1. Tropical Legumes I
Tropical Legumes II Annual Meeting
16–20 September 2009, Bamako, Mali

2. Outline
• Overview of TLI phase I
o Objectives, Activities
o Partners
o Achievements
o Lessons
• Transfer of TLI Outputs to TLII
• Overview of TLI phase II
o Rationale
o Partners
o Links with ongoing initiatives
o New Activities
o Integration between phase I and phase II
o Predicted outputs for TLII in phase II

3. Overview of TLI phase I

4. Improving tropical legume productivity for
marginal environments in sub-Saharan Africa (TLI)
To develop the key genomic resources that are
currently lacking in legumes (including cross-legume
molecular markers for comparative genomics), identify
molecular markers for traits of importance to resource-
poor farmers (biotic stresses and drought tolerance),
and improve “molecular” breeding capacities in sub-
Saharan Africa
10 Million US$, 2007-2009, 1st May 2007

5. TLI Objectives
1, Improve groundnut productivity
2, Improve cowpea productivity
3, Improve common bean productivity
4, Improve chickpea productivity
5, Develop cross-species resources for comparative biology
6, Provide training and capacity building

6. TLI Activities
♦ Objectives 1 to 4
• Germplasm for genetic studies and breeding -- development + characterization
• Generate genomic resources -- genetic studies and breeding
• Molecular markers and genes for biotic stress resistance (crop specific)
• Molecular markers and genes for drought tolerance
• Fluctuating annual rainfall and uneven annual distribution
• Enhancement of locally adapted germplasm -- target traits
♦ Objective 5
• Orthologous markers for cross genome analysis
• Comparative analysis of the Arachis species complex
• Genome divergence at orthologous loci
♦ Objective 6
• Project planning and training workshops
• Support to local facilities

7. National Program Partner Institutions
Groundnut Cowpea Bean Chickpea Capacity Building
East Africa
Ethiopia SARI EIAR EIAR
University
KARI,
of KARI,
Kenya Egerton
Nairobi/KA Egerton University
University
RI 9 countries
Naliendele Naliendele Research 14 institutions
ECABREN 2 networks
Tanzania Research LZARDI Station; ECABREN;
; ART
Station ART; LZARDI
West Africa
Burkina Faso INERA INERA
Cameroon IRAD IRAD
Niger INRAN INRAN
Senegal ISRA ISRA ISRA
Southern Africa
Chitedze
Chitedze Research
Malawi Research SABRN
Station; SABRN
Station
Zimbabwe

8. Other Partner Institutions
Cross species
resources for
Groundnut Cowpea Bean Chickpea
comparative
genomics
University of
University of
ICRISAT California- CIAT ICRISAT
California-Davis, USA
Riverside, USA
USDA/ Washington
Catholic University of
IITA RIKEN (Japan) State University, ICRISAT
Brasilia, Brazil
Pullman, USA
University of University of University of
University of California–
EMBRAPA, Brazil California- Davis, California- Davis, California- Davis,
Riverside, USA
USA USA USA
University of Georgia, Purdue University, University of
CIAT
USA USA Frankfurt, Germany
DArT P/L, Australia DArT P/L, Australia IITA
Instituto Agronomico
NCPGR, India
de Campinas, Brazil
IIPR, India

9. Expected Outputs TLI phase I
-Extensive evaluations of diverse germplasm
-High-throughput genotyping systems
-Trait specific genetic markers / marker–trait associations
-Development and transferring of modern breeding tools
- Building capability of NARS breeding programs

10. Achievements

11. Groundnut diversity studies
Phenotyping of reference collection
1) Diseases
•Malawi - ELS and rosette
•Tanzania - rust and rosette
•Mali and Senegal – LLS
Altogether 19 sources of disease resistance identified
2) Drought Range of variation for pod yield (India)
Highly contrasting drought -tolerant ICGVSM ICG12879
Germplasm (yield and trait based) was identified
87003
Florunner
JL24 TMV2 ICG3421
ICG3746
and knowledge that farmer-preferred varieties 900
are highly sensitive to intermittent drought 800
has been obtained
700
600
Pod yield
500
400
300
200
100
0

12. Cowpea diversity studies
 500 genotypes characterised for drought tolerance in
Senegal, Burkina Faso, Nigeria and USA.
 200 promising genotypes selected and evaluated
for grain yield and drought tolerance traits. The
same five ‘drought QTLs’ identified from
genetic analysis of RIL populations -- robust
QTL for to drought tolerance in many genetic
backgrounds
 Diversity analysis with 1536 SNP loci of breeding
lines from IITA, Cameroon, Burkina Faso and
California compared to IITA/GCP Reference
Collection -- high degree of relatedness within
breeding programmes

13. Common bean diversity studies
Population structure of 200 genotypes of CIAT core collection well understood
through molecular marker analysis (Blair et al. 2009)
 useful for comparison of drought tolerance sources within each genepool
 analyzed in Lattice design experiments with stratification by genepool origin
and drought or irrigated treatments
 phenotypic data for seed size, weight, height and length across genepools
proven useful for association analysis with markers
 sites in Ethiopia, Kenya, Malawi, Zimbabwe, Tanzania, Mozambique,
Colombia used for testing of reference collection
DJ1 DJ2 G M1 M2 NG1 NG2 P1 P2

14. Chickpea diversity studies
 Phenotyping reference collection (300 lines) – two seasons
- drought related traits e.g. root traits, HI, yield
- insect resistance in both field and lab conditions
- δ13C, SLA and SCMR
 Interspecific population (131 RILs) - insect resistance
 Two intraspecific populations
ICC 4958 x ICC 1882 -264 RILs - root traits, HI, 13-C
ICC 283 x ICC 8261- 281 RILs - root traits, HI
Natural field conditions Detached leaf assay
 The reference collection (305 lines) was
evaluated for resistance to pod borer. About
25 genotypes were identified as being less
susceptible. These lines were evaluated and
selected for multi-site testing and breeding by
National programmes.

15. Groundnut genomic resources
 About 3,200 microsatellite markers are now available (only 300 at the
beginning)
 The first cultivated groundnut map completed (RIL between TAG24 and
ICGV86031)
T04 ISC04
T05 ISC05
T08WW PodWtWW08
T08WS PodWtWW08
TE04 SeedWtWW08
TEbis04 SeedWtWS08
TE05 HaulmWtWW08
TE08WS HaulmWtWW08
TE08WW
SLAHar04
SLAPreTrt05
SLAPreTrt04
SLAHar05
SLA04
SLA05
LA04
LA05
SPADPreTrt04
SPADStresStrt04
SPAD7UndrStres04
SPAD005
SPAD505
SPAD1005
SPAD1505
Wateruse04
Initialbiomass04
Finalbiomass04
Deltabiomass04
Shootbiomass04
Delta13C04
TDM05
InitialDryWt05
DWINC05
ShootDWWW08
ShootDWWS08

16. Cowpea genomic resources
 SNP discovery in EST covering 13 cowpea accessions, several RIL
parents, African and broader germplasm accessions - 10,000 high
confidence SNPs
 Selection of 1536 SNP set (1 SNP per gene, high polymorphic information
content in African breeding lines) ->90% of 1536 markers (1375) worked
 Now exploring single-plex for customized breeding applications utilizing
these validated SNPs
 Creating a high-density consensus map Homozygotes
AA Homozygotes
BB
Ilumina BeadStudio output
for 1 SNP, 128 RIL Heterozygotes
AB

17. Seven mapping populations genotyped and used to develop ~1,000
SNP consensus map
680cM; 11 LG; 1 marker/0.7cM - Muchero et al 2009, PNAS

18. Common bean genomic resources
• SSR marker development based on multiple sources, such as small insert
genomic libraries, ESTs and BAC end sequences.
• SNP markers have been based on cDNA sequences from subtractive libraries
for drought tolerant/susceptible genotypes, candidate genes and cross-legume
sequences.
ATA – rich SSR
Source: Blair et al. (2008) Genome
Small Insert - SSR
Total : 417 SSRs discovered in 18,000 small
insert clones from 3 libraries
Source: Blair et al. (2009b) Genome
EST-SSR
Discovered through hybridization screening of
18,000 cDNA clones and sequencing of positive
hits at 5’ and 3’ ends
Source: Blair et al. (2009a) BMC Plant Bio
CEL I and 768 Illumina arrays w/ Obj 5
Source: Galeano et al. (2009) Crop Sci

19. Chickpea genomic resources- large scale markers
 1655 SSR markers were developed and 1416 of these were screened on
parental genotypes of inter- and intra-specific mapping populations
 An expanded DArT array with 15,360 clones was completed
 The first Illumina® GoldenGate Assay (768 SNPs) developed and genotyping
completed for reference mapping population (in collaboration with Obj 5)
Genotyping data for ca. 2000 marker loci compiled
on the international reference mapping population
Varshney et al. 2009; COPB