoter isolation
Four salt stress and three more general abiotic stress
inducible promoters were isolated from various
rice cultivars and cloned into reporter constructs,
along with six putative promoter sequences from
rice enhancer trap lines. These constructs await
transfer into rice for further analysis. Three drought
inducible promoters were isolated from wheat and
the inducibility of these will be screened using
northern blots. Of particular importance has been
the evaluation and use of the Rab17 promoter. This
promoter has been extensively used in developing
drought tolerant transgenic wheat and barley lines.
Analysis of early grain specific promoters has
been continuing. ACPFG has lodged six patent
applications covering the grain promoters from
wheat and barley.
Protein structure resources
Maria Hrmova and colleagues received several
grants that will further ACPFG’s capacity to resolve
protein structures. They include grants that will
give ACPFG researchers access to a shake-free
crystallographic cabinet, the South Australian
Facility for Small and Large Molecule X‑Ray
Diffraction Structure Determination and BioCars:
A Synchrotron Structural Biology Resource, based
in the USA.
In situ hybridisation/
Immunolocalisation
RNA in situ hybridisation revealed the expression
pattern of two aquaporins in grapevine, which
was confirmed with protein immunolocalisation.
The development of a more sensitive RNA in situ
detection method enabled detection of AtHKT1;1
in Arabidopsis root. A selection of probes were
tested on a range of plant material to directly
compare sensitivity and expression patterns with
both the old and improved detection methods.
Hybridisation stringency experiments optimized
sense and antisense probe conditions with the
new method.
Immunolocalisation of antibodies to a drought
transcription factor included a comparison of
fluorescent detection with two colorimetric
alternatives, to address problems with barley
leaf autofluorescence.
Antibody production
Monoclonal antibodies to six separate targets
were raised successfully in 2008. DNA-based
antibody production technology remains a work
in progress. Seven polyclonal antibodies and four
monoclonal antibodies were sent to Neubody
for marketing to the wider research community.
ACPFG will receive a percentage of the profits
from the sales of these antibodies.
2008 ACPFG Annual Report 31
Aligned Programs | Cell Walls
CELL WALLS
Cell walls are dynamic structures that represent
key determinants of overall plant shape, plant
growth and development, and responses of plants
to environmental and pathogen-induced stresses.
Walls play centrally important roles in the quality and
processing of plant-based foods for both human and
animal consumption, and in the production of fibres
during pulp and paper manufacture. In the future, wall
material that constitutes the major proportion of cereal
straws and other crop residues will find increasing
application as feedstocks for renewable biofuels and
composite manufacture.
While the chemical structures of most wall
constituents have been defined in detail, the actual
synthesis of the polysaccharides remains unclear
and many of the enzymes involved in making or remodelling them also remain largely undefined.
However, there have been exciting recent advances in
our understanding of cellulose biosynthesis in plants,
and of the genes and enzymes which play a key role
in mixed-link glucan synthesis, a polysaccharide that
has particular implications for human health.
Current research in the cell wall group seeks to
expand our knowledge of both cellulose and mixedlink glucan biosynthesis. The former is achieved
through our association with DuPont-Pioneer in the
USA, which is further supported by a Linkage Grant
from the ARC, and the latter by our participation in the
Food Futures Flagship to engineer higher fibre grains.
Cellulose Biosynthesis
Through the ACPFG, the cell wall group of the
University of Adelaide has developed research
collaborations with DuPont-Pioneer in the area
of cellulose biosynthesis in maize and barley.
The work has been supported by an ARC Linkage
Grant from 2006 to 2008. A number of extremely
beneficial visits have been made by Adelaide-based
staff to DuPont-Pioneer laboratories in both Des
Moines and Wilmington. In particular, Margaret
Buchanan, a PhD student supported by the ARC
Linkage Grant, and Jill Taylor have been able to
work with Pioneer in their facilities.
At the end of 2008, a second substantial ARC Linkage
Grant was awarded to the current Chief Investigators
to allow this project to continue into 2009 and beyond.
Rachel Burton
Rachel Burton completed
Honours in Microbiology
at the University of
Bristol, UK, and then
moved to the John Innes
Centre (JIC) in Norwich
for her PhD. Following
a postdoctoral position
at the JIC investigating
starch biosynthesis in peas
and potatoes, she moved
to Adelaide in 1995 to
take up a postdoctoral
position in Geoff Fincher’s
laboratory. She worked on
genes involved in cellulose
biosynthesis, which were
first described in plants
in 1996. Since then she
has developed a broader
interest in plant cell wall
polysaccharides and with
colleagues in Adelaide
and Melbourne made
the seminal discovery,
published in Science, that
the cellulose synthase-like
F (CslF) genes are mixedlink glucan synthases.
This polysaccharide is
beneficial for human
health and important in
the malting and brewing
industries. Her current
work, still based in Geoff
Fincher’s lab, seeks to build
on this discovery through
participation in the Food
Futures Flagship scheme.
32 2008 ACPFG Annual Report
Aligned Programs | Cell Walls
Barley leaf sections probed with the beta-glucan antibody, detected with Alexafluor488. The control (left) shows endogenous
polysaccharide, while the transgenic (right) shows enlarged cells with increased amounts of beta-glucan, especially in the
vascular cells. Photographs by Natalie Kibble.
Mixed-Linkage Glucan Biosynthesis
Through the Food Futures Flagship, we have
continued our successful collaboration with groups
at CSIRO in Canberra and at UQ towards the goal
of increasing the amount of soluble dietary fibre in
grain, particularly wheat, for human benefit.
The barley CslF gene family has been defined,
leading to our first joint publication “The genetics
and transcriptional profiles in the cellulose
synthase-like HvCslF gene family in barley” in Plant
Physiology in March 2008.
Using barley as a model, we have over expressed
some of the mixed-link glucan synthase genes,
the CslFs, in transgenic plants, leading to the
accumulation of higher amounts of mixed-link glucan.
Work on the barley CslH gene in 2008 has
demonstrated that this gene is also a mixed-link
glucan synthase. A full patent was submitted in
December 2008 and this work will be published
in early 2009.
A successful pilot pig feeding trial was carried out
at Gatton in Queensland, where pigs fed a diet
containing a higher arabinoxylan content showed
marked positive differences in a number of assays
when compared to the control pigs. This will form the
basis of a much bigger trial to be carried out in 2009.
2008 ACPFG Annual Report 33
Aligned Programs | Nitrogen use efficiency
NITROGEN USE
EFFICIENCY
Nitrogen (N) plays a role in almost all plant activities, so plants need plenty of it
to grow properly. To satisfy this need, farmers worldwide apply about 90 million
tonnes of nitrogen fertiliser to crops each year. This vast quantity is necessary as
many crops are extremely inefficient at using nitrogen – cereals, for example,
use only 30 per cent of the nitrogen that is applied as fertiliser.
Apart from being economically wasteful, this
practice is also costly to the environment, nitrogen
pollution of waterways being a worsening problem
globally. Use of nitrogen fertiliser also adds to
greenhouse gases through the emission of nitrous
oxide, a gas with more than 300 times the global
warming power of carbon dioxide and which, by
conservative estimates, accounts for more than seven
per cent of the human-influenced greenhouse effect.
Why are crop plants so inefficient in their use of nitrogen? Is it, perhaps,
because the breeding of high yielding varieties has been carried out under
conditions of readily available nitrogen? The nitrogen use efficiency (NUE)
group at ACPFG aims to improve the overall NUE of cereals by increasing
the efficiency of accumulation of nitrogen and the efficiency with which this
nutrient is used once inside the plant.
NUE research at ACPFG centres around two important collaborations with
American companies. The first, with DuPont Pioneer, aims to develop a
greater understanding of NUE. The second, with CSIRO Plant Industry and
Arcadia Biosciences, focuses on improving NUE in cereals by over-expressing
a nitrogen assimilation gene for the enzyme alanine aminotransferase. This
is a very applied project focussing on testing the efficacy of the Arcadia NUE
technology in wheat and barley.
34 2008 ACPFG Annual Report
Trevor Garnett
Mamoru Okamoto
Trevor Garnett has a
Mamoru Okamoto received
Bachelor of Science
a Master of Science in
with Honours from the
Agriculture from the Tokyo
University of Adelaide and
University of Agriculture
a PhD from the University
and Technology, followed
of Tasmania. Trevor’s PhD
by a PhD in Botany at
investigated nitrogen
the University of British
transport in Eucalyptus
Columbia, Vancouver,
roots using ion-selective
Canada. For his PhD he
microelectrodes. Following
characterized the gene
his PhD Trevor studied
regulation of all high-
iron transport into wheat
affinity nitrate transporters
grains, before spending five
in Arabidopsis thaliana.
years managing a project
Then at the University
supported by the Australian
of California San Diego
Centre for International
he studied nitrate signal
Agricultural Research in
transduction and nitric
collaboration with scientists
oxide synthesis in plants.
in China and Laos, to find
He joined ACPFG in July
pastures adapted to adverse
2008 and leads the wheat/
environments. Since 2006,
barley NUE group. The
Trevor has been managing
group focuses on improving
a collaboration between
crops to utilize nitrogen
ACPFG and DuPont
nutrient more efficiently
Pioneer in the US, aimed
with forward and reverse
at improving the NUE of
genetics approaches.
maize, wheat and barley.
Alex Johnson
Alex Johnson obtained
a Master of Science and
PhD from the Horticulture
Department of Virginia
Tech in the US before
moving to the University
of Cambridge in 2001
to begin a postdoctoral
position with Mark Tester
in the Department of Plant
Sciences. During his three
years at Cambridge, Alex
developed a library of
enhancer trap lines that
is used to study cell typespecific gene expression in
rice. He moved to Adelaide
in 2004 and has used
these lines to investigate
salinity tolerance and
metal transport processes
in rice. He is leader of the
High-Iron Rice Project
and is a member of the
Salinity Focus Group.
Iron deficiency is the most common nutritional
deficiency disorder in Australia and the world.
Over two billion people, or 30% of the world’s
population, suffer from iron deficiency, with
symptoms including poor mental development,
depressed immune function and anaemia.
Infectious diseases further increase the incidence
of anaemia in resource-poor countries, meaning
that developing countries are disproportionately
affected. Within Australia, up to 10% of women,
teenage girls and toddlers are iron deficient.
Increased loading of iron into cereal grains through
genetic modification represents a powerful and
sustainable approach towards increasing daily iron
intake for people suffering from iron deficiency.
Wheat and rice, the two most widely consumed
cereal species in developing countries, transport
only a small fraction of leaf iron to the developing
grain. Furthermore, the small amount of iron
translocated to the grain accumulates almost
exclusively in outer grain tissues – the hull, embryo
and aleurone – which are removed during milling
and polishing. Taken together, these observations
highlight the need for new cereal cultivars with
enhanced iron translocation from vegetative to
grain tissues (also known as iron remobilisation)
and increased iron accumulation in inner grain cell
types (namely the endosperm, which survives the
milling and polishing process).
Research and activities
In collaboration with the HarvestPlus Challenge
Program, we aim to increase the iron content of
cereal grains by identifying rate limiting steps in
the delivery of iron to cereal endosperm. Using
cell type-specific expression tools, we are driving
the expression of iron transporters and chelators
in specific cell types of rice hypothesised to be
important for iron translocation within the plant and
for loading into developing rice grain. The project
received a financial boost in 2008 with a successful
application to the ARC Linkage scheme for a
collaborative two year project with HarvestPlus,
valued at nearly $300,000.
Constitutive upregulation of
nicotianamine synthase activity
increases the micronutrient content
of rice grain
Nicotianamine is a well known chelator of
metals in plants and may play important roles
in the delivery of micronutrients, such as iron
and zinc, to developing seeds. To generate rice
lines with elevated levels of nicotianamine, the
three nicotianamine synthase (NAS) genes of rice
were constitutively overexpressed in transgenic
Nipponbare rice. We used inductively coupled
plasma atomic emission spectroscopy analysis
(ICP-AES) to analyze seed micronutrient content of
the transgenic plants. Iron and zinc concentrations
were significantly higher in brown rice of all three
of the transgenic populations relative to controls.
After milling, polished rice retained 20-30% of seed
iron and 76-84% of seed zinc. One of the lines had
a threefold increase in iron content and twofold
increase in zinc content relative to controls. The
iron levels in many of the transgenic lines either
meet or surpass the HarvestPlus target of 14 parts
per million in milled rice grain.
2008 ACPFG Annual Report 35
Aligned Programs | Iron-rich rice
High-IRON RICE
COMMUNICATION
Cobi Smith
Cobi Smith returned
to ACPFG in 2008 as
Communications Manager.
She has degrees in
The communications and education management role was split in 2008
to allow greater focus on public participation and improving internal
communications, complementing ACPFG’s well established education
outreach programs.
journalism and international
studies, in which she
incorporated biology,
chemistry, development
studies and environmental
security. After working
as a sub-editor for an
environment-focused
newspaper she became an
Australian Broadcasting
Corporation journalist,
working for Adelaide and
rural South Australian
newsrooms. She moved
to ACPFG in 2005,
launching the magazine,
Vector. In 2006 she
Media
Media relations for ACPFG is also changing in response to a new political environment, in which
adaptation to climate change and food security are high on the news agenda. Focus has moved away from
reactionary coverage generally regarding the use of GM, towards coverage considering the role technology
can play in solving global and Australian problems. ACPFG hosted a film crew from Japan’s national
broadcaster, NHK, who were producing a documentary on food security. Peter Langridge appeared in a
French television documentary on GM and the world food supply. The Australian Financial Review ran a
feature on our drought and salinity research, how it may be commercialised and how this could contribute
to global food security. Mark Tester reviewed a book in Science discussing whether farming would be more
sustainable incorporating both organic and GM production methods. This new media focus is in addition to
our discovery-based coverage associated with new grants and research outcomes.
The Australian Science Media Centre has become a valuable service, connecting our scientists with journalists
reporting on relevant issues. We increased the number of scientists available for public comment in 2008,
which is raising the profile of these individuals and better reflecting the diversity of activities at ACPFG.
moved to Cambridge,
UK, where she worked for
organisations including
Vector magazine
an educational publisher,
university, science news
service and technology
commercialisation
consultancy. She is
Issues seven and eight of Vector were printed and distributed in 2008, receiving positive feedback locally
and internationally. The magazine continues to be the main medium for communicating ACPFG news to
stakeholders and interested parties, with more than 1,000 people on the hard-copy distribution list, roughly
the same number of copies distributed at events, and content indexed by Google available online.
completing a research
degree in science
communication through
Australian National
University’s (ANU) Centre
for the Public Awareness
of Science (CPAS).
Internal communications
Quarterly reporting was restructured in early 2008 to better reflect the needs of shareholders and clarify for
contributors what information was most useful.
IT upgrades allowed ACPFG’s stock images and staff photos to be moved to a central network accessible to
most staff, facilitating quicker production of marketing materials and presentations.
36 2008 ACPFG Annual Report
Communication
Rachel Burton, Darren Plett and Trevor Garnett at a public participation event in Adelaide.
Public participation
In collaboration with ANU’s CPAS, ACPFG hosted three public participation events in Adelaide and
Canberra during National Science Week. Rachel Burton, Trevor Garnett and Darren Plett presented
to public audiences, who decided in which of ACPFG’s research programs they would like to invest
their taxpayer dollars. Participants were surveyed about science funding, their decision making and
event evaluation. These results will be analysed and published in 2009 by Communications Manager
Cobi Smith as part of her ANU research.
Website
ACPFG staff at the UQ took over design of the new website in 2008, allowing the site to be
managed in-house, while basic maintenance of the existing website continued in Adelaide.
Many people were involved in writing a new research section, which is completed and will be
unveiled with the launch of the new website in 2009.
Media releases
GM canola ban ‘disappointing’
8 February
A worldwide mission to solve iron deficiency
11 June
Adelaide becomes home to super greenhouse
28 July
UniSA turns maths minds onto plant genome research
28 July
‘Metabolomics Australia’s’ Victorian node officially opened
12 November
2008 ACPFG Annual Report 37
EDUCATION
Monica Ogierman
Monica Ogierman began
in 2008 as Education
Manager. She has a
Bachelor of Science with
Honours, majoring in
biochemistry, from the
University of Adelaide.
Much of her career then
focused on researching
bacterial pathogens that
infect humans. After
graduating with a PhD from
the University of Adelaide,
she worked as a molecular
biologist at the Women’s
and Children’s Hospital.
She received an Alexander
von Humboldt fellowship
which enabled her to work
in Tübingen, Germany,
for two and half years,
The role of the Education Manager has been defined so that while running
education programs is still a high priority, greater emphasis is placed on
managing and recruiting a vital resource of ACPFG – our postgraduate and
honours students. While we are world-class research facility, we also strive
to be a first-class teaching facility.
The role of education is to interface between
scientists and the community, particularly
secondary school students, as they will be either
producers or consumers of science. It’s vital they
understand the latest science and technology
available in society. Through education, we
demystify gene technology and its use in plant
breeding and food production.
The dual challenge we face is finding suitable
PhD and Honours students and then managing
them once on board, to ensure our high standard
of research and education is maintained. We also
need to ensure they have a good experience at
ACPFG and leave as first-class research scientists.
studying the iron transport
mechanisms of bacteria
at the molecular level.
Student recruitment
Throughout her career as a
research scientist, Monica
gave many presentations
and realised she had a
passion for talking to people
about science. She then
left research to become
territory manager for a
life science company and
then National Business
Development Manager
for a global scientific
recruitment company,
before moving to ACPFG.
Monica attended career fairs nationwide to promote
postgraduate opportunities at all ACPFG nodes.
These included UA, UQ, Flinders University, and
an online chat session with students at the Virtual
Careers Fair run by Graduate Careers Australia.
Cobi Smith attended the graduate job fair ‘Tertiary
to Work’ in Canberra. Monica attended the UA
Open Day to increase awareness about ACPFG
among students and their parents. ACPFG was a
Gold sponsor at Ausbiotech’s annual career night,
which generated much interest from biotechnology
students from South Australian universities.
Monica Ogierman, Belinda Griffiths, Roger Parish from
La Trobe University and Heather Bray.
Student management
Two student management committees were
formed this year. These committees, composed of
postdoctorate scientists representing all ACPFG
research groups, mentor students through their
academic /research programs, make decisions
about student projects and advise the EMG.
Many undergraduate students attended our ‘Tour
‘N’ Talk’, which provided an opportunity for
students interested in doing honours, postgraduate
studies or summer scholarships to see our facilities
and discuss research opportunities directly with
our scientists. 10 summer scholars from UA and
Flinders University entered our program at the end
of 2008.
Monica Ogierman demonstrating for students in Mount Gambier.
38 2008 ACPFG Annual Report
A Get into Genes magazine was launched,
thanks to Heather’s previous efforts with Monica’s
predecessor, Belinda Barr. The magazine was
distributed to schools and received excellent
feedback.
PhD committee members
(from left): Ute Baumann,
Alex Johnson, Monica
Ogierman, Nick Collins,
Nataliya Kovalchuk and
Rachel Burton. Absent:
Dave Edwards.
PhD Committee
The PhD committee established guidelines for the
selection, distribution and management of PhD
students at the Adelaide ACPFG node; assessed
and screened potential students for suitability;
and then mentored them through the process of
applying for university scholarships. As part of
the new guidelines, the committee will assess
final projects offered to PhD students and make
recommendations to the EMG to ensure timely
completion of the projects.
Masters and Honours Committee
Members of the Masters and Honours Committee
are Andrew Jacobs, Delphine Fleury, Olivier
Cotsaftis and Tim Sutton. This committee assisted
honours students with their oral presentations and
other deadlines.
Get into Genes
Monica Ogierman and Heather Bray from the
Molecular Plant Breeding Cooperative Research
Centre collaborated in managing the successful
Get into Genes program. Belinda Griffiths joined
the team in January 2008 as Education Officer to
run workshops in Victoria. The team revamped the
program in 2008, with changes to the workstations,
worksheets and oral presentations.
Stuart Roy (second from
right) working with science
teachers in an ACPFG lab.
The program received over 2000 students across
South Australia and Victoria. The Get into Genes
team presented at various teachers’ conferences. In
addition to building relationships with teachers, we
provided contextual research examples for teachers
to take back to the classroom.
Get into Genes workshops were incorporated
into UA education programs. ‘Aim for Adelaide’
promoted science to more than 50 year nine
students from schools with a low university
participation rate. Gifted science and maths
students from more than 30 schools were
encouraged to consider science as a career option
in the ‘Maths and Science Life Impact’ program.
Get into Genes Victoria relocated to a new
custom-fitted laboratory in the Faculty of Science,
technology and Engineering at La Trobe University.
Both La Trobe University and the University of
Melbourne have committed to funding Get into
Genes Victoria until the end of 2009. Belinda
Griffiths designed and ran the first Get into Genes
professional development workshop for Diploma
of Education students, giving new teachers the
confidence to teach biotechnology. More workshops
are planned for 2009 in both SA and Victoria.
Rural outreach in Mount Gambier, Barham and
Corryong reached over 250 students and generated
good radio publicity. Biotechnology Australia
sponsored the Mount Gambier trip.
Get into Genes collaborators include CSIRO
Science Education Centre, GrowSmart, SARDI,
Gene and Nanotechnology Information Service
and Biotechnology Australia.
Outreach events
We are now actively encouraging our practicing
scientists to participate in education programs. Stuart
Roy was involved in a professional development
program for science teachers, ‘building new science
into the curriculum for schools: biotechnology’,
hosted by the Australian Science and Mathematics
School. He ran several half-day, hands-on
workshops for science teachers to develop a better
understanding of agricultural biotechnology. Teachers
came to ACPFG and phenotyped plants, extracted
DNA and investigated the structure of a plant root
using the confocal microscope. Sergiy Lopato and
Andrew Jacobs were scientific advisers for thirdyear University of Adelaide biotechnology students
studying commercialisation and business writing.
Education staff and volunteer scientists ran a
booth at the Royal Adelaide Show and Science
Alive, South Australia’s premier National Science
Week event. We performed more than 2,000 DNA
extractions with the public, promoting the message
that genes are naturally in food. Our Museum Hub
display during National Science week provided
information about ACPFG research to the public,
with an estimated 4,000 people viewing the display.
2008 ACPFG Annual Report 39
CONFERENCES
& MEETINGS
January 12–16
February 22–25
March 31–April 3
April 5–10
February 20 –22
February 14–15
March 19
March 25–30
April 6–8
April 5–10
June 8–12
June 11–12
June 15–20
June 22–26
June 25–27
June 30 –July 3
July 7–9
August 1–5 August 21
August 24–30
August 31–September 2
September 4
September 15–18
September 16–20
September 21–26
September 21– 25
September 24–27
September 30 –October 1
October 13–28
October 28–29
November 20
Peter Langridge, Professor Geoff Fincher, Dr Nick Collins and Andrew Chen, PAG XVI San Diego
Geoff Fincher, Elsevier Editor Meeting, Singapore
Geoff Fincher, DuPont Pioneer – Des Moines and Wilmingto, USA
Geoff Fincher, Tim Sutton, Yuri Shavrikov, 10th IBGS Conference, Alexandria, Egypt
Cobi Smith, Rights and obligations of scientists and researchers in universities and public sector research agencies, Canberra
Trevor Garnett, Australian Academy of Science – Enhancing the quality of the experience of post docs and early career researchers, Canberra
Cobi Smith, Science communication in informal education environments workshop, Perth
Andreas Schreiber, Mathematical Evolutionary Biology, Naracoorte
Alex Johnson, Plant Stress: Global Challenges and Opportunities Workshop. Pennsylvania State University, USA
Geoff Fincher, Tim Sutton, Yuri Shavrikov, 10th IBGS Conference, Alexandria, Egypt
Geoff Fincher, Maria Lombardi and Margaret Buchanan, Cell Wall Meeting, Asilomar, USA
Peter Langridge, Triceae genome meeting, Clermont-Ferrand, France
Geoff Fincher, Scottish Crop Research Institute, Dundee, Scotland
Peter Langridge, EPSO Conference, Presqu’ile de Giens, France
Cobi Smith, Public Communication of Science and Technology (PCST)-10, Malmo, Sweden
Peter Langridge, Delphine Fleury, Durum Conference, Bologna, Italy
Monica Ogierman, Conference of the Australian Science Teachers Association, Gold Coast
Geoff Fincher, Plant Polysaccharide Workshop, Stockholm, Sweden
Rachel Burton, Trevor Garnett, Darren Plett and Cobi Smith, Australian Science Festival Events, Canberra
Peter Langridge, Delphine Fleury, Aurelie Evrard, Margaret Pallotta, Ainur Ismagul, Dion Bennett, Yuri Shavrukov, James Edwards, Sergiy
Lopato, Natliya Kovulchuk and Andrew Chen, International Wheat Genetics Symposium, Brisbane
Geoff Fincher, 58th Australian Cereal Chemistry Conference, Surfers Paradise
Sharla Hall, Resource Capture by Crops: Integrated Approaches, University of Nottingham, UK
Geoff Fincher, 10th European Society for Agronomy Conference, Bologna
Peter Langridge, Generation Challenge Programme Meeting, Bangkok, Thailand
Maria Hrmova, 11th Bratislava Symposium on Saccharides, Slovakia
Rachel Burton, Emily Grace, Deepa Jha, Trevor Garnett, Christian Preuss, Andrew Chen, Michael Dow, Chunyuan Huang, Inam Ullah,
Joanna Sundstrom and Bujun Shi, Combio 2008, Canberra
Geoff Fincher, Plant Genomics European Meeting 7, Albena, Bulgaria
Geoff Fincher, Milano Bioforum Meeting
Maria Hrmova, ‘X-Ray Methods in Structural Biology’, Cold Spring Harbor Laboratory, New York State, USA
Michael Gilbert, AusBiotech National Conference, Melbourne
Michael Gilbert, The Clinical Oncological Society of Australia 35th Annual Scientific Meeting, Sydney
40 2008 ACPFG Annual Report
STUDENT LIST
ACPFG PhD Students
Completed, Adelaide
Project Title
Supervisors
Byrt, Caitlin
Salinity tolerance in durum wheat
Tester
Carter, Scott
Non specific cation channels of plants and yeast
Kaiser, Tester
Chen, Andrew
Positional cloning of a reproductive frost tolerance gene from barley
Collins, Fincher, Baumann
Drew, Damian (submitted)
Characterisation and functional analsys of putative salt tolerance
genes, monodehydroascorbate reductase and PpENA1 from the
moss, Phsycomitrella patens
Fincher, Tester, Hrmova
Grace, Emily
The control of phosphate transport in barley by micchorizal infection
Smith, Tester, Smith
Hassan, Mahmood (accepted 08)
A genomic approach to boron stress tolerance in wheat
Baumann, Sutton, Oldach
Plett, Darren
Cell specific manipulation of gene expression in rice to increase
salinity tolerance
Tester, Jacobs, Johnson
Sheikh-Jabbari, Jafar (submitted)
Functional analysis of novel genes involved in the interaction
of Rhynchosporium secalis and barley
Langridge, Oldach
Completed, Melbourne
Project Title
Supervisors
Widodo
A proteomic study of barley root plasma membrane
Patterson, Bacic, Tester, Newbigin, Roessner
Commenced, Adelaide
Project Title
Supervisors
Kaur, Sukirat
Genetics and physiology of tin – a gene in wheat for dry
environments?
Collins, Spielmeyer, Chandler
Kyriacou, Bianca
Molecular approaches to increasing the iron content of rice grain
Stangoulis, Tester, Johnson
Schwerdt, Julian
Structural basis for catalysis and substrate specificity of xyloglucan
endotransglycosylases from barley (HvXETs), the key cell wall
re-modelling enzymes
Hrmova, Fincher, Streltsov
Tiong, Jingwen
Functional characterisation of barley ZIP7 zinc transporter
Huang, McDonald
Ongoing, Adelaide
Project Title
Commenced
Supervisors
Dolman, Fleur
Functional characterisation of plant cytosolic thioredoxins
2004
Baumann, Juttner, Comis
Elsden, Joanne
Map based cloning of a malt quality QTL in barley
2004
Chalmers, Collins, Langridge,
Eglinton
Ilanzoo, Ali
Genomics of drought tolerance in cereals
2004
Langridge, Tester, Schnurbusch,
Collins
Malone, Jenna
Analysis of signal pathway protein-protein interactions in
signal pathways shared by biotic and abiotic stresses
2004
Oldach, Comis
Reinheimer, Jason
Breeding for frost tolerance in winter cereals
2004
Eglington, Collins
Rivandi, Alireza
Cloning and the physiological characterisation of a sodium
exclusion gene from barley
2004
Collins, McDonald, Tester,
Schnurbusch
Rusinova, Irina
Discovery of functional relationships among genes using
microarray data
2004
Schreiber, Baumann
Tran, Michael
Investigating the role of untranslated regions in mRNA that may be
involved with stability translation and localisation in abiotic stress
2004
Schultz, Baumann
Edwards, James
Genetic mapping of drought related traits in hexaploid wheat
2005
Schnurbusch, Langridge
Hall, Sharla
Mapping QTLs associated with root traits in wheat
2005
Huang, Schurbush
Lombardi, Maria
Early vigour in cereal seedlings
2005
Burton, Fincher
Morran, Sarah
Characterisation of AP2 domain transcriptional factors from
early wheat grain
2005
Lopato, Langridge
2008 ACPFG Annual Report 41
STUDENT LIST
Ongoing, Adelaide
Project Title
Commenced
Supervisors
Pillman, Katherine
Transcription factors involved in cold and salt tolerance in barley and
arabidopsis
2005
Jacobs, Langridge, Lopato
Smart, Alex
Stress response and characterisation of the thioredoxin h family in
cereals
2006
Jacobs, Langridge
Buchanan, Margaret
Stem strength determinants in cereal crops
2006
Fincher, Burton
Sundstrom, Joanna
Regulation of HKT gene expression in plants
2006
Tester, Cotsaftis, Roy
White, Heath
Identification of kinase substrates in critical stress–signalling
pathways and modulated expression for improved drought tolerance
2006
Lopato, Juttner, Langridge
Bennett, Dion
Drought and heat tolerance
2007
Langridge, Schnurbusch
Dow, Michael
Characterisation of transcription factors important in regulating
salinity tolerance
2007
Tester, Jacobs
Krishnan, Mahima
Cell-type specific expression of salt tolerance genes in barley
2007
Jacobs, Tester, Johnson
Preuss, Christian
Phosphorus use efficiency and drought resistance in wheat: through
an understanding of root traits
2007
Huang, Tyerman
Rajendran, Karthika
Mapping for salinity tolerance in Triticum monococcum
2007
Roy, Tester
Ongoing, Melbourne
Project Title
Commenced
Supervisors
Liu, Dawei
The study of the biology of abiotic stress in cereals using functional
genomics
2005
Bacic, Patterson
Ramesh, Sushma
Differential proteomic analysis of abscisic acid responses in rice
2005
Bacic, Patterson
Bowne, Jairus
The study of the metabolic response of cereals to abiotic stress
2006
Bacic, Roessner
Erwin, Tim
The development and application of bioinformatics tools for the
analysis of high throughput metabolomic data
2006
Bacic, Roessner, Likic
Ongoing, Brisbane
Project Title
Commenced
Supervisors
Woon, Peter
Genome diversity and response of organisms to environmental
factors
2006
Brusic, Basford
Duran, Chris
The development and application of bioinformatics tools for the
integration and analysis of crop genetic and genomic data
2007
Edwards, Basford
Imelfort, Mike
To establish and apply novel genome sequencing and assembly
methods as well as novel genome annotation and interrogation tools,
with specific application to cereal genomes
2007
Edwards, Basford
ACPFG Masters Students
Masters, Adelaide
Project Title
Commenced
Supervisors
Javadiyan, Shahri
Role of AtAMT1;2 in nitrogen uptake and plant growth
2007–2008
Kaiser
Liang, Bing
Cloning of barley COBRA genes and studying of their functions
2007–2008
Zhang, Fincher
Tan, Hwei Ting
Analysis of key glycosyltransferase (GT) families in barley
2007–2008
Burton, Fincher
Varanashi, Partha
Barley cellulose synthases involved in secondary cell wall formation
and stem strength: generation of cDNA constructs for functional
analysis.
2007–2008
Hrmova, Fincher
Yang, Nannan
Analysis of the stress-inducible promoter of TdDHN8/Wcor410 from
wheat using transient expression assays
2007–2008
Lopato, Eliby
Masters, Brisbane
Project Title
Commenced
Supervisors
Appleby, Nicola
Identification and characterisation of molecular genetic markers from
DNA sequence data
Converted
from PhD
Edwards, Basford
42 2008 ACPFG Annual Report
STUDENT LIST
ACPFG Honours Students
Honours, Adelaide
Project Title
Commenced
Supervisors
James Preuss
HvHRA1, a His-rich Arabinogalactan protein, functions in metal
binding with implications for biofortification
Jan 08
Schultz, Johnson, Tester
Corrine Callegari
Fine mapping of a Na+ exclusion QTL in Arabidopsis
July 08
Roy, Tester
Honours, Melbourne
Project Title
Commenced
Supervisors
Guimaraes, Geraldo
Metabolomics of transgenic rice overexpressing a sodium-ATPase
2008
Bacic, Roessner, Patterson
ACPFG Summer Scholars Students
Summer Scholars 08/09
Project area
University
Supervisor
Conway, James
Isolation and cloning of maize cellulose synthase promoters
Adelaide
Burton
Fabrizio, Jacqueline
Manipulation of beta-glucan levels in transgenic barley plants
Adelaide
Collins
Hezrin Shahrin, Nur
Physical mapping of genes in barley
Adelaide
Fleury
Holtham, Luke
Nutrient use efficiency in wheat and barley
Flinders
Garnett
Nagarajan, Yagnesh
Protein expression of curdlan synthase that is involved in bacterial cell Flinders
wall biosynthesis
Hrmova
Reid, Nicolas
Analysis of drought/cold inducible promoters from wheat
Flinders
Lopato
Sadras, Francisco
Characterisation of grain-specific promoters from wheat
Adelaide
Kovalchuk
Schiling, Rhiannon
Creation of transgenic plants for characterisation of a candidate gene
for sodium exclusion in Arabidopsis
Adelaide
Roy
Vardini, Harsha
Sequence clustering and assembly of the Arabidopsis transcriptome
Flinders
Schreiber
Webber, Michael
Enhancing the salinity tolerance of rice
Flinders
Jacobs
Work Placements
Time of Visit
Origin
Supervisor
Chris Hope
February
Flinders University
Collins, Sutton
Matthew Anderson
February
Flinders University
Collins, Sutton
Sandra Schmöckel
July to October
University of Potsdam
Roy
Catherine Huang
September to November
University of California
Roy
Tufan Oz
December to December 09
Middle East Technical University
Sutton
Matthew Langford
July to November
TAFE SA
Shadiac
Work Placements
2008 ACPFG Annual Report 43
PATENT LIST
Gene promoters
Flower active transcriptional control sequences
2008904485, Provisional
description: Promoter expressed in seed during early grain development
applications: Avoid seed abortion and sterility during drought conditions; increase grain yield
Plant egg cell transcriptional control sequences
WO 2007/092992 A1, National Phase
description: Plant egg cell specific promoter
applications: Induce female sterility in plants; produce hybrid cereals increasing yield up to 20%; engineer the apomixis trait
Plant seed active transcriptional control sequences
PCT/AU2008/001359, National Phase
description: Endosperm and aleurone specific promoter in a plant seed
applications: Increase grain yield; manipulate the quality of grain; change grain size
Seed active transcriptional control sequences
2008904229, Provisional
description: Very strong ubiquitous expression of the promoter GL7 from before anthesis through to grain maturation
applications: Increase grain yield, protein content and grain size
Specific expression using transcriptional control sequences in plants
WO 2007048207A1, National Phase
description: Endosperm specific cell promoter in a plant seed
applications: Increasing grain yield; manipulating the quality of grain; changing grain size
Tissue specific expression
2008900432, PCT
description: Embryo specific promoter
applications: Increase grain yield
Transcriptional control sequences
WO 2008/052285 A1, National Phase
description: Plant egg cell & pollen specific promoter
applications: Engineer female reproductive sterility; induce female sterility in plants; produce hybrid cereals increasing yield up to 20%;
engineer the apomixis trait
Transcriptional regulators for reproduction associated plant part tissue specific expression
WO 2007/137361 A1, National Phase
description: Plant endosperm and male specific promoter
applications: Increase grain yield; engineer female reproductive sterility
44 2008 ACPFG Annual Report
PATENT LIST
Grain Quality
Polysaccharide synthases
WO 2007014433A1, National Phase
description: Genes encoding polysaccharide synthases producing (1,3):1,4) β-D-glucans encoded by members of the CslF gene family
applications: Functional foods (high β-glucan level); human disease prevention (high β-glucan level); improved growth performance
(low β-glucan level); enhance beer processing (low β-glucan level); molecular marker
Polysaccharide synthases (H)
2007907071, National Phase
description: Genes encoding polysaccharide synthases producing (1,3):1,4) β-D-glucans encoded by members of the CslH gene family
applications: Functional foods (high β-glucan level); human disease prevention (high β-glucan level); improved growth performance
(low β-glucan level); enhance beer processing (low β-glucan level); molecular marker
Polysaccharide transferase
WO 2008/011681 A1, National Phase
description: Genes encoding polysaccharide transferases (xyloglucan endotransglycosylases). Can potentially influence the strength,
flexibility and porosity of plant cell walls.
applications: Agro-industrial processes (paper & pulping); malting and brewing; bioethanol production; functional food (dietary fibre
and ruminant digestibility)
Quantitative trait locus for grain polysaccharides
2008902999, Provisional
description: A region of the barley 3H chromosome has been identified by association mapping which is likely to contain elements or
gene/s involved in beta-glucan synthesis. These novel genes are not members of the previously defined HvCslF or HvCslH families.
Involved in control of beta-glucan synthesis in cereal grain
applications: Functional foods (high β-glucan level); human disease prevention (high β-glucan level); improved growth performance
(low β-glucan level); enhance beer processing (low β-glucan level); molecular marker
Micronutrient transport
Boron transporter
WO 2008/083441 A1, PCT
description: Genes encoding boron transporters; essential for protecting plants from boron deficiency and toxicity
applications: Increase or decrease levels of boron in plants; molecular marker
2008 ACPFG Annual Report 45
PATENT LIST
Salinity tolerance
Cation channel activity
2008904951, Provisional
description: Genes encoding putative non-selective cation channels; may be the main sodium entry pathway in plants
applications: Production of salt tolerant plants; improve fertiliser use efficiency
Salinity tolerance in plants
2008904596, Provisional
description: Protein kinase involved in directing plant response to salt stress
applications: Production of salt tolerance
Vascular plants expressing Na+ pumping ATPases
WO 2006037189A1, National Phase
description: Genes encoding sodium pumping ATPases; a sodium efflux system
applications: Improve plant salinity tolerance
Tools and methods
Targeting vector
WO 2006/135974 A1, National Phase
description: DNA constructs for cloning genes of interest into target chromosomal loci in plants; can also be used for determining
unknown gene function
applications: Research and development tool
Transcription factors
Modulation of plant cell wall deposition
PCT/AU2008/001539, PCT
description: Homeodomain/leucine zipper polypeptide which modulates plant cell wall deposition including secondary cell wall
deposition
applications: Increase or decrease stem strength; decrease lodging; biofuel production
Modulation of plant cell wall deposition via HD-ZIP1
2008905026, PCT
description: Expression of HD-Zip1 increasing secondary cell wall biosynthesis and deposition; HD-Zip1 expression modulates plant
size, flowering time and tillering
applications: Avoid lodging; regulate flowering time
46 2008 ACPFG Annual Report
2008 ACPFG Annual Report 47
PUBLICATION LIST
1.
Appleby N, Edwards D and Batley J. 2009. New technologies for ultrahigh throughput genotyping in plants. Ed. Somers D, Langridge P, and
Gustafson JP. Methods in Molecular Biology, Humana Press (USA) (In
press)
2.
Batley J and Edwards D. 2008. Mining for single nucleotide
polymorphism (SNP) and simple sequence repeat (SSR) molecular
genetic markers. In: Bioinformatics for DNA Sequence Analysis. Ed.
Posada D. Methods in Molecular Biology, Humana Press (USA) (In press)
3.
Boden SA, Langridge P, Spangenberg G and Able JA. 2008. TaASY1
promotes homologous chromosome interactions and is affected by
deletion of Ph1. Plant Journal. 57,487–497
4.
5.
6.
7.
8.
Brownfield L, Wilson S, Newbigin E, Bacic A and Read S. 2008.
Molecular control of glucan-synthase-like protein NaGSL1 and callose
synthesis during growth of Nicotiana alata pollen tubes. Biochemical J.
414,43–52.
Burton RA, Jobling SA, Harvey AJ, Shirley NJ, Mather DE, Bacic A and
Fincher GB. 2008. The genetics and transcriptional activity of the
cellulose synthase-like HvCslF gene family in barley (Hordeum vulgare
L.). Plant Physiology 146, 1821–1833.
Chen A, Baumann U, Fincher GB and Collins NC. 2009. Flt-2L, a locus
in barley controlling flowering time, spike density and plant height.
Funct Integr Genomics (in press)
Chen A, Brûlé-Babel A, Baumann U and Collins NC. 2008. Structure
– function analysis of the barley genome: the gene-rich region of
chromosome 2HL. Funct Integr Genomics doi: 10.1007/s10142-0080099-2
Chiovitti A, Kraft G, Bacic A, Craik D J and Liao M-L. 2008. Kappabeta-carrageenans from Australian red algae of the Acrotylaceae
(Gigartinales, Rhodophyta). Phycologia 47, 35–40.
9.
Clark T. 2008. Protein Sequence Databases. In Applied Bioinformatics
Ed. Edwards D, Hanson D and Stajich J. Springer (In press)
10.
Collins NC, Shirley NJ, Saeed M, Pallotta M and Gustafson JP. 2008.
An ALMT1 Gene Cluster Controlling Aluminium Tolerance at the Alt4
Locus of Rye (Secale cereale L.). Genetics 179: 669–682.
11.
Collins NC, Tardieu F and Tuberosa R. 2008. Quantitative trait loci
and crop performance under abiotic stress: where do we stand?
Plant Physiology 147: 469–486.
12.
Conn VM, Walker AR and Franco CMM. 2008. Endophytic
actinobacteria induce defense pathways in Arabidopsis thaliana.
Molecular Plant Microbe Interactions: 21, 208–218.
13.
Duran C, Appleby N, Edwards D and Batley J. 2008. Molecular genetic
markers: discovery, applications, data storage and visualisation. Current
Bioinformatics. (In press)
14.
Duran C, Edwards D and Batley J. 2008. Molecular marker discovery
and genetic map visualisation. In Applied Bioinformatics Ed. Edwards D,
Hanson D and Stajich J. Springer (In press)
48 2008 ACPFG Annual Report
15.
Duran C, Edwards D and Batley J. 2008. Genetic maps and the use of
synteny. In: Plant Genomics. Ed. Somers D, Langridge P, and Gustafson
JP. Methods in Molecular Biology, Humana Press (USA) (In press)
16.
Edwards D and Batley J. 2008. Bioinformatics: fundamentals and
applications in plant genetics, mapping and breeding. Principles and
Practices of Plant Genomics. Eds. Kole C and Abbott AG. Science
Publishers, Inc., (USA). pp 269–302.
17.
Edwards D. 2008. Bioinformatics. In: The World Wheat Book. Eds.
Bonjean A, Angus W and Van Ginkel M. Lavoisier (France) (In press)
18.
Feuillet C, Langridge P and Waugh R. 2008. Cereal breeding takes a
walk on the wild side. Trends Gent. 24: 24–32.
19.
Feuillet C, Langridge P and Waugh R. 2008. Meeting report. The
aaronsohn-itmi workshop. Israel J Plant Sci. 55:315–319.
20.
Fincher GB. 2009. Biochemistry, Physiology and Genetics of Endosperm
Mobilization Following Germination in Barley. In: Barley: Production,
Improvements and Use. Ed. Ullrich S. Wiley-Blackwell (in press).
21.
Fincher GB. 2009. Revolutionary Times in our Understanding of Cell
Wall Biosynthesis and Re-Modelling in the Grasses. Plant Physiol 149,
27–37.
22.
Fincher GB. 2009. The Evolution of (1,3;1,4)-β-D-Glucans in Cell
Walls of Grasses. Current Opinions in Plant Biology, doi:10.1016/j.
phi.2009.01.002 (in press).
23.
Grace EJ, Cotsaftis O, Tester M, Smith FA and Smith SE. 2008. Arbuscular
mycorrhizal inhibition of growth in barley cannot be attributed to
extent of colonisation, fungal P uptake or effects on expression of plant
phosphate transporter genes. New Phytologist.
24.
Haegi A, Bonardi V, Dall’Aglio E, Glissant D, Tumino G, Collins NC,
Bulgarelli D, Infantino A, Stanca AM, Delledonne M, Valè G. 2008.
Histological and molecular analysis of Rdg2a barley resistance to leaf
stripe. Molecular Plant Pathology, 9: 463–478.
25.
Hrmova M and Fincher GB. 2009. Functional genomics and structural
biology in the definition of gene function. Methods in Molecular
Biology, Plant Genomics. Vol 513. Eds. Somers DJ, Gustafson JP and
Langridge P, in the press. Humana Press, New York
26.
Hrmova M, Farkas V, Harvey AJ, Lahnstein J, Wischmann B, Kaewthai
N, Ezcurra I, Teeri TT and Fincher GB. 2008. Substrate specificity and
catalytic mechanism of a xyloglucan xyloglucosyl transferase HvXET6
from barley (Hordeum vulgare L.). FEBS J 276, 437–456.
27.
Huang CY, Roessner U, Eickmeier I, Genc Y, Callahan DL, Shirley N,
Langridge P and Bacic A. 2008. Metabolite profiling of barley (Hordeum
vulgare L) plants reveal distinct responses to phosphate deficiency. Plant
& Cell Physiology 49, 691–703.
28.
Imelfort M, Batley J, Grimmond S and Edwards D. 2008. Genome
sequencing approaches and successes. In: Plant Genomics. Ed. Somers
D, Langridge P, and Gustafson JP. Methods in Molecular Biology,
Humana Press (USA) (In press)
Publication LIST
29.
Imelfort M, Duran C, Batley J and Edwards D. 2008. Discovering genetic
polymorphisms in next generation sequencing data. Plant Biotechnology
Journal. (Accepted December 2008)
43.
Reynolds M and Tuberosa R. 2008. Translational research impacting on
crop productivity in drought-prone environments. Current Opinion in
Plant Biology 11: 171–179.
30.
Imelfort M. 2008. Sequence Comparison Tools. In Applied Bioinformatics
Ed. Edwards D, Hanson D and Stajich J. Springer (In press)
44.
31.
Izanloo A, Condon AG, Langridge P, Tester M and Schnurbusch T. 2008.
Different mechanisms of adaptation to cyclic water stress in two South
Australian bread wheat cultivars. J. Exp. Bot. 59:3327–3346
Reynolds M, Saint Pierre C, Saad ASI, Vargas M and Condon AG. 2008.
Evaluating potential genetic gains in wheat associated with streeadaptive trait expression in elite genetic resources under drought and
heat stress. Crop Science S–173–189.
45.
Roy SJ, Gilliham M, Berger B, Essah PA, Cheffings C, Miller AJ,
Widdowson L, Davenport RJ, Liu L.-H, Skynner MJ, Davies JM,
Richardson P, Leigh RA and Tester M. 2008. Investigating glutamate
receptor-like gene co-expression in Arabidopsis thaliana. Plant, Cell &
Environment 31: 861–871.
46.
Sanchez DH, Siahpoosh MR, Roessner U, Udvardi M and Kopka J.
2008. Plant metabolomics reveals conserved and divergent metabolic
responses to salinity. Physiologia Plantarum 132, 209–219.
47.
Schnurbusch T, Langridge P and Sutton T. 2008. The Bo1-specific PCR
marker AWW5L7 is predictive of boron tolerance status in a range of
exotic durum and bread wheats. Genome 51(12): 963–971.
48.
Schreiber AW, Shirley NJ, Burton RA and Fincher GB. 2008. Combining
transcriptional datasets using the generalized singular value
decomposition. BMC Bioinformatics, 9: 335, doi:10.1186/1471–2105–
9–355).
49.
Schulte D, Close TJ, Graner A, Langridge P, Matsumoto T, Muehlbauer
G, Sato K, Schulman AH, Waugh R, Wise RP, Stein N 2008. The
International Barley Sequencing Consortium (IBSC) – at the threshold of
efficient access to the barley genome Plant Physiol 149, pp. 142–147
50.
Somers D, Gustafson P and Langridge P Eds. 2008. Methods in plant
molecular biology. Hidari press.
51.
Sørensen I, Pettolino P, Wilson SM, Doblin MS, Johansen B, Bacic A
and Willats WGT. 2008. Mixed linkage (1 3),(1 4)-β-D-glucan is
not unique to the poales and is an abundant component of Equisetum
arvense cell walls. Plant Journal 54, 510–521.
52.
Tester M and Langridge P. 2008. Crops aren’t invasive. New Scientist,
197:24.
53.
Tracy FE, Gilliham M, Dodd, AN, Webb AAR and Tester M. 2008.
Cytosolic free Ca2+ in Arabidopsis thaliana are heterogeneous and
modified by external ionic composition. Plant, Cell & Environment 31:
1063–1073.
54.
Tran MK, Schultz CJ and Baumann U. 2008. Conserved upstream open
reading frames in higher plants. BMC Genomics 9:361.
55.
Webster JM, Oxley D, Pettoliino FA and Bacic A. 2008. Characterisation
of secreted polymers from suspension cultures of Pyrus communis.
Phytochemistry 69, 873–881.
56.
Williams M, Langridge P, Trethowan R, Dreisigacker S and Crouch J.
2008. Genomics of wheat, the basis of our daily bread. Chapter 22
p515–548. In “Genomics of Tropical Crop Plants.” Series: Plant Genetics
and Genomics: Crops and Models , Vol. 1 Moore, Paul H.; Ming, Ray
(Eds.) 2008, XXIV, 582 p
32.
Jones CE, Schwerdt J, Bretag TA, Baumann U and Brown AL. 2008.
GOSLING: a rule-based protein annotator using BLAST and GO.
Bioinformatics doi: 10.1093/bioinformatics/btn486.
33.
Langridge P and Baumann U. 2008. Self-incompatability in the Grasses.
Self-Incompatability in Flowering Plants - Evolution, Diversity and
Mechanisms. Chapter 13: 275–287. VE Franklin-Tong (ed.). SpringerVerlag Berlin.
34.
Langridge P and Gilbert M. 2008. From Gene Discovery to Paddock
Reality. online http://www.regional.org.au/au/asa/2008/plenary/
biotechnology/5944_langridgep.htm.
35.
Li M, Singh R, Bazanova N, Milligan AS, Shirley N, Langridge P and
Lopato S. 2008. Spatial and temporal expression of endosperm transfer
cell-specific promoters in transgenic rice and barley. Plant Biotechnol J.
6,:465–76.
36.
Lightfoot D, Boetcher A, Little A, Shirley N and Able A. 2008.
Identification and characterisation of barley (Hordeum vulgare)
respiratory burst oxidase homologue family members. Functional Plant
Biology, 2008, 35, 347–359.
37.
Munns R and Tester M. 2008. Salinity tolerance in higher plants. Annual
Reviews of Plant Biology 59, 651–681.
38.
Myriskava R, Jenoe J, Gils A, Ismagul A, Weyen J and Gils M. 2008.
Expression of active Streptomyces phage phiC31 integrase in transgenic
wheat plants. Plant Cell Rep 27:1821–1831
39.
Natera S, Ford K, Cassin A, Patterson J, Newbigin E and Bacic A.
2008. Analysis of the Oryza sativa plasma membrane proteome using
combined protein and peptide fractionation approaches in conjunction
with mass spectrometry. Journal of Proteome Research 7,1159–1187.
40.
41.
42.
Pien S, Fleury D, Mylne JS, Crevillen P, Inzé D, Avramova Z, Dean C
and Grossniklaus U. 2008. ARABIDOPSIS TRITHORAX1 dynamically
regulates FLOWERING LOCUS C activation via histone 3 lysine 4
trimethylation. PlantCell 20,580–8.
Qu Y, Egelund, J, Gilson PR, Houghton F, Gleeson PA, Schultz CJ and
Bacic A. 2008. Identification of a novel group of putative Arabidopsis
thaliana β–(1,3)–galactosyltransferases. Plant Molecular Biology 68,
43–59.
Rajendran K, Tester M and Roy SJ. 2008. Quantifying the three main
components of salinity tolerance in cereals. Plant, Cell & Environment,
32: 237–249
2008 ACPFG Annual Report 49
ACPFG STRUCTURE
BOARD
EXECUTIVE
MANAGEMENT
GROUP
RESEARCH FOCUS GROUPS
Drought
Salinity
Nutrients
Boron
Cold
MANAGEMENT
RESOURCES
Resources
Mutant Populations
Genome Structure
Resources
Promoter Isolation
Protein Structure Resources
In Situ/Hybridisation
Immunocalisation
Antibody Production
50 2008 ACPFG Annual Report
RESEARCH
SUPPORT
Research Support
Information Technology
Intellectual Property
Regulatory Compliance
Education
Communication
Commercialisation
Finance
ALIGNED
PROGRAMS
Aligned Programs
Cell Walls
Nitrogen Use Efficiency
High-Iron Rice
SUMMARY OF
CONTRIBUTIONS
Summary of Contributions 2008
Australian Research Council
$2,223,986
Grains Research and Development Corporation
$2,000,000
South Australian Government
$1,749,875
University of Adelaide
$1,000,000
University of South Australia
Nil
University of Melbourne
$150,000
University of Queensland
$50,000
Total Grants Received
$7,173,861
Other Income
In 2008, Australian Centre for Plant Functional Genomics Pty Ltd earned $11,779.91 in interest on funds deposited with the Adelaide Bank.
In-kind contributions received
South Australian Government*
University of Adelaide
$500,000
$5,298,513
University of South Australia
University of Melbourne
Nil
$774,804
Victorian DPI
University of Queensland
Total In-kind contributions received
$42,625
$565,486
$7,181,428
* Agreed annual value of Plant Genomics Centre funding
2008 ACPFG Annual Report 51
CONTACTS
University of Adelaide
Plant Genomics Centre
Hartley Grove, Urrbrae SA 5064
Postal address:
PMB 1, Glen Osmond SA 5064
ACRONYMS
P: +61 8 8303 7423
F: +61 8 8303 7102
E: acpfg@acpfg.com.au
AGT
Australian Grain Technologies www.acpfg.com.au
ANU
Australian National University
ARC
Australian Research Council
BAC
Bacterial artificial chromosome
CIMMYT
International Maize and Wheat Improvement Centre
cM
Centimorgans
CPAS
Centre for the Public Awareness of Science
CRC
Cooperative Research Centre
CSIRO
Commonwealth Scientific and Industrial Research Organisation
DNA
Deoxyribonucleic acid
DRE
Drought-responsive element
EMG
Executive Management Group EST
Expressed sequence tag
GC-MS
Gas chromatography-mass spectrometry
GCP
Generation Challenge Programme
GM
Genetically modified
School of Mathematics and Statistics
University of South Australia
Mawson Lakes SA 5095
GRDC
Grains Research and Development Corporation
IPK
Leibniz Institute of Plant Genetics and Crop Plant Research
LC-MS
Liquid chromatography-mass spectrometry
P: +61 8 8302 6479
F: +61 8 8302 5785
E: desmond.lun@unisa.edu.au
miRNA
Micro ribonucleic acid
MPBCRC
Molecular Plant Breeding Cooperative Research Centre
NCRIS
National Collaborative Research Infrastructure Strategy www.unisa.edu.au/maths/phenomics
NSW DPI
New South Wales Department of Primary Industries
PCT
Patent Cooperation Treaty
QTL
Quantitative trait loci
QUT
Queensland University of Technology
SNP
Single nucleotide polymorphism
SSR
Simple sequence repeat
TILLING
Targeting induced local lesion in genomes
UA
University of Adelaide
P: +61 7 3365 2810
F: +61 7 3365 1177
E: k.e.basford@uq.edu.au
UM
University of Melbourne
UNESCO
United Nations Educational, Scientific and Cultural Organisation
UniSA
University of South Australia
www.acpfg.imb.uq.edu.au
UQ
University of Queensland
University of Melbourne
Melbourne Node
Tony Bacic
School of Botany
University of Melbourne
Parkville Vic 3052
P: +61 3 8344 5041
F: +61 3 9347 1071
E: abacic@unimelb.edu.au
www.plantcell.unimelb.edu.au
University of South Australia
University of Queensland
Queensland Node
Kaye Basford
School of Land Food Sciences
The University of Queensland
Brisbane Qld 4072
52 2008 ACPFG Annual Report
Australian Centre for Plant Functional Genomics | 2008 Annual Report
A program initiated by
The Commonwealth Government of Australia
And funded by
The Australian Research Council
The Grains Research and Development Corporation
Support also provided by
The Government of South Australia
Additional financial support from
The University of Adelaide
The University of Melbourne
The University of Queensland
Research providers
The University of Adelaide
The University of Melbourne
The University of Queensland
The University of South Australia
www.acpfg.com.au
Drought
Boron
Nutrients
Cold
Salinity
Bioinformatics
‘omics
Genome Analysis
Resources
Cell Walls
Nitrogen Use Efficiency
High-Iron Rice
2008
Annual
Report