Name:
Professor Matthew Bellgard
Subject of fellowship:
Modular and Scalable Bioinformatics approaches to agricultural and biomedical research and
development
Theme 3: Biological Resource Management for Sustainable Agricultural Systems
Host Institution:
National Center for Genome Resources, Santa Fe, New Mexico
Host Supervisor:
Dr. Ernie Retzel and Dr Callum Bell
Dates of Fellowship:
November 3, 2012-January 28, 2013
I consent to this report being posted on the Co-operative Research Programme's website.
Relevance:
a. To the Co-operative Research Programme objectives:
The four major objectives are 1) To provide a sound scientific knowledge base to agricultural
policy-making; 2) To contribute to an informed public debate on current and emerging agro-food
issues and to help resolve conflicting views in Member countries (through sponsorship of
conferences); 3) To contribute to scientific advances in this field (through sponsorship of
fellowships), and 4) To promote scientific understanding and standards between major regions of
OECD.
As both the Murdoch University and the National Center for Genome Resources, Santa Fe, New
Mexico are interested in advanced genomics and advanced bioinformatics applied to both
agricultural and biomedical applications, this fellowship brought together two group leaders for
an extended opportunity to collaborate on understanding the appropriate biological experimental
design and analytical approaches to building sustainable information-based systems. The
fellowship also strengthened newly formed collaborations with:
• USDA (Texas) and Landcare Research, New Zealand
• Kansas State University (invited seminar) to progress plant biosecurity research and
development.
• Office of Rare Diseases, National Institutes of Health (invited seminar)
b. To the Theme: (Theme 3 The Food Chain)
It is widely recognized that the increasing world population and socio-economic shifts in the
population leading to changes in diet will require the doubling of grain and fiber crop production
by 2030. This doubling of output will require a significant genetic base change because the
availability of land for cultivation is being dramatically reduced due to urbanization and the cost
of resources such as fertilizers is increasing. Devising new varieties of wheat, through genetic
means, with dramatically improved yield is thus directly relevant to this theme objective by
employing the latest biotechnologies to identify candidate genes that can be transferred into
breeding programs. There is an urgency to make sophisticated easy-to-use computational tools
coupled with the latest DNA sequencing technologies available to plant breeders so that their trial
designs are based on integrating vast amounts of molecular sequence data. Decisions on
progressing germplasm will then have a greater success rate for realizing yield gains in an
environment of climate change. The approach taken for this project will be applicable to other
regions of the wheat genome as well as analyses carried out in other species in the food chain.
Initiatives such as the International Wheat Genome Sequencing Consortium is committed to a
coordinated effort to improve wheat germplasm through integration of: i) improved genetic
material; ii) curated, readily accessible genetic and genomic resources (including high throughput
DNA markers/platforms); iii) phenotyping; and iv) new methodologies (including GM
approaches, breeding methods). This proposal leverages upon efforts such as IWGSC in order to
accelerated progress using new high throughput DNA approaches and making the results and
methods readily available to key stakeholders such as molecular mappers, pre- and plant breeders,
molecular biologists and growers.
c. To agricultural and food policy:
Policy makers now consider large scale conflicts resulting from food shortages to be significant
factors in considering world security in the next 10 -20 years. This concern was highlighted by
the food riots caused by a spike in grain prices in 2007-2008. It is known that the impact of
starvation is higher than that of any human endemic disease. The majority of developing
countries require an active and efficient agricultural sector if they are to overcome hunger and
poverty. Increased investments in agriculture are a requirement for overall economic growth. It is
postulated that the gravity of the current food crisis is the result of 20 years of under-investment
in agriculture and neglect of the sector. Directly or indirectly, agriculture provides the livelihood
for 70 percent of the world's poor. [The Food and Agriculture Organisation (FAO http://www.fao.org) summit on Food Security 16-18 November 2009].
The FAO also sees the need to provide consistently sufficient, high quality food and feed
products through a sustainable agricultural system. This requirement takes into consideration: i)
increasing food production by 2% per year until 2050; ii) recognizing that there has been little or
no grain yield improvement over the last 10 years; iii) climate change, reduced and unevenly
distributed water resources, limited expansion of arable lands; and iv) agricultural policies
difficult to coordinate, and agricultural research is not a priority in many countries. In Europe,
wheat and barley are the most important cereal crops. Targets traits for wheat and barley are
yield, adaptation to climate change (e.g. drought, heat, cold tolerance), durable resistance to biotic
stress (e.g. viruses, fungi, new pests and diseases and invasive species) and quality of grain coproducts (e.g. protein, starch, allergenicity).
The deployment of new Information based technologies utilizing the Internet is required to
implement the outputs of fast evolving biotechnologies to achieve the “crop/plant improvement
revolution” required for doubling the yields of a major food source such as wheat by 2030. The
nature of contemporary web-based information exchange means that the outputs from the project
will drive new international collaboration as urgency for new break-throughs in genome-based
(genetic) solutions increases.
Objectives of the Fellowship:
This fellowship will:
Fast-track crop improvement to meet increase demands on global sustainable food safety through
the identification of candidate genes controlling relevant traits. This fellowship will:
(1) allow me to understand and work closely with experts in third generation DNA sequencing
technologies and work with them to refine computational approaches to analyse this data; and
(2) Establish more general computational pipelines for third generation sequencing technologies
that can be directly transferable to other species using the new open source Internet-based
analytic environment, YABI, developed by the Centre for Comparative Genomics
(http://ccg.murdoch.edu.au/yabi).
Major Achievements:
1. Use of next generation and third generation DNA sequencing platforms applied to:
• Lupin transcriptome: lupin crop species inoculated with different strains of rhizobium species
of varying nitrogen fixation efficiencies.
• Further sequencing of cattle tick genome using third generation DNA sequencing
2. Work towards deployment of Yabi (http://ccg.murdoch.edu.au/yabi ) developed at the Centre
for Comparative Genomics, Murdoch University system at NCGR
3. Submission of two grants to USDA (Agriculture and Food Research Initiative) – Feb 2012.
Follow-up:
a. We anticipate a manuscript will be submitted to a peer-reviewed scientific journal in April/May
2013 that will describe the lupin nitrogen fixation and rare disease research.
b. This fellowship has initiated and enabled an ongoing collaboration with NCGR. Professor
Bellgard has been offered (and accepted) an Adjunct Research Fellow appointment at NCGR.
One NCGR staff member has presented in the Plant and Animal Genomics (PAG-Asia Singapore,
March 2013) Workshop run by Dr Bellgard and has visited the CCG in Perth, Western Australia
to progress collaborations on lupin and cattle bioinformatics. The fellowship enabled several
face-to-face meetings with scientists at USDA, NIH (Washington), Kansas State University as
well as collaborative research with Landcare Research New Zealand.
Satisfaction:
The fellowship was what I expected and will enhance my CV. International collaborations are
viewed with great favor at Murdoch University. No practical problems encountered. No
improvements necessary.
Advertising the Programme:
I learned about the Programme from a colleague in the USDA who had a successful OECD
fellowship in 2009.