The New Genebank CGIAR Research Program

Michael Abberton; Ahmed Amri; Denise Costich; David Ellis; Luigi Guarino; Aslaug Haga; Alice Muchigi; Alexandra Jorge;

Charlotte Lusty; Thomas Payne; Nicolas Roux; Ruaraidh Sackville-Hamilton; Hari Upadhyaya

(IITA, ICARDA, GCDT, CIMMYT, CIP, ICRAF, ILRI, Bioversity, ICRISAT)

CGIAR: The Consultative Group on International Agricultural Research

Agricultural research for development

Collaboration to help developing countries:   Identify needs   Build, implement and monitor R&D partnerships   Conserve, evaluate and share genetic diversity   Build capacity in agricultural R4D

$1 invested in CGIAR research àà $9 / year in benefit to developing countries   Higher in some cases e.g. 21:1 benefit:cost for rice

improvement in Vietnam, Philippines, Indonesia

www.cgiar.org

CGIAR holds ~10% of global accessions in ~0.5% of world’s genebanks

Accessions

AfricaRice Rice 20,000

Bioversity Banana, Plantain 1,298

CIAT Beans, Cassava, Tropical forages 65,635

CIMMYT Maize, Wheat 155,129

CIP Potato, Sweet potato, Andean Roots & Tubers 16,495

ICARDA Grain legumes, Wheat, Barley, Forage & range crops 135,406

ICRAF Trees 5,144

ICRISAT Dryland cereals, Grain cereals 156,313

IITA Banana, Plantain, Maize, Cowpea, Cassava, Yam 28,286

ILRI Tropical forages 18,291

IRRI Rice 116,817

Total 712,568

Phenotypic  variability  in  germplasm  conserved  at  ICRISAT  

Small millets Sorghum Pearl millet

Pigeonpea Chickpea Groundnut

Distribution of germplasm from CGIAR centres   Approx 600,000 samples / year   ~ 70% improved material   ~ 75% to developing countries.

Developing 76%

Developed 12%

In transition

7%

CGIAR 2%

Not specified

3%

Global distribution, by CG genebanks, of germplasm originally sourced from India,

1979-2009

  Source: Lopez-Noriega, I., Galluzzi, G., Halewood, M., Vernooy, R., Bertacchini, E., Gauchan, D. and Welch, E., 2012. Flows under stress: availability of plant genetic resources in times of climate and policy change. CCAFS discussion paper series. CIAT: Cali. Available at: http://hdl.handle.net/10568/21225

First Objective Crop and tree diversity is secured in perpetuity

Long-term storage Medium-term storage

Safety duplication

Plan and Partnership for

Managing and Sustaining CGIAR-held Collections of PGR

Second Objective

Conserved germplasm is clean, available and disseminated

Regeneration & characterisation

Disease testing & cleaning

Introduction of new accessions

Multiplication & dissemination

Third Objective

Use of conserved diversity is informed and facilitated

Managing information

GENESYS

Fourth Objective

Crop diversity is conserved with a rationalized, cost-effective and

globalised system Partnerships and exchange of services

Rationalisation and optimisation

Establishing QMS and staff retention plan

What makes an efficient effective rational global system?

Conservation

Use

Svalbard

Safety backup

Long term collection

Genebank active collection

Breeding/working collection

Farmers

Trad

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gene

bank

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Mak

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eful

Improving genebanks

  Adding new accessions to collections   Ensuring rational effective addition to fill gaps

  Optimise collection structure   Rationally eliminate duplicates   Classify accessions / reduce redundancy / balance

representation of genepool. How?   Rationally limit the size based on diminishing returns

  Sample tracking   QA for regeneration, seed processing and distribution

Making genebanks more useful

  Designing collections for breeding & research   Trait-specific subsets   Core collections   Focused Identification of Germplasm Strategy (FIGS)

  Pre-breeding 1:   Base broadening   Wide hybridization

  Pre-breeding 2:   Gene discovery: genotyping, phenotyping, association genetics

    Collections for Breeding Pre-breeding 1 Pre-breeding 2

  Crop Trait-specific Core FIGS Base-broaden

Wide Hyb geno pheno GWAS

Bioversity Banana X X       X X   Plantain X X       X X  

CIMMYT Maize   X X X   X X X Wheat   X X   X X X X

ICARDA

Grain legumes   X X X X X X X Wheat   X X   X X X X Barley   X X X X X X X Forages     X     X X  

ICRAF  

Multipurpose trees

X X   X   X X  

Fruit trees X X   X   X X  

IITA

Banana   X       X X   Plantain   X       X X   Maize                

Cowpea   X     X X X   Cassava   X       X X  

Yam   X       X X   ILRI Forages   X       X X X IRRI Rice X X   X X X X X

Survey of 7 CGIAR genebanks

Genebank   Collaborators/Partners  Bioversity   Institute of Experimental Botany, Cornell, BGI, DarT

(Australia),KULeuven, IITA, CIRAD U. Wageningen, Int. Musa Testing Programme  

CIMMYT   Seeds of Discovery (MasAgro)  

ICARDA   GRDC-Australia, Helsinki University  

ICRAF   Kunming Institute of Botany, China Forest Research Institute, Burkina Faso, INIA-Peru, PROSEMA-Peru, IARD, Cameroon Forest Research Institutes of Ghana, Burkina Faso, Malawi, Tanzania DARS of Malawi, Forest Commission\DRSS, Zimbabwe  

IITA   IITA breeders, Bioversity, Cornell University of California, CIAT  

ILRI   IITA Biotech, ILRI - Beca Hub; ASARECA, Africa-Brazil Innovation Marketplace  

IRRI   Rice SNP consortium, Rice 3k Sequencing Project, Global Rice Phenotyping network, INGER, Cornell  

Focused identification of germplasm for specific traits (FIGS)

A rational approach to exploiting large genetic resource collections Efficient and effective methods to mine genebanks for useful traits to breeders Deliver priority trait best bet subsets to requestors

Utilization of genetic

resources

Quantification of trait-environment

relationship

A priori information

Develop trait subsets

Sunn pest –

RWA resistance –

- resistance to Syrian bio-type

– 2 new functional genes

Salinity –

FIGS successes

T. boeoticum

New  gene�c  diversity  for  wheat    transferred  from  wide  crosses    

T. urartu

T. dicoccoides

yellow rust resistance

leaf rust resistance

earliness

high productive tillering

spike productivity

plant productivity

plant height

drought tolerance

Sunn pest resistance

Russian wheat aphid resistance

Septoria tritici resistance

Ae. speltoides

Grain Yield of Lines derived from Durum wheat x wild Triticum and Aegilops species

Wild Species of Oryza

O. minuta O. alta

O. ridleyi O. officinalis

O. brachyantha O. longistaminata O. rufipogon

Ø Insect resistance

Ø Disease resistance

Ø Tolerance of abiotic stresses

Ø QTLs for yield

Traits

Ø Nutrition?

Ø Industrial uses?

Ø Male sterility

Wide hybridization in rice

IR56 (No Salt)

IR56 (EC 24 )

O. coarctata (EC 24)

F1 IR56 x O. coarctata (EC 24)

BC1 IR56 x O. coarctata//

IR56 (EC 24)

Salt tolerance from Oryza coarctata

15 years of crossing produced

1 viable plant!

Use  

Rice  Diversity  as  Founda�on  Conserved  Germplasm  

Breeding  Lines  Specialized  Gene�c  Stocks  

Current    problems  

Drought  tolerance  

conserva�on  

dissemina�on  

Genotype-­‐phenotype  associa�on  

Durable  disease-­‐pest  resistance  

Problem  soils  

Future      challenges  

Public  gene�c  diversity  research  pla�orm  for  rice  

C4  Rice    Grain  quality    

Summary of rice progress

  8,000 accessions purified

  2,000 samples genotyped with 700k SNP chip   Designed from pool of 27M SNPs from 150 genomes

  >3,000 samples sequenced by NGS   17.059 TeraBases total of filtered, trimmed reads   Average 14.02 X depth coverage per line   820k average SNPs per genotype (about 1 SNP/500 bp)

  Genetic populations established for discovery   Indica, japonica and wild MAGIC   CSSLs, RILs …

  Global phenotyping network established

Seeds of Discovery (SeeD): An initiative to systematically explore

and mobilize novel genetic variation into maize and wheat breeding

programs Sarah Hearne, Martha Willcox, Juan Burgueño,

Carolina Saint-Pierre, Matthew Reynolds, Samuel Trachsel, John Hickey, Jiankang Wang, Sukhwinder Singh, Peter Wenzl,

Marc Ellis, Ky Mathews, Gregor Gorjanc, Janez Jenco, Armando Espinoza Banda, Alejandro Ortega Corona

2013 Research Projects in the Maize Germplasm Bank

CML Genetic Fingerprinting Project   12 most-often requested accessions   560 (and counting) lines (1960s-present)   No quality guarantee in place (yet!) Transgenic Pollen Monitoring System   First pollen traps set up last week   Positive control plots being planned for Iowa (2014) Controlling Ear Rot in Maize Landrace Nurseries   Devastating post-pollination seed loss   Two factors being tested o  Pre- and post-pollination fungicide treatments o  Harvest time (early versus late)

Defining the species in the genus Tripsacum, sister genus to Zea

Thanks to all who have contributed:

A collaboration between donors, policy makers, genebanks, geneticists, sequencers,

pre-breeders, phenotypers, breeders, informaticians in all sectors