TL-I Objective 2 Phase 2 Draft Workplan – Nov. 20, 2009

“Improving Cowpea Productivity for Marginal Environments in SSA”

UC Riverside and IITA (Jeff Ehlers, Phil Roberts, Tim Close, Ousmane Boukar) N. Cisse - ISRA, Senegal I. Drabo - INERA, Burkina Faso R. Chiulele - Eduardo Mondlane University, Mozambique

200mm

800mm

Partners located across semi-arid “cowpea zone”: IITA – Kano, Nigeria

INERA, Saria, Burkina Faso ISRA, CNRA-Bambey, Senegal

Eduardo Mondlane Univ., Maputo, Mozambique

Mozambique

Senegal Burkina Faso

Nigeria

UCR Field Station mimics Africa

Rationale   Cowpea is a key component of

cropping systems, food security in SSA

  Cowpea productivity impacted by: • Drought, heat; Macrophomena, bacterial

blight, flower thrips, aphids, Striga,nematodes

  Solution – Cowpea varieties that resist these stresses

  “Modern Breeding” speeds delivery

•  Apply the outputs of current TL-1 in new breeding strategies (MARS, MABC)

•  Transfer Phase I outputs to TL-2   High-throughput SNP genotyping   Markers for drought and biotic stress resistance   Agarose-gel based markers from SNPs

TL-1 UCR/IITA

TL-2 IITA

CRSP Senegal

CRSP Burkina

TL-2 Mali

TL-2 Niger

TL-2 Nigeria

TL-1,2 Moz. EMU, IIAM IITA

TL-2 Tanz.

TL-1 Linkages to 8 African partners

CRSP Angola

  Drought tolerant germplasm and drought QTL identified

  Key QTL for resistance to flower thrips, Macrophomina, root-knot nematode

  High-throughput SNP genotyping •  Essential tool for MARS, MABC •  Select single-plex SNPs– custom assays

  High density SNP consensus map (Muchero et al., PNAS, 2009)

Phase 2 will build on current outputs of TL-1 & TL-2

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680cM; 11 LG; 1 marker/0.7cM

Phase I Outcomes, deliverables to TL-2 and Phase 2 Workplan & Outcomes

TL-1 and TL-2 Germplasm Screening

Genomic Resources

Phenotyping, Marker Development

TL-1 and TL-2 Population development

High-throughput SNP genotyping platform

640 access genotyped 1536 SNPs (50 TL-2 FPV, Elites)

>1,500 Accessions phenotyped drought tolerance

Sources of drought tolerance

TL-1 MAGIC population

1,200 RIL genotyped 1536 SNPs

Consensus map w/1000 SNPs

SNP QTLs Drought, Striga, Macro, Nematodes, Thrips

1,200 RIL Phenotyped- Drought tolerance & biotic resistance

Crosses made and advanced

Elite x Elite Populations

MARS ; MABC

2014

Phase I Phase II

Activity

Tools

Output

Outcome

Release DT cultivars, Parents

then Identification of genes for important traits

TL- 2 IITA/NARS MAS & MABC; Test, release varieties

Data Management Genotyping, MARS Tools QTL Analysis

TL-1 MAGIC population

Training

Agarose gel markers

cDNA, EST sequencing

High-throughput SNP genotyping platform

8 elite x elite , 2 cycles MARS; 8 MABC sets of lines

24 advanced lines w/superior performance under drought; 8 MABC lines

Test - MARS efficiency, practicality

3 PhDs trained

7 NARS breeders trained

Transfer. Outcome

Activity 1: Develop MAGIC population

SNP genotypes for the eight prospec3ve parents for linkage group 1 are shown below as an example.

Activity 2: Develop genomic resources in support of marker-assisted breeding

•  Customized sets of markers for MARS ; genotype data production in support of MARS breeding

•  Genotyping data analysis to optimize MARS (breeding values, selection indices)

•  Genetic analysis for QTL discovery in MARS populations

Activity 3: Employ MARS and MABC to develop improved breeding lines

•  2 populations per partner, 300 lines/population •  Conduct MARS cycles 1 and 2 in elite x elite crosses •  Selection and performance testing of advanced lines

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Phenotyping of parents (Phase 1 Output)

Sow Parents, Cross, Harvest F1(greenhouse) Sowing of 6 F1; Harvest F2

Sowing of 6 F2; Harvest 6 F3 (300 each)

Sow F3; Genotype F3; Harvest F4 seed

Phenotype F4 Families; select 10% Genotype 5/family, recombine selected 4 F5 (Crosses)

Sow Recombined (F1), Harvest 4 F2 Genotype 400 F2, select 100; harvest F3 selected Phenotype 100 F3, Select 10% -, Harvest F4 seed

Genotype 5/family, recombine selected F4, also advance selects to F5-tests Genotype, advance F5 to F6

Performance evaluation to determine progress

Genotyping Needs/popln 92 10x5 300 300

30x5

10x5

10x2 400

10x5

10x5

10x5

10x5 100 300

No. of Populations 2 2 6 2 6 2 2 6 6 2 6 6 6 6

Total=10,727 samples to be genotyped 184 100

1800 600 900 100 40

2400 300 100 300 300 600

1800

**Yellow and Blue filled areas are for populations initiated for TL-1 Phase 2 and under the Top-Off funding in 2009, respectively; Red indicates work already completed during Phase 1 as part of Phase 2; Light blue and light yellow indicates new cycle being initiated for TL-1 Phase 1 ‘Top-Off’ and Phase 2 populations, respectively. Top-Off populations (SuVita2/Mouride and IT93K-503-1/IT84S-2246) currently consist of 92 F4 families each, with phenotyping being conducted at UCR, Senegal and Burkina Faso. The 6 Phase 2 MARS founder populations (Table 2) will consist of 300 F3:4 families.

Cross Partner #

polymorphic markers

Known resistance/tolerance traits present in population

IT98K-1111-1/IT84S-2246* IITA 256 heat, multiple

IT96D-610/ IT97K-499-39 IITA 114 drought, Striga

KVx525/SuVita2 Burkina 143 Striga (race 1,2,3)

IT84S-2246/IT93K-503-1 Burkina /UCR 143 multiple*, drought, Macrophomina

Mouride/SuVita2 Senegal/UCR 226 Striga (races 1,2,3), bruchids, bacterial blight,CAbMV

IT93K-503-1/Yacine Senegal 306 drought, Macrophomina, Striga (races 1,3,4), aphid, bacterial blight, CAbMV

SuVita2/Melakh Mozambique 301 aphid, bacterial blight, CAbMV

IT84S-2246/IT95K-1491 Mozambique 220 aphid, thrips, bruchids, multiple

Biparental populations to evaluate MARS

  Also - Phenotyping 2 populations for heat and aphid tolerance marker discovery

Activity 3: Employ MABC to develop improved breeding lines

•  MABC to introgress/validate QTL into local varieties –  QTL validation – 4 Drought , flower thrips, Macrophomena –  MABC lines for release in TL-III

Activity 4. Capacity Building

•  Two PhD students at UC Riverside   Senegal (Penda Sarr)   Mozambique (Arsenio Ndeve)   Jointly supported by TL-I and USAID CRSP   MABC and MARS breeding

•  One PhD student at WACCI   Burkina Faso (Joseph Batieno)   GCP CB supported

•  English training now

•  Workshop for TL-1 and TL-2 breeders in MAS, MARS, MABC w/MBP   Use their own genotypic and phenotypic data

2014 Vision for Cowpea

  Modern cowpea breeding implemented •  Several African NARS •  Modern breeding strategies (e.g. MARS) evaluated •  Improved breeding lines developed, transferred to TL-III

  Local varieties with enhanced performance near release •  Introgress drought tolerance, biotic stress QTL using MABC •  Released in TL-III

  New tools and resources available •  A MAGIC population for cowpea research community •  New SNP-QTL markers for drought and heat tolerance plus aphid

and bacterial blight resistance

  Enhanced capacity in modern breeding •  3 African PhD students and 7 NARS scientists

trained in modern breeding

Impacts:

  Modernization of cowpea breeding to expedite delivery of improved varieties

  Greater cowpea production in drought-prone environments

  Enhanced breeding potential from: •  Elite drought tolerant breeding lines

•  More powerful tools (genotyping platform,

consensus map)

  Increased capacity/sustainability in modern breeding •  3 African PhD students & 7 NARS scientists

trained in modern breeding

Thank You

Phase II Outputs for MBP:

  MAGIC population available for gene discovery

  Genotypic and phenotypic data from 2 cycles of MARS

  300 additional RIL genotyped, even better map

Outputs for TL-III

  Validated markers for Drought Tolerance, Macrophomena, Bacterial Blight, Flower Thrips & Striga resistance

  More SNP markers for drought from elite x elite analysis

  New markers for heat tolerance, aphid resistance

  1,000 SNPs validated for use in flexible genotyping platforms

  8 ‘improved local’ candidate varieties from MABC

  24 advanced breeding lines from MARS