the new genebank cgiar research program - nordgen · the new genebank cgiar research program ......
TRANSCRIPT
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
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
ition
al
gene
bank
ne
twor
ks
Mak
ing
gene
bank
s
mor
e us
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
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