Why and how to build up a network of excellence on Triticeae - - PowerPoint PPT Presentation

European Triticeae Genomics Initiative (ETGI) 1st Workshop at the 4th Plant Genome European Meeting Amsterdam, Sep 21st, 2005

Why and how to build up a network of excellence on Triticeae genomics in Europe?

Nils Stein, Catherine Feuillet

European Triticeae Genomics Initiative (ETGI)

• 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

• f 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, and

affordable food for the world’s growing population as well as in the development of renewable resources to replace the limited fossil resources

• EU depends on our crop production to maintain the health and prosperity of its

population (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 molecular biology.

• EU economy relies heavily on agriculture - 17 million farms; 8% of EU25

workforce is employed in the agricultural sector; and the EU seed market equals 8.4 billion € annually, largest regional market (representing 30% of the global market)

• EU needs to have a knowledge based bio-economy and Plant Genomics will

provide 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

Wheat Barley

Maize 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 most important cereal crops grown in Europe Europe is a key player in barley and wheat research (scientific know-how and breeding history)

Wheat and barley are the most important cereal crops in Europe

Technology platform: Strategic research Agenda 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 varying

environments, 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 efficiency reduce 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 feed non-food use: starch industry renewable resources (ethanol)

Barley: malting (brewing industries)

animal feed renewable resources (ethanol) human nutrition

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

(Transcriptomic Proteomic)

Comparative genomics Genetics (QTL, association) Ecophysiology Identification of genetic loci involved in target trait phenotype

Isolate the genes, understand regulation and function

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 mapped BAC libraries 7 libraries from diploid (3), tetraploid (1) and hexaploid (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 barley genomics

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 abiotic resistance 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 yet possible 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 better exploitation of genetic diversity set up the foundation for sequencing the genomes

European Triticeae Genomics Initiative (ETGI)

• 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?

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 Breeding Research (MPIZ), Cologne, Germany (4. Risoe National Institute,Roskilde, Denmark)

A European Competence Network for Barley Genome Research

Risoe MPIZ IPK 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 Barley Genome Net Network of bilateral and 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 adaption
• f barley to drought environments)
• BIOEXPLOIT (EU FP6) (Disease

resistance and diversity)

• GABI-Genoplante (Rye-Barley

Diversity) plentiful cooperations at the international level

European barley genomics network

White 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 barley genome thereby providing a platform:

• for systematic gene isolation in barley
• for future genome sequencing
• for elucidating the genetic basis of complex

traits for accelerated crop improvement

• for understanding the complex functionality of

the cereal genome Phase I (short/medium term) WP1 whole genome physical map of barley WP2 genetic anchoring of physical map WP3 concerted development of germplasm and mapping populations for high- throughput phenotyping WP4 sample sequencing of targeted regions in 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 Gramineae

Mapping Programme)

HEALTHGRAIN (EU FP6) (nutrition, health, grain

technology and quality)

BIOEXPLOIT (EU FP6) (Disease resistance and

diversity)

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 G enome Sequencing Consortium

www.wheatgenome.org

IWG SC 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 G

• als

. . . . . . . . . . . . . . . . . . . . . . . . . . . .

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.

European Triticeae Genomics Initiative (ETGI)

• 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

• f 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?

Why a European Triticeae Genomics initiative?

The barley and wheat communities have a long and successful history

• f 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 wheat and barley ESTs (http://wheat.pw.usda.gov/genome/)

NSF project: Structure and Function of the Expressed Portion of Wheat Genomes (16000 EST mapped

• n 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 and

Bacterial Artificial Chromosome Resources to access the Barley Genome »

• Wheat D genome (NSF) « Assessment of the Insular

Organization 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 the wheat genome »

• IWGSC: International Wheat Genome Sequencing

Consortium

It is time to establish a coherent, basic cereal genomics research program 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

European Triticeae Genomics Initiative (ETGI) Next steps for establishing the network

• Write a white paper of the ETGI
• Apply for a SSA (next February 2006: (takes one year before

funding comes)

• First business meeting to discuss organisation of the ETGI

(committees…)

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

workpackages

How do we raise funding for the projects?

• First steps: Physical map (barley genome= 5 M Euros, 7 wheat

chromosomes (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 the

physical 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

European Triticeae Genomics Initiative (ETGI)

Acknowledgments

Organisers: Willem Stiekema, Dominique Job Secretariat: Marianne Selten