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The New Genebank CGIAR Research Program - Nordgen · PDF fileThe New Genebank CGIAR Research Program ... 1979-2009 < Source: Lopez-Noriega, ... Survey of 7 CGIAR genebanks . Genebank

Apr 28, 2018

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  • 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 $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 worlds 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

    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 genec 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

    Insect resistance

    Disease resistance

    Tolerance of abiotic stresses

    QTLs for yield

    Traits

    Nutrition?

    Industrial uses?

    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 Foundaon Conserved Germplasm

    Breeding Lines Specialized Genec Stocks

    Current problems

    Drought tolerance

    conservaon

    disseminaon

    Genotype-phenotype associaon

    Durable disease-pest resistance

    Problem soils

    Future challenges

    Public genec diversity research plaorm 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 Burgueo,

    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 th

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