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TL1 proposal: common bean




  TL2 annual Meeting, Bamako Mali – Nov. 2009




        (Objective 3 – Tropical Legumes I)
Objective 3 Common bean – Major Outcome flows to TL-1 Phase II


          Germplasm                        Genomic                     Marker                  Population                        Activity
          Screening                       Resources                  Associations             development


                                                                                                                              2007

Germplasm phenotyped               SSR platform (1500) from                                                                          Tools
 (604) drought tolerance             EST, BAC, etc., and
                                      genotyping sets            MAS crosses (CBB,          Adv Backross
                                   1st gen. SNP platform (768)    BCMV, Bruchid)         populations created (5)

         Germplasm genotyped                                                             Intra-genepool Elite x
                                                                   QTL populations




                                                                                                                   Phase I
                                                                  phenotyped (deep         Elite Crosses (40)                   Operation
                                       Mapped markers /          rooting and carbohyd.
Sources of drought                      Physical map                  translocation)      Inter-genepool lines
    tolerance                                                                             (DAB and CBIB lines)
                                                                   Advanced lines
              Diversity Sets:                                      and segregating
                                                                     populations            Early generation
              Ethiopia, Kenya,        QTL for deep rooting                                  populations and
                ECABREN /             and for carbohydrate                                  advanced lines
                SABRN and                 translocation
              Reference Coll.                                                                                                   Outcome
                                                                                                                              2010




                                                                                                                   Phase II
      Deep rooting sources            SNP confirmation             Marker-assisted         Adv. Backcross and
                                                                   backcrossing to           MARS breeding
                                      For Intra-genepool
                                                                   develop improved          populations for
                                         populations
                                                                     local varieties         Andean drought
                                                                                                tolerance

                                                                                                                              2014
Act. 1: Evaluate rooting depth of
        parental sources

 •  Extending work
    on reference and
    regional
    collections
    (G. Makunde,
    Ph.D. thesis)
Act. 2: Validate SNPs for inter- and intra-
            gene pool crosses
                             Mesoamericans


•  For 50 donor and
   recipient genotypes

•  For introgression to
   Andeans

•  For use in MARS




                               Andeans
Act. 3: Deploy insect and disease
         resistance genes

•  Confirm MAS in
   advanced lines
   –  BCMNV
   –  Storage insects
   –  Bacterial Blight


•  RGA for Bacterial
   blight
Act. 4: Deploy drought
 tolerance traits from
    inter-gene pool
                                        o
                                        o
                                        o
                                        o


  crosses in Andean
                                        o




       gene pool                   Pod           Pod
                               Partitioning    Harvest
                                  Index         Index



             •  Characterize traits in 40 parentals
             •  Develop & test visual scales
             •  QTL for Pod Harvest Index & deep
                rooting
             •  Test 60 Andeans for heat tolerance
Act. 5: Pyramid drought tolerance traits
through MARS and Advanced Backcross
           in Andean gene pool
                               P1               P2
•  Genotype 2 AB
   populations                         F1

•  Genotype &                        F1-BC1
   phenotype 4 RIL
   populations for MARS
                                     F1-BC2
•  3 more populations for
   MARS                                X

•  Pyramiding from AB
   and RILs
                            Advanced Backcross Lines
Advanced
Backcross
Scheme


    Andean
  Red Mottled        2 AB-QTL            Microsatellites and SNPs
   Cultivars        Populations
  CAL96 (Uga)        selected
 CAL143 (Mwi)


                    Phenotype
                                  Genotype
                                                  Genetic Map


                    QTL identification
 Mesoamerican
Drought Tolerance
    Sources
     SER16          Line distribution
     SER48
Marker
Assisted
Recurrent
Selection
Scheme


                                                                       DNA extraction
                                                                       Genotyping

Lines Derived and                                                      QTL analysis
Recombination Cycles
                                  F3.5: Drought
                                   Multi-location trials option
                                  Phenotyping for QTL analysis

Double & Multiple                                                 F3.4: Families
                                                                  Lowland site
          crosses


 F1: Simple cross                Cycle 1
Drought tol. X And. commercial   starts                           F3: Plant select.
                                                                  Low P + MAS for R gene
                                                                  Highland site

                F1 to F2              F2: Drought
                                      Single Plant Selection
                                      Lowland site
Act. 6: Training of students in
 drought tolerance and MAS
    •  Training students in MARS
    •  Short course in CIAT


   Act. 7: Data storage and
         management
Proposed Act. 8: Testing the out-sourcing of
      marker analysis with partners

  •  Samples currently cost $8 in Africa (paid by
     special project using unique method)

  •  Outsourcing would cost $2-3

  •  Accuracy of markers would be verified
    –  Bacterial blight
    –  Storage insects

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39 Matthew Blair Tli Objective3 Phase Ii Work Plan

  • 1. TL1 proposal: common bean TL2 annual Meeting, Bamako Mali – Nov. 2009 (Objective 3 – Tropical Legumes I)
  • 2. Objective 3 Common bean – Major Outcome flows to TL-1 Phase II Germplasm Genomic Marker Population Activity Screening Resources Associations development 2007 Germplasm phenotyped SSR platform (1500) from Tools (604) drought tolerance EST, BAC, etc., and genotyping sets MAS crosses (CBB, Adv Backross 1st gen. SNP platform (768) BCMV, Bruchid) populations created (5) Germplasm genotyped Intra-genepool Elite x QTL populations Phase I phenotyped (deep Elite Crosses (40) Operation Mapped markers / rooting and carbohyd. Sources of drought Physical map translocation) Inter-genepool lines tolerance (DAB and CBIB lines) Advanced lines Diversity Sets: and segregating populations Early generation Ethiopia, Kenya, QTL for deep rooting populations and ECABREN / and for carbohydrate advanced lines SABRN and translocation Reference Coll. Outcome 2010 Phase II Deep rooting sources SNP confirmation Marker-assisted Adv. Backcross and backcrossing to MARS breeding For Intra-genepool develop improved populations for populations local varieties Andean drought tolerance 2014
  • 3. Act. 1: Evaluate rooting depth of parental sources •  Extending work on reference and regional collections (G. Makunde, Ph.D. thesis)
  • 4. Act. 2: Validate SNPs for inter- and intra- gene pool crosses Mesoamericans •  For 50 donor and recipient genotypes •  For introgression to Andeans •  For use in MARS Andeans
  • 5. Act. 3: Deploy insect and disease resistance genes •  Confirm MAS in advanced lines –  BCMNV –  Storage insects –  Bacterial Blight •  RGA for Bacterial blight
  • 6. Act. 4: Deploy drought tolerance traits from inter-gene pool o o o o crosses in Andean o gene pool Pod Pod Partitioning Harvest Index Index •  Characterize traits in 40 parentals •  Develop & test visual scales •  QTL for Pod Harvest Index & deep rooting •  Test 60 Andeans for heat tolerance
  • 7. Act. 5: Pyramid drought tolerance traits through MARS and Advanced Backcross in Andean gene pool P1 P2 •  Genotype 2 AB populations F1 •  Genotype & F1-BC1 phenotype 4 RIL populations for MARS F1-BC2 •  3 more populations for MARS X •  Pyramiding from AB and RILs Advanced Backcross Lines
  • 8. Advanced
Backcross
Scheme
 Andean Red Mottled 2 AB-QTL Microsatellites and SNPs Cultivars Populations CAL96 (Uga) selected CAL143 (Mwi) Phenotype Genotype Genetic Map QTL identification Mesoamerican Drought Tolerance Sources SER16 Line distribution SER48
  • 9. Marker
Assisted
Recurrent
Selection
Scheme
 DNA extraction Genotyping Lines Derived and QTL analysis Recombination Cycles F3.5: Drought Multi-location trials option Phenotyping for QTL analysis Double & Multiple F3.4: Families Lowland site crosses F1: Simple cross Cycle 1 Drought tol. X And. commercial starts F3: Plant select. Low P + MAS for R gene Highland site F1 to F2 F2: Drought Single Plant Selection Lowland site
  • 10. Act. 6: Training of students in drought tolerance and MAS •  Training students in MARS •  Short course in CIAT Act. 7: Data storage and management
  • 11. Proposed Act. 8: Testing the out-sourcing of marker analysis with partners •  Samples currently cost $8 in Africa (paid by special project using unique method) •  Outsourcing would cost $2-3 •  Accuracy of markers would be verified –  Bacterial blight –  Storage insects