why and how to build up a network of excellence on...

European Triticeae Genomics Initiative (ETGI)

1st Workshop at the 4th Plant Genome European MeetingAmsterdam, Sep 21st, 2005

Why and how to build up a network ofexcellence on Triticeae genomics in

Europe?

Nils Stein, Catherine Feuillet

Institut National de la Recherche Agronomique


• What is the added value of the ETGI network and projects for the EU? What genomic tools, resources and strategies have to be developed to address the next challenges of a knowledge-based bio-economy and build the foundation of sustainable agricultural systems?

• How do we interact with existing international and European initiatives to build state-of-the-art research on Triticeae genomics in Europe and become major contributors of the international efforts?

• What is the best method for creating synergies between the barley and wheat genomic efforts?

• What are the next steps necessary for establishing a European network in Triticeae genomics and funding the priority scientific projects of the network?

• Europe has to play a role in the future production of safe, healthy, andaffordable food for the world’s growing population as well as in thedevelopment of renewable resources to replace the limited fossil resources

• EU depends on our crop production to maintain the health and prosperity of itspopulation (food and drink industry is the leading industry sector: 700 billion €annual turnover and 2.6 million workforce)

• EU farmers need to keep up with their international competitors (Canada, USA for wheat) by promptly applying advances in plant genetics and molecularbiology.

• EU economy relies heavily on agriculture - 17 million farms; 8% of EU25 workforce is employed in the agricultural sector; and the EU seed marketequals 8.4 billion € annually, largest regional market (representing 30% of theglobal market)

• EU needs to have a knowledge based bio-economy and Plant Genomics willprovide the foundation to solve these challenges

EU economy relies on plant derived products

Wheat and barley are the most important cereal crops in Europe

EU crop production (harv area Ha)FAO 2004

WheatBarleyMaize

Rapeseed

Rye

Oats

Triticale

Potatoes

Sugar Beets

Tomatoes

wheat (87 Mt vs 64 in USA) and barley (42 Mt vs 12Mt in Canada) are the mostimportant cereal crops grown in Europe

Europe is a key player in barley and wheatresearch (scientific know-how and breedinghistory)

Wheat and barley are the most important cereal crops in Europe

Technology platform: Strategic researchAgenda and Action plan adresses four main

challenges:

1. Healthy, safe and sufficient food and feed

2. Sustainable agriculture, forestry, and landscape

1. Improve plant productivity and quality: yield stability under varyingenvironments, high quality of harvest products, adaptability to end use, functional food

2. Reduce and optimise the environmental impact of agriculture: disease R to reduce pecticide application, Nitrogen efficiencyreduce fertiliser input

3. Green products

4. Competitiveness, consumer choice

Wheat and Barley: two cereal crops with different nutritional, agronomical, ecological and regional importance

Wheat: human nutrition (bread, pasta, cookies….)animal feednon-food use: starch industry

renewable resources (ethanol)

Barley: malting (brewing industries)animal feedrenewable resources (ethanol)human nutrition

Target traits for EU economy: high food quality, yield stability, environmental impact (N efficiency, water efficiency, disease resistance)

Structural genomics

Functionalgenomics(Transcriptomic Proteomic)

Comparative genomics

Genetics (QTL, association)

Ecophysiology

Identification of genetic loci involved in target trait phenotype

Isolate the genes, understand regulation andfunction

Mutant collections,Genetic engineering

Marker assisted Breeding (MAS),Exploitation of genetic diversity

Crop improvement

Wheat Barley

Markers (EST, SSR) ~600‘000 EST (16‘000 mapped)

3‘212 SSR mapped

~400’000 EST (>2’000 mapped)

900 SSR mappedBAC libraries 7 libraries from diploid

(3), tetraploid (1) andhexaploid (3) wheat

2 libraries + 1 in preparation + non arrayed libraries

Genes isolated Lr10,Pm3,Lr21,Vrn1,Vrn2, Q

mlo,ror2,Mla,Rpg1,rym4

DNA arrays 55’000 genes >20’000 genes(53’000 genes)

Development of molecular tools for wheat and barleygenomics

The genomes of wheat and barley need to become more accessible to allow for targeting traits quicker

Large number of populations, genetic maps and genetic loci identified in the last 20 years. Most important agronomic traits are QTL based

in Wheat and Barley: ~ 900 genetic loci correspond to more than 100 different morphological and physiological protein, biotic and abioticresistance phenotypes.

bottleneck = map-based cloning, labourious and long (7-10 years projects)

Best way to accelerate is to get the genome sequence (e.g., rice), not yetpossible in wheat and barley but:

Physical maps anchored to the genetic maps in both species would:

accelerate gene cloning and gene characterisation

Support the development of markers for efficient MAS and betterexploitation of genetic diversity

set up the foundation for sequencing the genomes


• What is the added value of the ETGI network and projects for the EU? What genomic tools, resources, and strategies have to be developed to address the next challenges of a knowledge-based bio-economy and build the foundation of sustainable agricultural systems?




Member Institutions:

1. Institute of Plant Genetics and Crop Plant Research (IPK),Gatersleben, Germany.

2. Scottish Crop Research Institute (SCRI),Dundee, UK

3. Max-Planck-Institute of Plant BreedingResearch (MPIZ),Cologne, Germany

(4. Risoe National Institute,Roskilde, Denmark)

A European Competence Networkfor Barley Genome Research

Risoe

MPIZIPK

SCRI

General objectives:

(1) Exchange of information(2) Joint scientific events(3) Mutual use of research and test facilities(4) Joint use of resources(5) Development and promotion of joint projects(6) Promotion of the training of young scientists (7) Joint public relations work

European barley genomics network

Nordic Joint Commitee

BarleyGenomeNet

Network of bilateraland multilateral projects

• BarleyGenomeNet

• Nordic Joint Commitee: FI,DK,SE,NO genomics of endosperm development

bi- and multilateral projects:

EGRAM (EU FP4) (The European gramineae mapping programme)MABDE (EU FP5) (Mapping adaptionof barley to drought environments)BIOEXPLOIT (EU FP6) (Diseaseresistance and diversity)GABI-Genoplante (Rye-BarleyDiversity)

plentiful cooperations at the international level

European barley genomics networkWhite paper: Barley Genome Physical Map and Sequence

= initiating partners= EOI

UH

IPK

TUM

SCRI

Initiative of IPK(DE),SCRI(GB),UH(FI),EOI of numerous EU partners (NL,DK,IT,ES)

Generate a physical map of the whole barleygenome thereby providing a platform:

• for systematic gene isolation in barley

• for future genome sequencing

• for elucidating the genetic basis of complextraits for accelerated crop improvement

• for understanding the complex functionality of the cereal genome

Phase I (short/medium term)WP1 whole genome physical map of barleyWP2 genetic anchoring of physical mapWP3 concerted development of germplasm

and mapping populations for high-throughput phenotyping

WP4 sample sequencing of targeted regionsin the barley genome

WP5 bioinformatics

Phase II (long term)WP6 complete genome sequence of barley

A proposal for WP1 was submitted by IPK in cooperation with ACPFG, AUS and TUM, GER to „Pakt f. Forschung“, WGL- recommended for funding- descision pending, expected by Nov 14,

2005

European wheat genomics

Network of bilateral and multilateral projects

EGRAM (EU FP4) (European GramineaeMapping Programme)

HEALTHGRAIN (EU FP6) (nutrition, health, graintechnology and quality)

BIOEXPLOIT (EU FP6) (Disease resistance anddiversity)

IEB

Collaboration between academia, industry and governmental research organizations to:

build the foundation for advancing research for wheat production and utilization by developing DNA-based tools and resources that result from a sequenced wheat genome

facilitate international collaborations and coordination

. . . . . . . . . . . . . . . . . . . . . . . . . . . . International Wheat Genome

Sequencing Consortium

www.wheatgenome.org

IWGSC Current Membership. . . . . . . . . . . . . . . . . . . . . . . . . . . .

Australia

Canada

Czech Republic

France

India

Israel

Italy

Japan

Mexico

Switzerland

Turkey

United Kingdom

United States

50 individual members in 13 countries/ 16 Organizations from 9 countries

•Agricultural Research Council of Italy - Experimental Institute for Cereal Research of Fiorenzuola d’Arda

•Centro Internacional de Majoramiento de Maiz y Trigo (CIMMYT)

•Cereal Research Center, Agriculture & Agri-Food Canada (CRC, AAFC)

•ENEA Casaccia Research Centre: Plant Genetics and Genomics (Italy)

•Grains Research Development Corporation (Australia)

•Indo-Swiss Collaboration in Biotechnology

•Institut National de la Recherche Agronomique (INRA)

•Kansas State University

•Kansas Wheat Commission

•Montana Grain Growers Association

•Montana State University

•Murdoch University

•National Association of Wheat Growers (USA)

•Sabanci University (Turkey)

•The Institute for Genomic Research (TIGR)

•Wheat Genetics Resource Center

Short-Term and Mid-Term Goals. . . . . . . . . . . . . . . . . . . . . . . . . . . .

Develop a physical map and link it to the genetic map;

Sample sequencing and assessing alternative approaches for sequencing hexaploid wheat;

Sequence the genic regions of hexaploid wheat;

Annotate the genic regions; and

Obtain full-length cDNAs for all expressed genes.


• What is the added value of the ETGI network and projects for the EU? What genomic tools, resources and strategies have to be developed to address the next challenges of a knowledge-based bio-economy and build the foundation of sustainable agricultural systems?




Why a European Triticeae Genomics initiative?

The barley and wheat communities have a long and successful historyof cooperation at the international level

ITMI (1989, International Triticeae Mapping Initiative)

Genetic mapping of barley and wheat chromosomes

ITEC (1998)= joint EST sequencing effort that provided over 1 million wheatand barley ESTs (http://wheat.pw.usda.gov/genome/)

NSF project: Structure and Function of the Expressed Portion of Wheat Genomes (16000 EST mappedon deletion bins)

Barley and wheat Affymetrix chips (Barleybase)

TREP database (2001) = a collection of repetitive DNA sequences from different Triticeae species (http://wheat.pw.usda.gov/ITMI/Repeats/index.shtml)

TESC: EST-SSR coordination

ITMI (International Triticeae Mapping Initiative)2000: Reorganisation around 7 research areas including

Physical analysis:

•Barley (NSF)« Coupling Expressed Sequences andBacterial Artificial Chromosome Resources to access theBarley Genome »

• Wheat D genome (NSF) « Assessment of the InsularOrganization of the Wheat D Genome by Physical Mapping »

•3B physical mapping (INRA, IWGSC) «3B chromosome, a model to study the structure, function and evolution of thewheat genome »

• IWGSC: International Wheat Genome SequencingConsortium

It is time to establish a coherent, basic cereal genomics researchprogram in Europe

EU technology platform / Know-how transfer to:

• Construct physical maps• Develop marker and consensus maps, comparative genetics• New sequencing technology• Bioanalysis, sequence annotation platforms• Develop high throughput phenotyping• Develop, manage, and utilize Genebank, mutant collections (diversity)• Develop new methods for genetic studies (QTL, association genetics)• Use model genomes (rice, brachypodium for new probes)

To set the foundation for addressing the specific questions that are of importance for

Wheat: - preharvest sprouting, yield stability, protein content, disease resistance, water use, nitrogen efficiency….- Agreement on specific chromosomes with traits of interest?

Barley: - disease resistance (Pyrenophora, mildew), malting quality, Earliness, drought resistance, pre-harvest sprouting….- Whole genome map


Next steps for establishing the network

• Write a white paper of the ETGI

• Apply for a SSA (next February 2006: (takes one year beforefunding comes)

• First business meeting to discuss organisation of the ETGI (committees…)

• Organise first scientific workshop of the ETGI (2006), defineworkpackages

How do we raise funding for the projects?

• First steps: Physical map (barley genome= 5 M Euros, 7 wheatchromosomes (3B + 6 = 6 million euros) = 11 million Euros• Next projects•Total Cost Project= ~20 Million Euros

• Article 1.6.9: If collaboration built between the members states programs(Genoplante, GABI etc…) possibility to get support from the EU commission on the top of it

• State, region support (e.g., « Innovation in Cereals » Competence poles in France this year, « Pakt für Forschung » of Leibniz Association 2005…. )

• Calls of EU FP7 - proposal on tasks/goals as specified in the roadmap to thephysical map of the wheat chromosomes and/or the barley genome

• Marie Curie Research Training network for exchange of docs and postdocs, workshops

• Private sector support


Acknowledgments

Organisers: Willem Stiekema, Dominique Job

Secretariat: Marianne Selten

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