Tropical Legumes I

Tropical Legumes II Annual Meeting16–20 September 2009, Bamako, Mali

Outline• Overview of TLI phase I

o Objectives, Activitieso Partnerso Achievementso Lessons

• Transfer of TLI Outputs to TLII • Overview of TLI phase II

o Rationaleo Partnerso Links with ongoing initiatives o New Activities o Integration between phase I and phase IIo Predicted outputs for TLII in phase II

Overview of TLI phase I

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 Africa10 Million US$, 2007-2009, 1st May 2007

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

TLI Objectives

♦ 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

TLI Activities

Groundnut Cowpea Bean Chickpea Capacity Building

East AfricaEthiopia SARI EIAR EIAR

Kenya

University of

Nairobi/KARI

KARI,Egerton

University

KARI,Egerton University

TanzaniaNaliendele Research

Station

ECABREN; ART LZARDI

Naliendele Research Station; ECABREN;

ART; LZARDI

West Africa

Burkina Faso INERA INERACameroon IRAD IRAD

Niger INRAN INRANSenegal ISRA ISRA ISRA

Southern Africa

MalawiChitedze Research

StationSABRN Chitedze Research

Station; SABRN

Zimbabwe AREX AREX

National Program Partner Institutions

9 countries14 institutions 2 networks

Other Partner Institutions

Groundnut Cowpea Bean Chickpea

Cross species resources for comparative

genomics

ICRISATUniversity of

California-Riverside, USA

CIAT ICRISAT University of California-Davis, USA

Catholic University of Brasilia, Brazil IITA RIKEN (Japan)

USDA/ Washington State University, Pullman, USA

ICRISAT

EMBRAPA, BrazilUniversity of

California- Davis, USA

University of California- Davis,

USA

University of California- Davis,

USA

University of California–Riverside, USA

University of Georgia, USA

Purdue University, USA

University of Frankfurt, Germany CIAT

DArT P/L, Australia DArT P/L, Australia IITA

Instituto Agronomico de Campinas, Brazil NCPGR, India

IIPR, India

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

Achievements

Phenotyping of reference collection

1) Diseases•Malawi - ELS and rosette •Tanzania - rust and rosette•Mali and Senegal – LLSAltogether 19 sources of disease resistance identified

2) DroughtHighly contrasting drought -tolerant Germplasm (yield and trait based) was identified and knowledge that farmer-preferred varieties are highly sensitive to intermittent drought has been obtained

Groundnut diversity studies

ICGVSM 87003 Florunner

Range of variation for pod yield (India)

0

100

200

300

400

500

600

700

800

900

Po

d y

ield

JL24 TMV2ICG12879ICG3421ICG3746

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

Common bean diversity studiesPopulation 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

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-CICC 283 x ICC 8261- 281 RILs - root traits, HI

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.

Natural field conditions Detached leaf assay

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

T05

T08WW

T08WS

TE04

TEbis04

TE05

TE08WS

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

ISC04

ISC05

PodWtWW08

PodWtWW08

SeedWtWW08

SeedWtWS08

HaulmWtWW08

HaulmWtWW08

T04

T05

T08WW

T08WS

TE04

TEbis04

TE05

TE08WS

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

ISC04

ISC05

PodWtWW08

PodWtWW08

SeedWtWW08

SeedWtWS08

HaulmWtWW08

HaulmWtWW08

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

HeterozygotesAB

HomozygotesBB

HomozygotesAA

Ilumina BeadStudio output for 1 SNP, 128 RIL

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

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

Small Insert - SSR

Source: Blair et al. (2009b) Genome

Total : 417 SSRs discovered in 18,000 small insert clones from 3 libraries

EST-SSR

Source: Blair et al. (2008) Genome

Source: Blair et al. (2009a) BMC Plant Bio

Discovered through hybridization screening of 18,000 cDNA clones and sequencing of positive hits at 5’ and 3’ ends

Source: Galeano et al. (2009) Crop SciCEL I and 768 Illumina arrays w/ Obj 5

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

LG 1

CaM10300.0CaM124415.9CaM0514;CaM051551.2CaM091957.1M59_Mtmt;M93_Mtmt85.1STK42_El87.3STMS1390.2CPCB294.8M3185_Mt97.0CaM147799.8OG902578104.3cp680889;cp682003;cp490579OG903590cp677240;cp322948;cp679721

104.7

OPI63113.9TA113128.6cp490970141.3cp171266143.5cp173328144.2OG897728;OG897239149.1ACONa158.1OPG09_1168.5OPD03_3173.7ACONb177.2OPQ13_2183.5ISSR8481188.6PG7_PisG;M432_Mtm199.2ISSR8841;STK42_Eh202.7STK24_Ev205.7CAMCAT10205.9TC77488212.7OG897376;OG918864214.2cp323000;cp677227;cp677381cp491173216.3OG910457;H3H021217.1cp325818219.6cp490024;cp173046;cp350308cp491085;cp676494;cp490693OG898978

220.1

R36082y226.9C81;ICCM0245231.5cp490797;cp490675;cp350018ICCM0297OG894619;OG897323;OG903021OG899509;OG902765;cp350537

233.5

cp679622234.5cp490323234.8cp491438;cp488937234.9TC80236239.4H2A08240.1CaM0403;CaM0720;AJ005043240.6OG905379;AGL112;CaM0486241.0Gm212091;cp681088;OG897579241.4CaM1451;OG913108241.8OG901047;OG908473242.6OG900394243.9OG912303;cp490301246.0H1G16253.4TR43;TA1;TA8258.6P82_PisP260.5FP_i269.1OPC11_2285.0OPU17_3296.0R2609_2;OPC11_3;R2609_3297.2PR10_obe300.4ISSR858302.3TA203319.4ISSR888339.7TS52360.2STMS12377.1ISSR8884397.6ISSR8552428.9APF4.4439.8CAMCTA09;CAMCTA10442.7AAMCTA01444.3ACMCAC05445.5ISSR8801453.3cp679048463.6cp490477;cp678734468.9OG897499473.5OG910796;OG894192;cp171403cp350554;cp679353;cp491412477.2OG898940477.6cp679810;cp678432;cp173071OG905290479.7OG961504480.1C32482.5OPAB9_1488.4OG897333494.9OG902569495.7H1H24496.9OG902030;OG898304497.3cp678442;cp676401;OG897347cp679336;cp490906;cp350226cp350627;cp171322

497.7

cp489385497.9OG895237;OG894516498.1OG905292;cp678248;OG912880;APE4.3499.3OG948105503.1Mt106628503.3OG898883503.5ACCO506.7M107_Mtm;ISSR8842509.4GAA40512.3APF4.2513.4GAA50520.0IC_unten524.9XP_Ca_96;AAMCTA15527.6M859_Mtm528.2cp491035;cp678137;cp323728cp678822;cp678546;cp491097OG894864

535.1

OG930652535.9ICCM0289;Mt125375536.3cp325921540.6cp327812;cp327873;OG894483540.9OG895173541.3OG898575;OG902800543.8cp327943544.2cp326018544.4STMS21554.6Apero562.1APFF2.2569.0ISSR810584.0ISSR8601587.2M1118_Mt;P59_PisP589.7TA5R_TR4590.6GA11591.1OG896385597.2OG924216;OG906873;OG901542597.9OG896074;OG902716602.6cp679779;cp173541;cp323904cp324017;cp324081609.3cp325093609.8OG901896610.4OG915738;CaM0797611.6ACMCAC11613.7DMI1613.9CaM1301640.2CaM1326647.0CaM0955671.0CaM1761686.7CaM0284;CaM0686;CaM0076690.6CaM0215709.8CaM1543711.4CaM1770;CaM0870;CaM1298711.8CaM1978734.2CaM2101759.2

GA160.0P141_Pis11.5TR1936.2ISSR826261.5MSU393;AJ40464066.1AGL3OG895374;OG898285;OG89769467.4cp680621;cp68239367.9OG89406168.2OG89426268.6cp17229569.0M3223_Mt;M3188_Mt72.0OPU1875.0APAR178.3ICCM016682.7AGL179;OG924480;OG89574783.6cp489318;cp32280684.4M1023_Mt93.4OPD3_499.0ISSR8252108.3ISSR8553109.7CS27112.2Foc4;R2609_1112.9TA120R_T;APAR6;TA96;OPP06_4114.1AAMCTA12;CAMCTA07115.2M10_Mtmt116.4APFF2.4117.2Foc5;TA27118.8TA59119.3AB025002;AJ005041123.4H1H011124.7ICCM0030125.1H1P092125.2H2B061125.3H1F05;OG912685;OG901841ICCM0247;OG895601125.4AGL202;OG915900;OG923111OG918275;OG897346;AGL21;OG903853125.8CaM0233125.9CS27ASAP126.3OG896190;OG897209127.2CaM0173;ICCM0082129.1cp326233130.3cp326223;cp325101;cp325045cp325508;cp326716130.7OG899729;OG915207;cp327714cp327716;cp325794;cp325853cp325969;cp326060;OG919333;CaM0726

131.1

cp327859;cp326041131.3cp325216131.6cp325646132.0H1J07135.2H1A12135.3CaM0336138.5OG895412142.8OG924480;cp172164144.3CaM1648144.8CaM2064146.4ISSR8603156.9TS82165.4TAA60165.9TA194166.5TRb58167.0OPC14_4;R2607_2171.4M1035_Mt176.0Gluc_a_u184.9CaM1135198.8PR5201.7M251_Mtm207.0LN211216.7OPU17_1;OPQ11_1220.4OPP15_3;OPU03_1;OPN06_3221.0OPD05_1;OPP08221.9OPP15_1222.4OPM20X223.3TA37223.8ISSR8571230.3OPS02_1234.3AGL52;OG895274249.8OG903882250.6cp678796252.0cp490097;cp491092;cp490237OG896024253.9cp676706;cp680356;cp681533cp677297;cp682089;cp679116255.1DK242257.0M304_Mtm259.5M05_Mtmt;TA110262.2OPP06_3264.1AJ004960266.3RGA_DS268.9RGA_D272.3ISSR8681276.7ISSR864282.3HR_unten288.5AAMCTA10293.2AAMCTA05294.9AAMCTA03;AAMCTA04296.5AAMCTT07308.7PGI333.3M218_Mtc338.8M215_Mtc;M83_Mtmt339.5M237_Mtm341.7TC87369344.9cp489497;cp681259347.1cp489404;cp490744;cp491088cp491301;cp490226;Mt681737347.9OG961222350.8OG903783353.8OG918855355.5OPC14_1373.9APFF2.1380.7ISSR8661398.4IC_oben418.4

OPAB9_50.0CaM00859.9OG90862510.2OG897973;LG7314.5cp677013;cp489629;cp35057315.3cp488664;cp48941517.0DNABP22.4OG89424825.0PG10_Pis29.0STMS1531.1TA1433.4OPC15_453.3OPA17_260.7TR4468.1ACMCAC0171.3CAMCTA0473.5APFF2.3;OPJ13_2;CAMCAT07CAMCTA02;AAMCTA08;ACMCAC0475.5APDR2184.2OPD3_1101.7CaM1868116.5cp171521119.7H3A03;cp681792;cp490380cp678597;cp677806;cp490199cp490316;cp489132;cp171418cp681513

120.6

OG894408;OG899538;OG900871122.6OG899062;OG899640;OG902919123.8cp489518;cp322954;cp490337cp489881;cp681694;cp681488cp677717;OG894921;OG903023OG902834;OG902901;OG914910OG898034;OG903841;OG897351OG897956;OG898370;OG916065

124.6

H6G10124.8ICCM0284;CaM0620;CaM1125CaM1763;CaM0806;CaM0421125.0OG908356125.8OG914210126.6cp490788;Pc172283;OG897362cp679761127.4cp678637131.3CaM1377131.8OG907934;OG902560;OG901197132.8OG900075133.3OG901133134.1cp675974134.5OG896498;OG910601;cp680556cp679140;cp678144;cp676665cp172068;cp172153

134.9

cp679625140.7CISP5;OG913329141.4OG906936141.7CaM2168156.3CaM1084;CaM0251158.7H1L161158.9CaM1402;CaM0753;CaM0677159.0ICCM0191159.3CaM0743166.9OG899728167.8OG899657168.5OG900222;OG946804173.3OG906599;OG895029;OG922092OG896103181.0OG901904182.7OG894415;cp679880;cp682745cp350006;cp488839183.5cp682128183.6cp682478183.7OG909974184.0OG894314;OG919211;OG903717184.4CaM0063;cp490069184.6cp489647;cp678839186.0cp488971;cp679928;cp682560;cp682104188.0OG898533188.4cp679791;H3B08;H5A04190.9APE4.2;A2ga2_R6;ICCM0104192.9ACMCAC10;TS19R_TA;PR10_mit195.2APAR2195.4ICCM0242;ICCM0242199.5ISSR8402213.5XP_Ca_11;TR1222.3R2607_1;STK25_B223.9ps179_ps;OPN06_4226.1TGDH227.0TC79726230.2M86_Mtmt;ps169_ps232.9APDR23233.9TA80;TRa7;TA22;TA176235.3TA4L_TA1;TA3R_TS7236.6OPU03_5;OPD03_2;OPO04_2;OPC15_1238.6OPC20_1;OPC06_1238.9XP_Ca_42;M367_Mtm239.8TC88598239.9M51_Mtmt240.5TRAL246.0CaM0594258.5ICCM0284265.3CaM0464269.6CaM1101276.6TC78756294.8M24_Mtmt308.8cp676639;cp172996;cp680216312.2CaM0244;cp675609313.0OG894270;OG896567313.8cp173163;cp681531314.6cp324158;cp172290316.6OG896584319.0cp323841;cp680413;cp680836cp680100;OG916436330.4OG906822331.2cp172879333.2OG894755333.6cp489826;CaM1239;cp679581cp323760;cp322640338.4OG905619338.8cp325105;cp675405;cp676491OG906575;cp324065;cp490454cp680120;cp324115;cp679989cp491442;cp675253

339.2

cp325265;cp325803;cp325141cp325151339.6cp325981;cp680288;cp322687cp679505;cp679770;cp680400342.5cp325873344.9EST948345.9MTU07348.4ISSR8551362.5GA9364.6M241_Mtm372.3M19_Mtmt372.4TA106377.2AGL76381.1M361_Mtm;M320_Mtm385.5M3163_Mt386.4QOR;ps205_ps387.0GA34393.4RGA_Gv400.2STMS2411.4CAMCAG08;CAMCAG09440.6M1121_Mt455.4OPN06_5461.2M3186_Mt;M866_Mtm470.2TR3486.1OG961744494.6MSU40494.9TC88727502.3TS83;GA26508.2GA21;CaM0399;GAA41GAA39508.7OG897528512.3H1I16513.1RGA_D2r537.2

_RGA_A2.3ACMCAC082.5CaM06299.7CaM06249.8OG894002;OG89532913.5cp681290;cp17319214.3AGL7414.8OG89426515.8OG905434;cp680815;cp680932cp677464;cp350498;cp676134cp488955;cp681256;cp675751

16.3

OG89435116.7cp489460;OG894263;OG907978OG894920;Tp684972;OG895724OG908343

17.5

cp325639;cp326270;cp32646019.3cp32652819.7cp32656419.9ICCM012425.8cp491550;cp490442;cp49010134.0OG897016;OG89887239.8OG937303;OG917728;OG897513OG896613;OG908192;OG902630OG910318;OG903058

40.6

cp171270;cp490711;cp682845cp677288;cp172053;cp172088OG896253

41.8

OG894791;OG923107;cp173254cp172387;OG89897542.5P131_Pis45.4PG27_Pis48.3GA3152.0TS1959.1H1H2272.8CaM1129;CaM151580.3CaM0717;cp173050;cp172357cp490103;cp679895;cp675788cp489156;OG896348;CaM0658CaM0475

80.4

cp326014;cp325716;OG905013OG899689;OG917730;OG902906cp325884

81.2

H1H1181.8H1E2285.7H4F0991.4CaM0886101.6CaM1358117.5OG905195;OG895162126.8cp323821127.2OG897009;Gm212324127.6cp676885;OG960856;OG918946cp323880;cp324051;cp324951128.0cp677165;cp350651;cp488767cp489055;cp489840;cp489987128.8cp490507;cp677267;cp675299OG894098;Gm207793;OG903842Ms694351;cp677979

129.2

ICCM0093130.0H1F14;H2I01F;H5E02ICCM0282;CaM1354;ICCM0185ICCM0178;CaM2085;CaM1750CaM1020;CaM0600

130.4

CaM1132136.4ACMCAC12146.1AAMCTA06;AAMCTA02;AAMCTA07146.8CAMCTA01147.8STMS10153.4STMS14154.5STMS28155.1TA135155.4PG9_PisG;TR2;TR31TA34;STMS4155.6TA3R_TS7156.8TA120R_T156.9TA4L_TS1158.1STMS23;TR56158.8R3608_3161.9M3177_Mt;M01_Mtmt163.0OPO04_1163.6OPP15_2165.6APAR4;APBR;APAR5169.3CAMCAT06169.9PGMa171.5PGD6172.1C33173.5ISSR8903175.1TC88726180.0MSU380;AJ291816;TC88512180.4ICCM0159;ICCM0197182.9CaM1122;ICCM0062183.7TC84431190.0APC41203.2GA13212.8OPU03_4233.1CAMCTA08244.7MSL591;RNAH250.4AJ004917;TC76881253.5M16_Mtmt;PG6_PisG;AGT255.9OPC14_5257.3OG908776;OG910656263.8OG896261265.9OG914613266.3AGL23267.5TC78638268.9TA64273.5OG907937277.1OG903883;OG908710;OG928551Ca21249277.4cp676386;cp676452;cp682642cp679455;cp489463;cp678587OG903989

278.3

OG896159278.8OG905504;OG898599;OG933879280.3CaM1042280.7ISSR807284.1CAMCAT11284.3CaM0610287.7cp488860;OG929069;OG919458OG912320;AGL94;OG894927OG894612;cp172155;OG918895

288.2

cp677994;cp676615;cp679902cp350337;cp678699289.6cp682496;cp173150;cp173167291.4cp682494293.0P69_PisP301.1OPP06_1;OPP06_2305.7TC86212309.3ENOL310.8ICCM0045312.6OPL42;TA120R_T;APF4.3313.9CaM0799;OG901858;OG896979317.5OG898832;OG899490;OG916035Ca2009_3;cp173452318.8OG901180321.3OG903904;OG914943;OG910683OG918991;OG896448322.5TR26;STMS5328.2SAMS332.7ISSR8882354.7M213_mtc380.4CAMCAG11381.9OPD03_5383.7XP_Ca_78384.8CaM0862386.8OG897486;cp676571;cp491267cp171590;cp172237;cp681358387.3cp681608389.3OG910860390.5cp491231;cp682291;cp682299cp322975390.9OG901928393.4cp488624;cp677322;OG960456OG906875;cp488939393.8AJ012739401.6GAA45412.4M1027_Mt;M32_Mtmt416.9TA76421.1

OPD05_20.0OPO04_314.8OPA12_520.6ps163_ps41.6M209_Mtc49.7OPA12_150.3M1132_Mt;M91_Mtmt52.6CAMCAG07;CAMCAG0662.6APE4.1;CAMCAG0564.3Con_Pero;Pero66.1STMS667.5ISSR856269.5ISSR859270.6ISSR856174.7ISSR859175.0CPOX277.2OG946834;TC87800;OG902760cp67790781.3OG90537181.7OG89907282.1TC8625883.8H2E1384.2H3H12184.6M3183_Mt88.7P206_Psm;APDR22;P191_psa93.0OG914635;cp325980;cp681101cp682312;cp323423;cp48873399.7cp678635;cp679193;cp680081cp489357;cp491065102.4cp326437;ICCM0074;OG903027cp173427;cp326442104.2OPC183107.9ICCM0074110.6FIS_1;AJ276270121.9OG901547;OG905278126.7OG896873127.0ACMCAC07130.6C80133.1AJ489614134.8COAO136.0OG896040;cp491201;OG918556138.7M64_Mtmt143.5EST671143.7cp488703;cp677011147.6cp491099;cp489427;cp489903150.0cp489931150.9OG905443;OG900261152.4cp488731;cp489293;cp679199cp679688;cp491512153.2OG894196170.8cp490885;cp489326188.4OG908268188.8cp676152189.7Pyruvat_206.1CAMCTA11223.8TA4L_TA1233.3CAMCAG01;CAMCTA06241.7CAMCAT05242.7CAMCAT02243.8CAMCTA12245.4TSa62248.7TGAA44;GAA44259.6TA21278.4ICCM0034299.9TA78323.3CAMCTA03;AAMCTT04;ACMCAC06329.0OPC20_2331.0OPT18_2332.9OPA12_2;TA5L_TS7335.1MSU82339.5CaM0558341.8CaM0622;H1I18342.6cp682113;cp325968350.2ICCM0196;OG897618351.2AGL178;H1O12353.2cp173377;cp326427354.0cp327923;cp490690;cp679050cp488935;cp489344;cp679693cp489394

354.4

cp677139;cp682693;cp679896cp676498355.0OG897306356.1cp682222;cp681271;cp677961CaM0034;cp682791;cp350187cp350325;cp680065;cp677368cp675455;CaM1159;OG908917OG916106;OG927781;CaM0661cp677192

356.5

H5E11;H1C22357.3TA28363.6TAb140;TAA58;TAA59TA18365.5OPA12_3371.0CAMCAT04371.2CaM0286378.3TA180386.0CaM0598399.1OPG09_2412.3HR_Oben421.7ISSR8112439.9CaM0277479.0CaM0435492.9CaM0705495.1CaM0864511.5CaM0958524.8CaM1496535.8CaM1497;CaM1506;CaM1591544.2CaM2060563.8OPQ13_1577.5

AJ276275628.7

OPAB9_20.0PG3_PisG;OPC11_126.8Gluc_a_m29.3CAMCAT0131.2TC86606;SHMT32.5ISSR823149.2cp325702;cp327625;cp675973cp327902;cp32794770.5cp489237;cp67787872.6OG91274974.6HRIP;cp677636;cp326059PG25_Pis;OG90839675.4OG899054;OG89804675.8cp675317;cp49086777.9TC7670080.1M312_Mtm85.8PR10_unt87.4CALTL95.3OG904041;cp679047;OG898075OG894357;OG922990;OG89698197.7cp322634;cp322638;cp679524cp678616;cp67818798.1OG900259;OG916001;OG910388OG89584698.9OG896936;OG90005399.3OG90650799.7cp678950;cp682382102.6OG896495103.4OG894812;OG910203103.8OG896976;OG930121;OG910567AGL111;OG901743;OG894321OG901729

104.2

OG896911;OG896066105.3cp489600108.6OG898887;OG897003;OG910862109.0cp327870;OG901184;cp327974cp327881;cp327936;cp327868110.2M853_Mtm114.3ISSR8843127.0DSI138.1CAMCAT13140.0OPA14_1140.5TA4L_TA1143.8M570_Mtm144.1OG895877;Gm212512148.7cp676929;cp327807;OG908289OG919460;OG903969149.9cp680545;cp678117;cp678340cp675768151.5cp323461;cp327623;OG901549OG896540152.3OG900006153.1cp678768;cp677822;cp675905cp491458;cp675277;cp350553153.5cp491484;cp676464153.9cp327672;cp327869155.1ICCM0293155.8STMS11;GA24;GAA47161.1LN5A162.2REP164.5M400_Mtm;P32_PisP166.6TA4L_TA1168.2RL3;M12_Mtmt171.9OG895535;OG919735174.8Ct687595176.3LG99176.7cp490593;cp488743177.8cp678437;cp679062;OG903593178.6OG896007179.0ICCM0024181.1cp326008;cp327960181.7OG895578;OG897715;OG901985182.2ICCM0003;ICCM0004183.6OG910718;Ca128631186.9AAMCTT08191.3TA3L_TS6193.5TA130194.8ICCM0063;ICCM0249198.9cp323738;OG935579;OG922957OG899078199.7ICCM0065212.9OG922889230.9OG895956;OG906662;OG913321233.1CaM1529240.3GA2251.4M214_Mtc;M224_Mtc258.3CaM0232263.0OG896733;OG902016;OG901045tk_515;OG899516264.4OG908504;CaESTSin264.6cp677080;cp491502;cp680494cp350396;cp681085;cp490330cp488869

265.4

ICCM0127265.8CaM0480267.1cp676824;cp676868;cp678296267.5CaM0436;CaM1903;H1H13CaM0113;H1G20;H1H15CaM1666;CaM2049

268.0

CaM1637;H1B17270.9CaM0691271.9OG897326;OG900323281.3OG915802284.7CaM0446286.1CaM0909;OG903155;OG895060CaM0507287.5CaM1502287.9CaM0645288.9CaM1551290.0OG927609;Gm208481291.1OG894171291.5CaM1158291.7H1G22299.5AAMCTA13304.6ppPF306.4AAMCTT01311.9Pyruvat_314.5ACMCAC03318.5TR20;TA13321.2TA146;TA72321.7TA2323.0TS54335.9STMS26347.6ps189_ps349.5TA4R_TA1349.6TS72350.4ISSR8401350.8OPS13_2354.0OPT12_5360.3cp682025;cp490406372.1ICCM0068374.1OPD16_1378.9OPC14_2381.2ISSR8902385.0OPS13_3397.6OPT12_3408.6cp490039;OG913370;OG917721430.8OG895229431.2ICCM0212;AAMCTT03;OG897521OG903088433.7cp172089;ps190_ps;cp679174cp323966;OPC10_1;cp323611434.6CAMCAG10437.2ICCM0257;ACMCAC09439.4OG895163;OG946905;LUP51_CA441.9CYSPR2443.0OG902037444.6cp678644445.0cp172299;cp350492;cp488878cp491565;cp491143;cp489107cp489311;cp676816;cp677363

446.2

OG896166446.8STMS24455.0TA46456.9M477_Mtm;M336_Mtm465.9TC87270;CDC2467.0P124_Pis468.0ISSR842470.4M13_Mtmt471.9OG894099477.1cp675523;cp675919;cp677611cp350449477.8OG897469483.0OG899684483.8ISSR8901510.9

cp4894780.0Ca144021;OG901215;cp681450cp6819108.3OG8957609.4OPT12_116.3cp68178521.5ISSR868225.3STMS827.7AAMCTT0631.7ISSR88934.0OG894880;OG90307940.6cp675348;cp67557141.0OG90536341.4cp489370;OG916130;cp49140842.2OG91837343.4OPT12_4;OPJ13_148.6PG18_Pis51.3OG908250;M201_Mtm51.4CaM012352.6OG900269;LG103;OG89975153.1OG896702;OG904656;OG895900OG894358;Gm20919856.5cp171271;cp172050;cp17284557.3OG89496558.1cp491303;cp49152659.3OG899600;OG89605062.6P192_psa66.3P11_PisP;M71_Mtmt;R3608_168.4CaM0881;M3175_Mt;M3244_Mt70.9CAMCAT1273.8TA4L_TA179.9OG903928;OG902476;OG90098786.4CaM088098.0cp676716;cp489464;cp48906998.8cp489565;cp490810;cp490937100.0OPU17_2;Ts35;OPQ13_3113.5P110_Pis115.4CaM1778136.6OG894669163.7cp489257;cp490515;cp350038cp679231;cp491620;cp677260cp675429;OG895630

165.7

OG903813166.1OG903928167.8cp680271;cp678440;cp676553cp350039;cp172924;OG900987ICCM0205

169.0

cp680674;cp681903169.8OG898508;OG903939;cp677437170.6TC80362171.4ICCM0120;CAMCAG04175.3cp678275;cp679168;OG913047CaM0463;cp327899;cp324146177.1OG917719177.5cp682536;cp677049;cp679041cp491184178.3OG906843;cp489176;cp682538cp680662;cp677055;cp491350cp350118;OG899130

178.7

M1107_Mt;P106_1_P182.8OPAB9_3185.5DCS_6191.5CaM1939212.4CaM0416;CaM0574;CaM1809CaM0423237.4CaM0639238.4CaM1072243.7CaM1590246.5CaM0491252.3RGA_D22;RGA_D23268.9CAMCAT08271.3TA5L_TS3274.7OG918150;OG895545277.2OG895816;OG910676;OG902462OG896744;cp679202;cp488779cp350493;cp682214

277.6

cp678477;cp680535282.6ICCM0120292.9RGA_C302.1OPN06_2303.9Ps198_ps307.6CaM1536319.0cp172130;cp172152;Tp685729Mt133126334.7cp350116;cp350541335.1cp324020;cp327946;cp327739cp325842335.9GA4;M3179_Mt;OPC06_2340.0M103_Mtm;OPT12_2343.9Pyruvat_345.3M116_Mtm347.0ps175_ps347.1cp677807348.7OG925843;OG927739348.9OG915805;TCMO349.1cp491008;cp489932;cp490282cp171274;cp680370;cp172962OG896285;cp676692

349.5

OG896967;cp682554;cp490678350.3OG900450;OG894267350.7CaM0258357.4STMS17363.9M1026_Mt365.6TA5366.3TS43;STMS19367.6P93_PisP370.3M50_Mtmt;BTF3b371.6H2B202373.0CaM0698379.6H2B18383.2H2L102;H2J09;CaM1545H1H07;H1O01;OG915278OG897350;OG895358;OG915293OG936005;OG896202;OG895876CaM0805;OG900217;CaM1218

391.7

H4H11;CaM0740;CaM1228ICCM0123392.1cp327747392.5ICCM0134394.0TRPT396.0RGA_B;OPP07_1;STK86_DRGA_D2a399.6TS53;TA179;TR59401.1STMS7;TA71402.0TAASH403.6TA39404.6TA5L_TS1406.9TR29412.0GAA42417.7CaM1782437.1M932_Mtm448.3ICCM0076452.2OG903808;OG912629;OG895467OG903716;ICCM0081452.3ICCM0079;cp323897;cp323608cp679996;cp678399;cp327849452.7cp172370;H4F07;OG894043OG904027;OG907169454.8cp350631;cp491000456.0cp490581;cp490006;cp172234cp488709458.4cp682445458.6cp676840458.7CaM1036;cp489634;OG902902OG907096;OG894007;OG897198cp679277;cp678520

459.5

CaM0836468.1CaM0368;CaM1016491.2TA66R_TS516.6OPG09_4521.5OPB08_1525.3TA5L_TS3525.9OPB08_2526.8ACMCAC02;CAMCTA05532.6AAMCTA09534.3CAMCAT09;CAMCAT03535.8ISSR843539.4CaM1238563.3CaM1098568.2CaM1722569.6CaM1360571.3CaM0358579.3CaM0038586.7CaM1068591.3CaM0073609.6CaM0848611.8OPE32624.4OPAC43642.8CaM1417;CaM0111655.6H1N12;CaM1469664.6STMS25665.1TA196668.8TA125688.8OG896348712.5CaM0790739.2CaM0260740.5CaM1079743.4CaM2045750.4CaM0751754.4CaM0466;CaM1007;CaM1542CaM1668;CaM1149;CaM2155CaM1714

754.9

CaM1581;CaM1337;CaM0519CaM0632755.0CaM0656769.2CaM1658;CaM0340;CaM1975781.7CaM2162782.4CaM0443783.1CaM0795784.0CaM0599;CaM0345784.5CaM1827792.3CaM2186797.4CaM1620809.2CaM0025835.4CaM0578858.0CaM0997872.7CaM1207;CaM2016;CaM1493873.7CaM0050881.6CaM1607921.7CaM1679959.9CaM2080;CaM0317;CaM1961CaM1953;CaM1693;CaM1166CaM1247

962.6

CaM1257963.4CaM1783969.1M578_Mtm1012.6M1433P1015.4OG897369;OG8978841020.7AF4575901024.0MSU831027.6STMS221029.2STMS201041.9AIGP1045.9

OPG09_50.0M992_Mtm;MA225_Mt;CYSS13.2XP_Ca_2913.7AAMCTT0216.1CYSK16.2MSU8918.1S1E125.3CStC127.3GAA4630.8CAMCAG0334.8ICCM007238.6cp68075640.0OG90206340.8OG91958441.2cp680255;cp677086;cp49046342.2OG895142;OG92440544.8cp678287;cp678922;cp682300cp172945;cp681747;cp67735450.6OG91965551.0OG904000;OG89807851.4ICCM0130;cp679509;cp680549cp171561;cp172966;cp677302cp676753

54.4

Ca22434;OG89761955.6OG90696956.0OG90389858.1cp489035;cp173466;cp48922259.3cp68164959.5cp68192059.7CaM078762.6OG89823164.0Ts4567.4X60755;U7168.7FENR70.0G6PD73.9ACONc74.0PGMb80.3OG895690;OPQ11_290.3OG896172;OG89587194.9M599_Mtm98.0TA3R_TA2100.3AAMCTA11104.8AAMCTA14119.8TA3127.3M121_Mtm142.8OG901744;OG901711148.1Ca21567;cp350602153.8OG898271;OG919502157.1H1D24;H1C092;CaM0539H5B04;OG902768159.5APF4.1167.9TS12178.6CaM2036203.5

Total marker loci - 1821Inter-marker distance- 2.48cM

LG 4LG 3LG 5

LG 2

LG 6 LG 7

LG 8

Chickpea genomic tools - high density genetic maps

Nayak et al. 2009

34 sequence-confirmed candidate disease resistance genes and five QTLs mapped on the reference AA-genome pop. Other candidate resistance genes (LLS, rust, rosette) mapped

59 minor QTLs (5–15 % phenotypic variation) identified in three pops for drought-related traits

Groundnut marker discovery and validation

Genomic regions likely to be involved in leaf spot resistance indicated

Leal-Bertioli et al. BMC Plant Biology in press

Cowpea marker discovery and validation

Two RIL sets phenotyped for resistance to Fusarium wilt. A major gene for resistance to race 3 of Fusarium mapped and confirmed by analysis of closely related cultivars contrasting for the resistance

Similar QTL for resistance to root-knot nematodes and resistance to M.phaseolina identified from RIL phenotyping and isoline analysis

QTL for drought and flower thrips currently being validated

Common bean marker discovery and validation

Over 300 F1-derived families with at least one gene for resistance to bruchids (arcelin), common bacterial blight (CBB), or bean common mosaic necrosis viruses (BCMNV) were developed and screened with markers. Genetic crosses made with commercial seed types and drought-tolerant genotypes. 69 families advanced in Malawi

Based on trials for the DOR364 x BAT477 (DxB) population, a total of 24 yield QTL were identified in drought treatment and 11 under irrigation. Significant differences were also found in the BAT881 x G21212 (BxG) population

7B7F

10Q

7E

BMd10

ATA3

15F

FInBM201BM53BM2006L2B9J3D1H14N13S10B7D13N14C4E14Q6I10J13L7S1G14U

agb01107.3 cM

Df1

.1D

f1.2

,3

Ph1.

1, L

dg1.

2

Dm

1.2,

D

m1.

1,3

Spo1 .1

Ldg

1.1,

Ph

1.2Yl

dp1.

1

7B7F

10Q

7E

BMd10

ATA3

15F

FInBM201BM53BM2006L2B9J3D1H14N13S10B7D13N14C4E14Q6I10J13L7S1G14U

agb01107.3 cM

Df1

.1D

f1.2

,3

Ph1.

1, L

dg1.

2

Dm

1.2,

D

m1.

1,3

Spo1 .1

Ldg

1.1,

Ph

1.2Yl

dp1.

1

BM161

14G4G11C11H6D

BM68

BM171BM199ATA5BM140ATA2BMd27ATA2010O11V10H4N10S10E7N10N12F12M15G15M14K7K11IBM149BM195RBCS4Q9C1C2C13B4L4J14B15E6F13A4K

agb04117.3 cM

Pp4.

1,2,

Sep

4.1

Yld4

.1

BM161

14G4G11C11H6D

BM68

BM171BM199ATA5BM140ATA2BMd27ATA2010O11V10H4N10S10E7N10N12F12M15G15M14K7K11IBM149BM195RBCS4Q9C1C2C13B4L4J14B15E6F13A4K

agb04117.3 cM

Pp4.

1,2,

Sep

4.1

Yld4

.1

BM68

BM171BM199ATA5BM140ATA2BMd27ATA2010O11V10H4N10S10E7N10N12F12M15G15M14K7K11IBM149BM195RBCS4Q9C1C2C13B4L4J14B15E6F13A4K

agb04117.3 cM

Pp4.

1,2,

Sep

4.1

Yld4

.1

Chickpea marker discovery and validation

A genetic map (220 SSR loci) was built for ICC 4958 × ICC 1882. Phenotypic data for root traits and carbon isotope discrimination (CID) were collected. One ‘hotspot’ harboring several QTL for root-related (30 % phenotypic variation) and for CID (60 % phenotypic variation), and about four other minor effect QTL were identified

Analysis of insect resistance data together with genetic mapping data for 128 lines of the interspecific population ICC 4958 × PI 489777 provided two putative QTL contributing about 10 % phenotypic variation

Groundnut pre-breeding 28 populations made between adapted parents and disease resistance sources,

and 19 F2 populations phenotyped. All advanced to BC1F1, and 12 evaluated for resistance to rosette, eight to ELS and eight to rust.

Three RIL populations per disease advanced to RIL for QTL mapping in multi-location trials

Phenotyping for Rosette at ICRISAT Malawi7 rosette segregating F2:3 populations involving 3 adapted vars (CG7, JL 24, Chalimbana, ICGV-SM 87003 with the GRV Res lines ICGV-SM 90704 and ICGV-SM 94584)

6 ELS segregating F2:3 populations involving 3 adapted vars (JL24, ICG 12991 and ICGV 93437 with the ELS Res lines ICGV-SM 93555 and ICGV-SM 95714).

6 rust segregating F2:3 populations involving 3 adapted vars (JL24, ICG 12991 and ICGV 93437 with the Rust Res lines ICGV 94114 and ICGV 95342).

Cowpea pre-breeding

Breeding populations with thrips resistance and drought tolerance developed

15 elite × elite crosses for future MARS breeding advanced by two generations. The parents were all genotyped, allowing determination of the number of polymorphic markers segregating in a particular population. Two of these MARS populations advanced to the F4 generation

Common bean pre-breeding

SEA5 = cream coloredSEA15 = medium red seeded

CAL96 = K132 (Ugandan release, high marketability)CAL143 = Napilira (Malawi release, low P tolerant)BRB191 = BCMNV resistance source

• Development of Advanced Backcross populations across genepool boundariesSER16 = small red drought tolerance sourcesSER48 = medium red

• New good x good recombinant inbred line populations made for both mapping and crop improvement (marker assisted recurrent selection) • Emphasize less well-studied drought tolerance sources such as Durango-derived breeding lines crossed with commercial varieties

Chickpea pre-breeding

Three cultivars were selected for introgression of drought avoidance root traits through marker-assisted backcrossing: ICCV 92318, ICCV 92311, and ICCV 93954. Crosses were made with the donor parent (ICC 4958)

The second cycle of MABC was completed for introgressing QTL for root traits in one desi (ICCV 93954; donor parent ICC 4958) and two kabulicultivars (ICCV 92318 and ICCV 92311; donor parent ICC 8261)

To accumulate alleles for drought tolerance, MARS activities were initiated by making three crosses, one each for Kenya, IIPR- India and ICRISAT. These activities will be continued

Donors

Cultivars

Cross-species resources – Obj 5

Cross species genetic markers Species-specific genetic maps were developed for chickpea, cowpea, common

bean and diploid peanut The genetic maps are based on discovery of SNP in a set of 1,369 genes that are

conserved across crop legume species Orthologous markers connect the four legumes species to a network of legume

genome synteny (including soybean, pigeonpea). This network is composed of 876 orthologous genes. It allows researchers to infer the position of the majority of genes in these crop legumes

Arachis duranensis BAC library characterization

More than 4,000 SSRs identified. PCR primers designed for a subset of 1,535 SSRs, including 142 resistance-gene-associated SSRs

Ultra-long SSRs mined from SSR-enriched libraries in cultivated groundnut, resulting in 147 candidate SSRs, of which 83 were polymorphic. These markers increased the number of SSRs available for cultivated groundnut by about 25%

Cross-species resources – Obj 5

Building Capacity and Training

Phenotyping for drought-related traits across tropical legumes: concepts and practices (3–28 March 2008, ICRISAT, India). Twenty-four participants (TLI+TLII)

Phenotypic and genotypic data analysis (29 June–3 July 2009, Zaragoza, Spain). Seventeen researchers participated (TLI+TLII)

Infrastructure was secured for all African partner institutes. Phenotyping and informatics equipment were prioritised. E.g. Laser printers, portable rain out-shelters, portable weather stations,

renovation of lab space, photocopiers, screen houses for diseases, scanners, electronic balances, soil moisture sensos, desktop computers, freezers, seed storage containers, repairing irrigation systems and more (Table 1 in Ann 1)

One GCP grant per crop for training in phenotyping and molecular breeding of African partners

Lessons learned

IPR issues Subcontracts between PI institutions and NARS Insufficient seed available at the start of the project

Low multiplication rate of legumes Connectivity of some partners Transfer of materials, procurement of equipment, acquisition of

import permits, and obtaining custom clearance

Different phenotyping protocols Genotype by environment interactions Multi-location testing

Transferable outputs of TLI toTLII

Groundnut phase I

Nine sources of highly contrasting disease resistance (2–4 units better than FPV, on a scale of 1 to 9) used in the development of populations

Highly contrasting drought-tolerant germplasm identified

ICGVSM 87003, JL24, TMV2 are highly sensitive to intermittent drought

Methods to screen for drought tolerance (controlled intermittent stress in the field and lysimetric system) that allows trait and yield assessment simultaneously

The first SSR-based genetic linkage map for cultivated groundnut

A number of BC lines in FMPV background using those sources of disease resistance that were available at the beginning of the project, ready for testing in PVS trials

At least three RIL populations for each disease (ELS, LLS, rust, GRV) that will provide QTL for the targeted disease resistance

One technician and one scientist in each of the national programmes of Tanzania, Malawi, and Senegal trained to employ phenotyping methods

Germplasm and genomic resources in support of applied breeding Eight sources of drought tolerance and two sources of resistance to ashy stem blight (caused by

Macrophomina phaseolina), eg, IT93K-503-1.

Genetic fingerprints (1350 loci) of 640 germplasm accessions, including 50 TLII varieties (promising varieties or parents). Marker polymorphisms between any two potential parental pairs known

Consensus genetic map with ~1,000 markers -- new trait-marker associations and a ‘backbone’ for MABC

Trait-linked QTL and molecular markers for marker-assisted breeding Agarose gel-based markers (from SNPs) for resistance to Cowpea Aphid-borne Mosaic, Cowpea

Mosaic Virus, Striga and several drought tolerance traits.

Five major SNP-based QTL for components of drought tolerance.

SNPs converted for use in single-plex genotyping platforms for biotic stress resistance (Macrophomina, foliage and flower thrips, root knot nematode, Fusarium wilt, cowpea aphid borne mosaic virus, cowpea mosaic virus, Striga) and agronomic traits (seed weight, flowering time)

Cowpea phase I

Reference collection (212 genotypes) distributed to shared sites between TLI and TLII and additional TLII sites in Ethiopia, Kenya, Malawi, Tanzania and Zimbabwe for parental identification and drought breeding

Regional collection varieties (208) disseminated among TLII partner countries including Ethiopia, Kenya, Malawi, Tanzania and Zimbabwe.

Markers and marker-assisted development of advanced lines for bruchid resistance distributed to TLII partner in Ethiopia (EIAR)

Additional MAS-based, BCMV and bruchid-resistant selections in the F3:5 generation available

Marker-assisted selections for CBB resistance and advanced lines or segregating populations distributed to TLII partners in Malawi (DARS and SABRN).

Drought tolerance QTL-containing lines available for testing and farmer preference studies with initial evaluations in Ethiopia, Kenya and Malawi

Common bean phase I

Common bean phase I Advanced lines from inter-genepool crosses of the Drought Andean Bean (DAB) and Crop

Breeding Institute Bean (CBIB) series for drought tolerance distributed for testing in Malawi and Zimbabwe

Advanced lines and segregating populations for drought tolerance combining the advanced lines from the DAB and SAB (Drought Andean Bean lines) series distributed in Malawi and prepared for distribution to ECABREN and SABRN networks. Early cycle recurrent selection populations also distributed to TLII.

Training of TLII students from Kenya (Felix Waweru), Malawi (Lizzie Kalolokesya) and Zimbabwe (Godwill Makunde) in data analysis, marker-assisted selection and drought phenotyping.

Already transferred 48 chickpea lines (including 14 elite genotypes from Ethiopia) fingerprinted Validation of root trait-associated markers on 14 elite genotypes of Ethiopia, 10 genotypes

of Kenya and 10 genotypes of India, all popular lines in these countries and used in farmer participatory evaluation in TLII

MABC for root traits initiated in elite chickpea varieties (JG 11, Chefe, KAK 2) used and recommended by TLII

MARS for enriching drought-tolerant alleles initiated using the genotypes recommended by the TLII

Scientists from Ethiopia (Million Eshete), Tanzania (Robert Kileo) and India (SK Chaturvedi and Aditya Garg) involved in TLII activities and trained in drought phenotyping and modern breeding.

MSc student (Tadesse Sefera Gela) from Ethiopia trained in molecular genomics and diversity analysis

Chickpea phase I

Ready for transfer by the end of phase I

Based on phenotyping, promising genotypes have been identified and can be used by TLII

Drought

India: ICC 7272, ICCV 92311, ICCV 10 and ICC 14595; ICCRIL03-0168, ICCRIL03-0041, ICC 708 and ICC 1882.

Kenya: ICC 8200, ICC 1510, ICC 15248, ICC 3325 and ICC 10393; ICC 1052, ICC 4958, ICC 15333, ICCRIL04-0239 and ICCRIL03-0135.

Ethiopia: ICC 11198, ICC 4495, ICC 7668, ICC 4918 and ICC 3325; ICC 4958, ICC 14435, ICC 14199, ICCRIL03-041 and ICCRIL04-0189

Pod borer

Kenya: EC 583250, EC 583264, EC 583311, ICC 144402 and ICC 16903 India: ICC 10393, ICC 1356, ICC 506, ICC 14402 and ICCV 10

Molecular markers associated with root trait QTL contributing up to 30 % phenotypic variation

Early generation MABC products ready for drought tolerance evaluation in Ethiopia, Kenya and India.

Large-scale SSRs (1655), DArT (15,360 features) and Illumina® GoldenGate Assay-based SNP (768 SNPs) genotyping platform.

Reference genetic map with > 1500 marker loci

Chickpea phase I

Overview of TLI phase II

Rationale

TLI phase II will emphasize the use and application of outputs obtained during phase I

Great advances made in development of genomic resources, so that their availability is not limiting for modern breeding

High-quality phenotyping still limiting for accurate marker-trait associations

A leap jump to apply molecular breeding in the four legumes

a new breeding paradigm using genomics-based resources = valuable experiences and lessons

Molecular breeding approaches MAS/MABC: based on pre-mapped single-locus traits

First used for qualitative traits Attempts under way to include oligo-QTL with large effects in the hope that they will apply across

a large range of genotypes and environments

MARS: recombination of favorable alleles to develop optimum genotypes for final testing Differs from traditional QTL or MAS studies in that de novo mapping is done on each breeding

population

Once the main QTL of interest are identified, they get recombined via several crossing cycles to develop lines with an optimum complement of QTL from both parents

At the end of the recombination process, genotypic instead of phenotypic data are used to select progenies to advance for final testing

No more characterization of contrasting germplasm (including reference sets, with exception of chickpea)

Elite lines identified will be used as parents to develop new populations Little extra development of genomic resources: cowpea, common bean, chickpea Markers for biotic stresses identified in phase I will be validated through

introgression into popular local germplasm Improved phenotypic screening methods will be applied in the MARS experiments

Characteristics of drought QTL (reduced genetic effects, large GxE, instability across backgrounds) support this move

Strong data management component will be included Human resource development embedded in the crop-objectives to strength the link

between learning and research. More resources allocated to improve NARS infrastructure

Evolution TLI phase I to phase II

Links with ongoing initiatives

The GCP Challenge Initiatives The Molecular Breeding Platform project Outside GCP the sequencing initiative for bean the sequencing initiative for cowpea

Cereals:1) Improving drought tolerance in rice for Africa2) Improving drought tolerance in sorghum for Africa3) improving drought tolerance in wheat for Asia

Legumes:4) Improving drought tolerance in chickpeas for Africa and Asia5) Improving drought tolerance in cowpeas for Africa

Root and tubers:6) Improving cassava yield in Africa's drought-prone environments

Comparative Genomics:7) Comparative genomics to improve cereal yields in high-aluminum and low-phosphorous soils

The 7 Challenge InitiativesFollowing an External Programme and Management Review (EPMR) in late 2007, GCP now focuses on seven trait–crop combinations, which concentrate half of resources available in GCP phase II

Molecular Breeding PlatformA project to develop and deploy a one-stop-shop functional and sustainable molecular breeding platform providing access to molecular breeding services, an information system and a toolbox of analysis and decision support applications

Breeding Inform

ation systemHigh densitygenotypingPhenotypic

characterizationA&DS

Choose parental material based on haplotype values, known genes, traits and adaptation

STLIMS

FDM

MSL

TSL

High densitygenotypingPhenotypicevaluation

STLIMS

FDM

MSL

TSL

A&DSDevelop crossing scheme based on genotype and phenotype compatibility

PIMPedigree information updated

Selection of lines based on QTL analysis / estimation of marker breeding valuesA&DS

Markergenotyping

PIM

ST LIMS MSL

Pedigree information updated

Selection of improved lines based on trait improvement and adaptation

PIM

A&DSPedigree information updated

Multi-locationtesting

A&DS Selection on index of marker values

ST FDM TSL

Public C

rop Information

GeneticResources

Improved Lines

Parental Material

Crossing Block

Nursery 1

Nursery 2

Evaluation TrialsGRSS

Cultivars& Breeding

Lines

GRSS

n cycles of selection and recombination

Interaction of breeding workflow and platform elements

GRSS

MSL

TSL

KeyInformation System

ST

LIMS

FDM

A&DS

PIM

SampleTracking

Pedigree Information

Laboratory Information

Field Data

Analysis & Decision Support

GeneticResourceService

Marker Service

TraitService

Platform Services

Genotyping services

Rationale: Many MAB projects rely on low throughput marker operations that cannot easily

accommodate growing applied MAB needs Use of many SNP markers requires labs with high tech equipment (robotics,

automated SNP platforms, LIMS) Large private breeding companies contract genotyping in specialized labs

Allows the breeders to focus on the use of the genotyping data rather than the generation of those data

Focus of academic SNP labs on high-density platforms (Illumina, etc.) is well suited to genomics studies but not to applied MAB projects

Specialized contract labs exist with extensive SNP genotyping experience and low costs (large-scale human, animal and plant projects)

Genotyping services to support MAB projects

Full-service lab from DNA extraction to genotypic scores Ability to accept dried leaf samples from all around the world

Flexible SNP platform (many markers on few samples to few markers on many samples)

Specialized contract labs for SNPs SSRs can still be done locally or in lower-throughput applications

High-throughput operation with robotics and LIMS Automated or at least high-throughput DNA extraction Automated scoring with high-quality scores Quick response time when needed (2-3 weeks for MABC and recurrent

selection projects) Validated QA/QC system in place Cost competitive

Objectives of TLI phase II

Validation of molecular markers and testing of molecular breeding approaches in drought-prone environments for traits important to sub-Saharan African farmers

Precision phenotyping to guarantee accurate marker-trait associations and to refine selection indices used by breeders

Data integration of all data-producing research activities in TLI, phase I and II, to ensure availability of high-quality, curated and publicly available data

Building capacity of African breeding programme partners, helping to institutionalise and expand modern breeding efforts in legumes

Activities Groundnut will increase the number of genomic resources and it will produce the first

molecular breeding products by introgressing rust and/or rosette disease resistance QTL identified in phase I in farmer-market preferred varieties of partner countries. A solid basis established towards molecular breeding for drought tolerance.

Cowpea will advance modern breeding by applying tools and knowledge for the optimization of MARS and MABC, developing lines and varieties with drought tolerance and biotic stress resistances identified from the analysis of elite x elite breeding populations

Common bean will deploy drought tolerance for Eastern and Southern Africa through AB-QTL and MARS. It will incorporate insect and disease resistances for dry land environments into the drought tolerant lines

Chickpea will develop drought tolerance varieties and pre-breeding lines with enhanced resistance to pod borer. While doing so, it will broaden the genetic base, and it will increase the available genomic resources to better enable MABC and MARS activities

Cross-cutting issues

Capacity building will enhance human resource capacity of sub-Saharan African scientists and it will improve infrastructure

Increased chances of adoption and pioneering NARS partners engagement in modern breeding

Combined endeavor with building capacity for drought tolerance breeding through the detailed study of cross-legume phenotyping and on data management by cataloguing all data generated in the project, including genomic data from Objective 5 in phase I

CowpeaGroundnut

Common bean Chickpea

Groundnut Cowpea Bean Chickpea Capacity Building

East Africa

Ethiopia SARI EIAR SARI; EIAR

Kenya University of Nairobi

Egerton University

University of Nairobi,Egerton University

Tanzania Naliendele Research Station ECABREN Naliendele Research

Station; ECABREN

West Africa

Burkina Faso INERA INERA

Senegal ISRA ISRA ISRA

Southern Africa

MalawiChitedze

Research Station, DARS

SABRN; DARS Chitedze Research Station; SABRN; DARS

MozambiqueUniversidade

Eduardo Mondlane

Universidade Eduardo Mondlane

Zimbabwe DR&SS DR&SS

National Program Partner Institutions

Groundnut Cowpea Bean Chickpea

Integration across crops: drought phenotyping, data and project management

(Obj. 5)

ICRISATUniversity of California–

Riverside, USACIAT ICRISAT

CIRAD, France IITACornell

University, USA

University of California, Davis,

USA

North Carolina State University, USA

University of Georgia, USA Riken, Japan NCGR, USA CIAT

Catholic University of Brasilia, Brazil

North Dakota State

University, USA

IIPR, India ICRISAT

EMBRAPA, Brazil IITA

West Africa Centre for Crop Improvement, Ghana

Other Partner Institutions

V. Vadez (ICRISAT, PI - Groundnut)J. Ehlers (UC-R, PI - Cowpea )M. Blair (CIAT, PI - Common bean)R. Varshney (ICRISAT, PI - Chickpea)D. Cook (UC-D, PI –Comparative genomics )C. de Vicente (GCP, TL1 Project Manager)

Thank you!