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What is Happening in Peanut Geno


									               What is happening
               in peanut genomics
                     in India

              Rajeev Varshney
   Senior Scientist- Applied Genomics, ICRISAT
Coordinator, Indian Groundnut Genomics Consortium
 Leader, Comparative Genomics & Gene Discovery
        (Generation Challenge Programme)
    Groundnut production in India

• 1st most important oilseed crop in India
       Area: 6.6 million ha
       Production: 5.9 million t
       Productivity of groundnut – 0.97 t ha-1

~ 20% of world production comes from India alone!
 Constraints in production

  Leaf              Rust
             Indian Groundnut
            Genomics Consortium
- Indian Council of Agricultural Research
 Three main partners:
 ICRISAT, Patancheru, A.P.
 (Intern. Crops Res. Inst. Semi-Arid Tropics)
 NRCG, Junagadh, Gujarat
 (National Research Centre for Groundnut)
 UAS, Dharwad, Karnataka
 (University of Agricultural Sciences)
         Team of multidisciplinary scientists
• Generation of microsatellite-enriched libraries and
  identification of ~500 microsatellite or simple sequence
  repeat (SSR) loci

• Generation of groundnut unigene-derived SNP markers and
  development of cost effective CAPS assay

• Construction of integrated genetic maps with SSR, SNP
  and DArT markers

• Phenotyping of mapping populations at three locations
  (ICRISAT, NRCG, UASD) over 3 years

• Identification of genes/QTLs associated with resistance
  to foliar diseases (rust and late leaf spot) and tolerance to
  drought (TE, SCMR and SLA)
What we already have done at ICRISAT…
          SSR marker development
 In silico approach after mining sequence data
     - Aeschynomenoid/ Dalbergoid and Genistoid clades of
        the Leguminoae (15 genera)
     - 6 genera Adesmia, Amorpha, Dalbergia, Chaetocalyx
        Lupinus and Stylosanthes: 411 seqs contained SSRs
.    - Primer pairs for 109 unique SSRs
     - 79 functional in one of six genera
     - 51 primer pairs functional in peanut

  BAC-end sequence derived SSRs (Doug Cook)
                                                          Genetic map construction
                     Ah1                        Ah2                       Ah3                      Ah4                      Ah5                            Ah6                          Ah7                       Ah8                     Ah9.1                Ah9.2                Ah10
               0.0         GM635a         0.0          GM630        0.0         GM626        0.0         TC3G01b      0.0         TC7C06             0.0         RI1F06_2A        0.0         seq18G01      0.0         GM698           0.0     seq7G02      0.0      seq2B09     0.0      XIP
                                          3.3          seq10D04
               5.9         GM635b         6.2          RN6F05
                                          7.6          GM633                                                                                         8.6         seq18E07                     seq19D01
              10.7         seq18G09_5B                                                                                            XIP245                                          9.8
                                          9.4          PM179                                                         11.0
              11.6         seq13A07
                                         14.5          TC6E01                               18.0         XIP219                                                                                                                                             14.6      GM672      13.9      seq
              14.5         GM669                                   15.5         seq16C06                             16.4         GM623                          seq1B09
                                                                                            24.3         XIP606                                     17.1                                                                                        gi1170_9A   16.2      TC2D06
              19.0         seq17E01                                                                                  18.9         TC1A02_7B                                                                                         18.6
                                                                                            26.5         XIP419                                     18.9         PM499
                                                                                                                                                                                                                                    20.7        Lec1_9A
                                                                                            28.1         XIP123      22.6         XIP689                                                                   22.5         seq8H01     22.7        PM436                 Ah193_1A
                                                                                            29.2         PM721                                      25.3         PM73                                                                           GM694
                                                                                                                                                                                                                                    26.8                                         27.1      seq
                                                                                            29.8         GM660       28.4         TC1A01                                                                                                        seq14H06
                                                                   30.3         seq13E09                                                                                                                                            28.8
                                                                                            31.5         GM679
                                                                                            33.8         XIP177                                                                                                                                             32.9      seq13A10
                                                                                                                     34.8         PM377             34.6         AC2C05                                                             34.5        TC5A06
                                                                                            35.9         XIP406                                                                                                                                                                  37.3      GM
                                                                                            37.4         TC9F10_8A   38.6         seq9H08a
                                         42.6          GM667                                39.2         TC6H03_6B
                                                                                            40.9         PM733a                                                                                                                                                                  43.7      seq
                                                                                                                     46.1         XIP171A
              48.4         TC3G01a
              50.1         TC3G01c                                                                                                                  50.8         seq2G04

                                                                                                                                                    62.0         TC9F04                                                                                                          61.8      PM

Ah9.2                  Ah10                     Ah11                      Ah12                     Ah14                Ah15                     Ah16                          Ah17                       Ah18                       Ah19                       Ah20
                                                                                                                                                                                                                                                                                 75.6      PM
    seq2B09          0.0      XIP287      0.0          TC11B04       0.0         TC4D09       0.0         PM427      0.0      XIP105          0.0           TC4G02          0.0          GM624       0.0          seq11G03        0.0         seq19D09_1B    0.0      GM641
                                                                                                                                                                                                     3.8          TC4F12_2A
                                                                                                                                                                            5.4          seq19B12
                                                                                              7.7         PM375      6.7      XIP108A
                                                                                                                                                                            9.0          TC9H09
                                                                    10.3         XIP524      10.8         GM629
    GM672        13.9         seq9G05                                                        13.2         GM736
                                                                                                                                                                           20.1          seq15C10
                                                                    22.5         seq19A05
    Ah193_1A                             23.6          GM647                                 23.9         seq18C05
                                                                    24.6         XIP165
                 27.1         seq19D06                                                       26.1         XIP108B

                                                                                                                                                                                                                                35.4          TC7E04
                 37.3         GM723b                                                                                                         36.7           GM618

                                         42.1          TC7H11_2A
                 43.7         seq19H03

                                                                                                                                             51.9           Gi4926
                                                                                                                                                                                                                                                Collab.     47.3      seq16G08

                 61.8         PM183      60.8          GM692                                 61.1         XIP136
                                                                                                                                             62.9           GM745
                                                                                                                                                                                                                                                D Bertioli, Brazil
                                                                                                                                             67.5           seq18A05
                                                                                                                                                                                                                                                G He, USA
                 75.6         PM418

                                                                                                                                                                                                                                                S Knapp, USA
         Cultivated x Cultivated
                                                                                                                                             83.0           seq19G07

                                                                                                                                                                                                Mapping water use
         TAG 24 x ICGV 86031 -RIL                                                                                                                                                               efficiency QTLs
            Molecular diversity
916 accessions at 21 SSR loci        Reference collection
                                     (300 genotypes)

                                     Exploring association
                   fastigiata: 488
                   hypogaea: 321
                   wild: 47          genetics approach
What we plan to do at ICRISAT
(under Troplical Legume Genomics project)…
          Generation Challenge Programme
• Launched in August 2003
• 10-year framework (2004–2008; 2009–2013)
• About US$16M annual budget
  – 75% Research
  – 15% Training and capacity building
  – 10% Management cost
• Major donors
  – European Community
  – DFID
  – The Bill & Melinda Gates Foundation
  – World Bank
  – Switzerland
• Target areas: Marginal drought-prone environments
  – Africa (SSA)
  – South and South East Asia
  – Latin America
• Mandate crops (CGIAR) – 22 crops
• A CGIAR Challenge Programme hosted at CIMMYT, Mexico
             GCP Research Structure
                         DB, Information Network               Jean-Marcel Ribaut
                                (SPL: T van Hintum)

                  Phenotyping               Phenotyping
        SP1                      SP2                           SP3
     Germplasm              Gene Discovery                     MAS
(SPL: J-C Glaszmann)      (SPL: R K Varshney)            (SPL: P Monneveux)

                           (SPL: C de Vicente)

            Breeding programmes
                                           (Delivery plans)
           Improved genotypes

         Improved germplasm in farmers’ fields
                 Tropical Legume I project
                          (GCP)            US $ 11 m

                 Activity 1:   Objective 5         Activity 3:     Activity 4:  Activity 5:
                  Explore       + Activity 2:   Identify Marker Identify Marker Improve
                 Diversity       Generate         Development     Development Germplasm
                                                    (Biotic)       (Abiotic)   Development
Objectives 1-4


                                                Objective 6
         Peanut                Common bean               Comparative Genomics
         Cowpea                Chickpea                  Training
           Objective 1- Peanut
           (PI: Dave Hoisington)
Project Activities
• Develop germplasm for genetic studies and modern
   – Bonny Ntare (ICRISAT, Mali)
• Generate genomic resources for genetic studies and
  modern breeding
   – Andy Paterson (University of Georgia, USA)
• Identify molecular markers and genes for biotic stress
   – David Bertioli (Catholic University, Brazil)
• Identify molecular markers and genes for drought
   – Vincent Vadez (ICRISAT, India)
• Improve locally adapted germplasm for target traits
  through modern breeding
   – Emmanuel Monyo (ICRISAT, Malawi)
                         Objective 5- Cross species
                         (PI: Doug Cook)
Objective 5:        Develop cross species resources for comparative genomics in tropical crop legumes

Activity 1:         Comparative Marker Development                                    Doug Cook
      Milestones:   1. Development of molecular marker database and web interface.
                    2. Development of 500 orthologous gene markers.
                    3. Associate genetic markers to bacterial artificial chromosome clones in each species

Activity 2:         Analysis of the Arachis-species Complex                          David Bertioli
      Milestones:   4. Diploid Arachis AA bacterial artificial chromosome clone end sequencing and SSR discovery
                    5. Mapping of orthologous genetic markers in diploid Arachis AA population
                    6. Identification of ultra-long SSRs in tetraploid Arachis
                    7. Genetic mapping of ultra-long SSRs in tetraploid Arachis

Activity 3:         Estimating Genome Divergence at Orthologous Loci                          Andy Paterson
                    8. DNA sequencing and divergence estimates for network of orthologous bacterial artificial chromosome clones
            Project partners
• Catholic University of Brasilia, Brazil
• Chitedze Research Station, Department of
  Research and Development, Ministry of
  Agriculture, Malawi
• EMBRAPA, Brazil
• ICRISAT, India/Malawi/Mali
• Insitut National de Recherche Agronomique du
  Niger (INRAN), Niger
• Institut Sénégalais de Recherche Agricole (ISRA),
• Naliendele Research Station, Department of
  Research and Development, Ministry of
  Agriculture, Tanzania
• University of Georgia, USA
         Take home message

   Community efforts
   Rapid advances in genomics
   Genome infrastructure available
   Applications to breeding
             Contributions and thanks
Genomics:                            OVERSEAS COLLABORATIONS
Rajeev Varshney                      UC-Davis: Doug Cook, R Varma
Dave Hoisington                      Catholic Univ: David Bertioli
Gautami, Ravi, Bryan, SomaRaju
                                     Tuskegee Univ: Guaho He
Genetic resources:
Hari Upadhyaya                       Univ of Georgia: Steve Knapp
Ranjana Bhattacherjee
Shyam Nigam, R Aruna                   Financial support:
Crop Physiology:                                National Fund,
Vincent Vadez                                   Indian Council of
                                                Agricultural Research
Statistics & Bioinformatics:
Subhash Chandra, Jayashree                      Generation
Collaboartions in India:                        Programme
NRC for Groundnut: T Radhakrishnan
UAS Dharwad: MVC Gowda, Khedikar                Department of

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