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2 Carmendevicente Tli

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    2 Carmendevicente Tli 2 Carmendevicente Tli Presentation Transcript

    • Tropical Legumes I Tropical Legumes II Annual Meeting 16–20 September 2009, Bamako, Mali
    • 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
    • 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 Africa 10 Million US$, 2007-2009, 1st May 2007
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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 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
    • 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.
    • 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
    • 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
    • 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 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
    • 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
    • Chickpea genomic tools - high density genetic maps Total marker loci - 1821 0.0 cp489478 Ca144021;OG901215;cp681450 8.3 cp681910 9.4 OG895760 16.3 OPT12_1 21.5 cp681785 25.3 ISSR8682 0.0 OPAB9_5 27.7 STMS8 9.9 CaM0085 0.0 OPAB9_2 31.7 AAMCTT06 0.0 CaM1030 0.0 OPD05_2 34.0 ISSR889 10.2 OG908625 26.8 PG3_PisG;OPC11_1 15.9 CaM1244 40.6 OG894880;OG903079 OPO04_3 Inter-marker distance- 2.48cM 51.2 CaM0514;CaM0515 14.5 OG897973;LG73 _ 14.8 29.3 Gluc_a_m 41.0 cp675348;cp675571 OPA12_5 31.2 CAMCAT01 57.1 CaM0919 15.3 cp677013;cp489629;cp350573 2.3 RGA_A 20.6 32.5 TC86606;SHMT 41.4 42.2 OG905363 cp489370;OG916130;cp491408 85.1 M59_Mtmt;M93_Mtmt 17.0 cp488664;cp489415 2.5 ACMCAC08 41.6 ps163_ps 49.2 ISSR8231 43.4 OG918373 87.3 STK42_El 22.4 DNABP 9.7 CaM0629 M209_Mtc 48.6 OPT12_4;OPJ13_1 CaM0624 49.7 70.5 cp325702;cp327625;cp675973 51.3 PG18_Pis 90.2 STMS13 25.0 OG894248 9.8 cp327902;cp327947 94.8 CPCB2 13.5 OG894002;OG895329 50.3 OPA12_1 51.4 OG908250;M201_Mtm 29.0 PG10_Pis 72.6 cp489237;cp677878 52.6 CaM0123 97.0 M3185_Mt 31.1 STMS15 14.3 cp681290;cp173192 52.6 M1132_Mt;M91_Mtmt 74.6 OG912749 53.1 OG900269;LG103;OG899751 99.8 CaM1477 14.8 AGL74 62.6 CAMCAG07;CAMCAG06 HRIP;cp677636;cp326059 OG896702;OG904656;OG895900 33.4 TA14 OG894265 75.4 56.5 OG894358;Gm209198 104.3 OG902578 15.8 APE4.1;CAMCAG05 PG25_Pis;OG908396 53.3 OPC15_4 OG905434;cp680815;cp680932 64.3 OG899054;OG898046 57.3 cp171271;cp172050;cp172845 cp680889;cp682003;cp490579 75.8 58.1 OG894965 104.7 OG903590 0.0 GA16 60.7 OPA17_2 16.3 cp677464;cp350498;cp676134 66.1 Con_Pero;Pero 77.9 cp675317;cp490867 59.3 cp491303;cp491526 cp677240;cp322948;cp679721 11.5 P141_Pis 68.1 TR44 cp488955;cp681256;cp675751 67.5 STMS6 80.1 TC76700 62.6 OG899600;OG896050 ACMCAC01 66.3 P192_psa 113.9 OPI63 36.2 TR19 71.3 16.7 OG894351 69.5 ISSR8562 85.8 M312_Mtm 68.4 P11_PisP;M71_Mtmt;R3608_1 128.6 TA113 61.5 ISSR8262 73.5 CAMCTA04 cp489460;OG894263;OG907978 87.4 PR10_unt 70.9 CaM0881;M3175_Mt;M3244_Mt 17.5 OG894920;Tp684972;OG895724 70.6 ISSR8592 95.3 CALTL 141.3 cp490970 66.1 MSU393;AJ404640 APFF2.3;OPJ13_2;CAMCAT07 73.8 CAMCAT12 143.5 cp171266 AGL3 75.5 CAMCTA02;AAMCTA08;ACMCAC04 OG908343 74.7 ISSR8561 97.7 OG904041;cp679047;OG898075 79.9 TA4L_TA1 67.4 OG894357;OG922990;OG896981 86.4 OG903928;OG902476;OG900987 144.2 cp173328 OG895374;OG898285;OG897694 84.2 APDR21 19.3 cp325639;cp326270;cp326460 75.0 ISSR8591 98.0 CaM0880 19.7 cp326528 cp322634;cp322638;cp679524 149.1 OG897728;OG897239 67.9 cp680621;cp682393 101.7 OPD3_1 77.2 CPOX2 98.1 98.8 cp676716;cp489464;cp489069 cp678616;cp678187 158.1 ACONa 68.2 OG894061 116.5 CaM1868 19.9 cp326564 OG946834;TC87800;OG902760 98.9 OG900259;OG916001;OG910388 100.0 cp489565;cp490810;cp490937 OPU17_2;Ts35;OPQ13_3 0.0 OPG09_5 ICCM0124 113.5 168.5 OPG09_1 68.6 OG894262 25.8 81.3 OG895846 P110_Pis 13.2 M992_Mtm;MA225_Mt;CYSS OPD03_3 119.7 cp171521 34.0 cp491550;cp490442;cp490101 cp677907 115.4 173.7 69.0 cp172295 99.3 OG896936;OG900053 136.6 CaM1778 13.7 XP_Ca_29 177.2 ACONb H3A03;cp681792;cp490380 39.8 OG897016;OG898872 81.7 OG905371 163.7 OG894669 72.0 M3223_Mt;M3188_Mt 99.7 OG906507 16.1 AAMCTT02 183.5 OPQ13_2 cp678597;cp677806;cp490199 OG937303;OG917728;OG897513 cp489257;cp490515;cp350038 75.0 OPU18 120.6 82.1 OG899072 102.6 cp678950;cp682382 165.7 cp679231;cp491620;cp677260 188.6 ISSR8481 cp490316;cp489132;cp171418 40.6 OG896613;OG908192;OG902630 103.4 OG896495 cp675429;OG895630 16.2 CYSK PG7_PisG;M432_Mtm 78.3 APAR1 cp681513 OG910318;OG903058 83.8 TC86258 MSU89 199.2 ICCM0166 103.8 OG894812;OG910203 166.1 OG903813 18.1 202.7 ISSR8841;STK42_Eh 82.7 122.6 OG894408;OG899538;OG900871 cp171270;cp490711;cp682845 84.2 H2E13 OG896976;OG930121;OG910567 167.8 OG903928 25.3 S1E1 205.7 STK24_Ev 83.6 AGL179;OG924480;OG895747 OG899062;OG899640;OG902919 41.8 cp677288;cp172053;cp172088 84.6 H3H121 104.2 AGL111;OG901743;OG894321 169.0 cp680271;cp678440;cp676553 123.8 cp350039;cp172924;OG900987 27.3 CStC1 205.9 CAMCAT10 84.4 cp489318;cp322806 OG896253 OG901729 93.4 M1023_Mt cp489518;cp322954;cp490337 OG894791;OG923107;cp173254 88.7 M3183_Mt ICCM0205 30.8 GAA46 212.7 TC77488 cp489881;cp681694;cp681488 105.3 OG896911;OG896066 169.8 cp680674;cp681903 42.5 93.0 P206_Psm;APDR22;P191_psa 108.6 170.6 OG898508;OG903939;cp677437 214.2 OG897376;OG918864 99.0 OPD3_4 cp677717;OG894921;OG903023 cp172387;OG898975 cp489600 171.4 TC80362 34.8 CAMCAG03 cp323000;cp677227;cp677381 108.3 ISSR8252 124.6 45.4 P131_Pis OG914635;cp325980;cp681101 109.0 OG898887;OG897003;OG910862 175.3 ICCM0120;CAMCAG04 38.6 ICCM0072 216.3 cp491173 109.7 ISSR8553 OG902834;OG902901;OG914910 48.3 PG27_Pis 99.7 cp682312;cp323423;cp488733 110.2 cp327870;OG901184;cp327974 cp678275;cp679168;OG913047 OG898034;OG903841;OG897351 52.0 GA31 cp327881;cp327936;cp327868 177.1 CaM0463;cp327899;cp324146 40.0 cp680756 217.1 OG910457;H3H021 112.2 CS27 cp678635;cp679193;cp680081 114.3 219.6 cp325818 112.9 Foc4;R2609_1 OG897956;OG898370;OG916065 59.1 TS19 102.4 M853_Mtm 177.5 OG917719 40.8 OG902063 cp489357;cp491065 127.0 ISSR8843 cp682536;cp677049;cp679041 cp490024;cp173046;cp350308 114.1 TA120R_T;APAR6;TA96;OPP06_4 124.8 H6G10 72.8 H1H22 178.3 cp491184 41.2 OG919584 ICCM0284;CaM0620;CaM1125 80.3 CaM1129;CaM1515 cp326437;ICCM0074;OG903027 138.1 DSI 220.1 cp491085;cp676494;cp490693 115.2 AAMCTA12;CAMCTA07 125.0 104.2 140.0 CAMCAT13 OG906843;cp489176;cp682538 42.2 cp680255;cp677086;cp490463 OG898978 CaM0717;cp173050;cp172357 178.7 cp680662;cp677055;cp491350 116.4 M10_Mtmt CaM1763;CaM0806;CaM0421 cp173427;cp326442 140.5 OPA14_1 cp350118;OG899130 44.8 OG895142;OG924405 226.9 R36082y 125.8 OG908356 cp490103;cp679895;cp675788 C81;ICCM0245 117.2 APFF2.4 80.4 cp489156;OG896348;CaM0658 107.9 OPC183 143.8 TA4L_TA1 182.8 M1107_Mt;P106_1_P cp678287;cp678922;cp682300 231.5 Foc5;TA27 126.6 OG914210 M570_Mtm 185.5 OPAB9_3 50.6 118.8 CaM0475 110.6 ICCM0074 144.1 191.5 DCS_6 cp172945;cp681747;cp677354 cp490797;cp490675;cp350018 cp490788;Pc172283;OG897362 148.7 OG895877;Gm212512 119.3 TA59 212.4 CaM1939 233.5 ICCM0297 AB025002;AJ005041 127.4 cp679761 cp326014;cp325716;OG905013 121.9 FIS_1;AJ276270 cp676929;cp327807;OG908289 CaM0416;CaM0574;CaM1809 51.0 OG919655 OG894619;OG897323;OG903021 123.4 81.2 OG899689;OG917730;OG902906 149.9 237.4 124.7 H1H011 131.3 cp678637 126.7 OG901547;OG905278 OG919460;OG903969 CaM0423 51.4 OG904000;OG898078 OG899509;OG902765;cp350537 cp325884 cp680545;cp678117;cp678340 238.4 CaM0639 cp679622 125.1 ICCM0030 131.8 CaM1377 81.8 H1H11 127.0 OG896873 151.5 243.7 CaM1072 ICCM0130;cp679509;cp680549 234.5 cp675768 234.8 cp490323 125.2 H1P092 132.8 OG907934;OG902560;OG901197 85.7 H1E22 130.6 ACMCAC07 246.5 cp323461;cp327623;OG901549 252.3 CaM1590 54.4 cp171561;cp172966;cp677302 152.3 CaM0491 234.9 cp491438;cp488937 125.3 H2B061 133.3 OG900075 91.4 H4F09 133.1 C80 OG896540 268.9 RGA_D22;RGA_D23 cp676753 239.4 TC80236 H1F05;OG912685;OG901841 134.1 OG901133 101.6 CaM0886 AJ489614 153.1 OG900006 271.3 CAMCAT08 55.6 Ca22434;OG897619 125.4 ICCM0247;OG895601 117.5 CaM1358 134.8 cp678768;cp677822;cp675905 274.7 TA5L_TS3 240.1 H2A08 134.5 cp675974 56.0 OG906969 240.6 CaM0403;CaM0720;AJ005043 AGL202;OG915900;OG923111 126.8 OG905195;OG895162 136.0 COAO 153.5 cp491458;cp675277;cp350553 277.2 OG918150;OG895545 125.8 OG896498;OG910601;cp680556 OG895816;OG910676;OG902462 58.1 OG903898 241.0 OG905379;AGL112;CaM0486 OG918275;OG897346;AGL21;OG903853 134.9 cp679140;cp678144;cp676665 127.2 cp323821 138.7 OG896040;cp491201;OG918556 153.9 cp491484;cp676464 277.6 OG896744;cp679202;cp488779 241.4 Gm212091;cp681088;OG897579 125.9 CaM0233 127.6 OG897009;Gm212324 143.5 M64_Mtmt 155.1 cp327672;cp327869 cp350493;cp682214 59.3 cp489035;cp173466;cp489222 cp172068;cp172153 cp676885;OG960856;OG918946 155.8 ICCM0293 282.6 cp678477;cp680535 241.8 CaM1451;OG913108 126.3 CS27ASAP 140.7 cp679625 128.0 143.7 EST671 292.9 ICCM0120 59.5 cp681649 242.6 OG901047;OG908473 cp323880;cp324051;cp324951 161.1 STMS11;GA24;GAA47 127.2 OG896190;OG897209 141.4 CISP5;OG913329 147.6 cp488703;cp677011 162.2 LN5A 302.1 RGA_C 59.7 cp681920 243.9 OG900394 cp677165;cp350651;cp488767 303.9 OPN06_2 129.1 CaM0173;ICCM0082 OG906936 128.8 REP 62.6 CaM0787 246.0 OG912303;cp490301 130.3 cp326233 141.7 cp489055;cp489840;cp489987 150.0 cp491099;cp489427;cp489903 164.5 307.6 Ps198_ps CaM1536 253.4 H1G16 156.3 CaM2168 cp490507;cp677267;cp675299 cp489931 166.6 M400_Mtm;P32_PisP 319.0 64.0 OG898231 cp326223;cp325101;cp325045 150.9 168.2 TA4L_TA1 334.7 cp172130;cp172152;Tp685729 258.6 TR43;TA1;TA8 130.7 158.7 CaM1084;CaM0251 129.2 OG894098;Gm207793;OG903842 OG905443;OG900261 Mt133126 67.4 Ts45 P82_PisP cp325508;cp326716 158.9 H1L161 Ms694351;cp677979 152.4 171.9 RL3;M12_Mtmt 335.1 cp350116;cp350541 260.5 OG895535;OG919735 68.7 X60755;U71 269.1 FP_i OG899729;OG915207;cp327714 CaM1402;CaM0753;CaM0677 130.0 ICCM0093 cp488731;cp489293;cp679199 174.8 335.9 cp324020;cp327946;cp327739 285.0 OPC11_2 131.1 cp327716;cp325794;cp325853 159.0 H1F14;H2I01F;H5E02 153.2 cp679688;cp491512 176.3 Ct687595 cp325842 70.0 FENR 159.3 cp325969;cp326060;OG919333;CaM0726 ICCM0191 176.7 LG99 340.0 GA4;M3179_Mt;OPC06_2 73.9 G6PD 296.0 OPU17_3 ICCM0282;CaM1354;ICCM0185 OG894196 343.9 M103_Mtm;OPT12_2 131.3 cp327859;cp326041 166.9 CaM0743 130.4 ICCM0178;CaM2085;CaM1750 170.8 177.8 cp490593;cp488743 345.3 Pyruvat_ 74.0 ACONc 297.2 R2609_2;OPC11_3;R2609_3 OG899728 178.6 cp678437;cp679062;OG903593 347.0 131.6 cp325216 167.8 CaM1020;CaM0600 188.4 cp490885;cp489326 M116_Mtm PGMb 300.4 PR10_obe 168.5 OG899657 179.0 OG896007 347.1 ps175_ps 80.3 302.3 ISSR858 132.0 cp325646 136.4 CaM1132 188.8 OG908268 181.1 ICCM0024 348.7 cp677807 90.3 OG895690;OPQ11_2 135.2 H1J07 173.3 OG900222;OG946804 146.1 ACMCAC12 cp676152 348.9 OG925843;OG927739 319.4 TA203 189.7 181.7 cp326008;cp327960 94.9 OG896172;OG895871 339.7 ISSR888 135.3 H1A12 OG906599;OG895029;OG922092 146.8 AAMCTA06;AAMCTA02;AAMCTA07 182.2 OG895578;OG897715;OG901985 349.1 OG915805;TCMO 181.0 OG896103 CAMCTA01 206.1 Pyruvat_ cp491008;cp489932;cp490282 98.0 M599_Mtm 360.2 TS52 138.5 CaM0336 147.8 183.6 ICCM0003;ICCM0004 349.5 cp171274;cp680370;cp172962 377.1 STMS12 OG895412 182.7 OG901904 153.4 STMS10 223.8 CAMCTA11 186.9 OG910718;Ca128631 OG896285;cp676692 100.3 TA3R_TA2 142.8 397.6 ISSR8884 144.3 OG924480;cp172164 OG894415;cp679880;cp682745 154.5 STMS14 233.3 TA4L_TA1 191.3 AAMCTT08 350.3 OG896967;cp682554;cp490678 104.8 AAMCTA11 ISSR8552 183.5 155.1 STMS28 CAMCAG01;CAMCTA06 193.5 TA3L_TS6 350.7 OG900450;OG894267 428.9 144.8 CaM1648 cp350006;cp488839 241.7 TA130 357.4 CaM0258 119.8 AAMCTA14 439.8 APF4.4 155.4 TA135 194.8 STMS17 146.4 CaM2064 183.6 cp682128 242.7 CAMCAT05 ICCM0063;ICCM0249 363.9 127.3 TA3 442.7 CAMCTA09;CAMCTA10 PG9_PisG;TR2;TR31 198.9 365.6 M1026_Mt 156.9 ISSR8603 183.7 cp682478 155.6 243.8 CAMCAT02 cp323738;OG935579;OG922957 366.3 TA5 444.3 AAMCTA01 TA34;STMS4 199.7 142.8 M121_Mtm 165.4 TS82 184.0 OG909974 CAMCTA12 OG899078 367.6 TS43;STMS19 445.5 ACMCAC05 165.9 TAA60 OG894314;OG919211;OG903717 156.8 TA3R_TS7 245.4 370.3 P93_PisP 148.1 OG901744;OG901711 ISSR8801 184.4 156.9 TA120R_T 212.9 ICCM0065 453.3 166.5 TA194 184.6 CaM0063;cp490069 248.7 TSa62 230.9 OG922889 371.6 M50_Mtmt;BTF3b H2B202 153.8 Ca21567;cp350602 463.6 cp679048 158.1 TA4L_TS1 373.0 468.9 cp490477;cp678734 167.0 TRb58 186.0 cp489647;cp678839 158.8 STMS23;TR56 259.6 TGAA44;GAA44 233.1 OG895956;OG906662;OG913321 379.6 CaM0698 157.1 OG898271;OG919502 240.3 CaM1529 383.2 H2B18 473.5 OG897499 171.4 OPC14_4;R2607_2 188.0 cp488971;cp679928;cp682560;cp682104 161.9 R3608_3 278.4 TA21 H2L102;H2J09;CaM1545 H1D24;H1C092;CaM0539 176.0 M1035_Mt 251.4 GA2 159.5 477.2 OG910796;OG894192;cp171403 188.4 OG898533 163.0 M3177_Mt;M01_Mtmt 299.9 ICCM0034 258.3 M214_Mtc;M224_Mtc H1H07;H1O01;OG915278 H5B04;OG902768 184.9 Gluc_a_u 163.6 OPO04_1 391.7 OG897350;OG895358;OG915293 cp350554;cp679353;cp491412 190.9 cp679791;H3B08;H5A04 323.3 TA78 263.0 CaM0232 OG936005;OG896202;OG895876 167.9 APF4.1 477.6 OG898940 198.8 CaM1135 192.9 APE4.2;A2ga2_R6;ICCM0104 165.6 OPP15_2 OG896733;OG902016;OG901045 PR5 169.3 APAR4;APBR;APAR5 329.0 CAMCTA03;AAMCTT04;ACMCAC06 264.4 CaM0805;OG900217;CaM1218 178.6 TS12 cp679810;cp678432;cp173071 201.7 195.2 ACMCAC10;TS19R_TA;PR10_mit tk_515;OG899516 392.1 H4H11;CaM0740;CaM1228 479.7 OG905290 207.0 M251_Mtm 169.9 CAMCAT06 331.0 OPC20_2 264.6 OG908504;CaESTSin ICCM0123 203.5 CaM2036 195.4 APAR2 PGMa 392.5 cp327747 480.1 OG961504 216.7 LN211 199.5 ICCM0242;ICCM0242 171.5 332.9 OPT18_2 cp677080;cp491502;cp680494 394.0 ICCM0134 482.5 C32 220.4 OPU17_1;OPQ11_1 172.1 PGD6 265.4 cp350396;cp681085;cp490330 396.0 213.5 ISSR8402 173.5 C33 335.1 OPA12_2;TA5L_TS7 TRPT 488.4 OPAB9_1 221.0 OPP15_3;OPU03_1;OPN06_3 cp488869 399.6 RGA_B;OPP07_1;STK86_D 494.9 OG897333 222.3 XP_Ca_11;TR1 175.1 ISSR8903 339.5 MSU82 265.8 ICCM0127 RGA_D2a 221.9 OPD05_1;OPP08 401.1 TS53;TA179;TR59 495.7 OG902569 222.4 OPP15_1 223.9 R2607_1;STK25_B 180.0 TC88726 341.8 CaM0558 267.1 CaM0480 402.0 STMS7;TA71 496.9 H1H24 OPM20X 226.1 ps179_ps;OPN06_4 180.4 MSU380;AJ291816;TC88512 342.6 CaM0622;H1I18 267.5 cp676824;cp676868;cp678296 403.6 TAASH 223.3 182.9 ICCM0159;ICCM0197 CaM0436;CaM1903;H1H13 TA39 497.3 OG902030;OG898304 TA37 227.0 TGDH 350.2 cp682113;cp325968 404.6 223.8 183.7 CaM1122;ICCM0062 268.0 CaM0113;H1G20;H1H15 406.9 TA5L_TS1 LG 8 cp678442;cp676401;OG897347 230.2 TC79726 TR29 230.3 ISSR8571 190.0 TC84431 351.2 ICCM0196;OG897618 CaM1666;CaM2049 412.0 497.7 cp679336;cp490906;cp350226 232.9 M86_Mtmt;ps169_ps 417.7 GAA42 cp350627;cp171322 234.3 OPS02_1 203.2 APC41 353.2 AGL178;H1O12 270.9 CaM1637;H1B17 437.1 CaM1782 249.8 AGL52;OG895274 233.9 APDR23 271.9 CaM0691 448.3 M932_Mtm 497.9 cp489385 212.8 GA13 354.0 cp173377;cp326427 250.6 OG903882 235.3 TA80;TRa7;TA22;TA176 OPU03_4 281.3 OG897326;OG900323 452.2 ICCM0076 498.1 OG895237;OG894516 233.1 499.3 252.0 OG905292;cp678248;OG912880;APE4.3 cp678796 236.6 TA4L_TA1;TA3R_TS7 244.7 CAMCTA08 cp327923;cp490690;cp679050 284.7 OG915802 452.3 OG903808;OG912629;OG895467 OG903716;ICCM0081 cp490097;cp491092;cp490237 238.6 OPU03_5;OPD03_2;OPO04_2;OPC15_1 354.4 cp488935;cp489344;cp679693 286.1 CaM0446 503.1 OG948105 250.4 MSL591;RNAH ICCM0079;cp323897;cp323608 253.9 238.9 OPC20_1;OPC06_1 CaM0909;OG903155;OG895060 452.7 cp679996;cp678399;cp327849 503.3 Mt106628 OG896024 253.5 AJ004917;TC76881 cp489394 287.5 CaM0507 cp172370;H4F07;OG894043 503.5 OG898883 cp676706;cp680356;cp681533 239.8 XP_Ca_42;M367_Mtm 255.9 M16_Mtmt;PG6_PisG;AGT cp677139;cp682693;cp679896 287.9 CaM1502 454.8 OG904027;OG907169 ACCO 255.1 cp677297;cp682089;cp679116 239.9 TC88598 257.3 OPC14_5 355.0 cp350631;cp491000 506.7 288.9 CaM0645 456.0 509.4 M107_Mtm;ISSR8842 DK242 240.5 M51_Mtmt 263.8 OG908776;OG910656 cp676498 cp490581;cp490006;cp172234 257.0 290.0 CaM1551 458.4 cp488709 512.3 GAA40 259.5 M304_Mtm 246.0 TRAL 265.9 OG896261 356.1 OG897306 291.1 OG927609;Gm208481 458.6 cp682445 513.4 APF4.2 262.2 M05_Mtmt;TA110 258.5 CaM0594 266.3 OG914613 cp682222;cp681271;cp677961 291.5 OG894171 458.7 cp676840 520.0 GAA50 267.5 AGL23 CaM1158 CaM1036;cp489634;OG902902 264.1 OPP06_3 265.3 ICCM0284 268.9 TC78638 CaM0034;cp682791;cp350187 291.7 459.5 OG907096;OG894007;OG897198 524.9 IC_unten 266.3 AJ004960 CaM0464 299.5 H1G22 269.6 273.5 TA64 cp350325;cp680065;cp677368 304.6 AAMCTA13 cp679277;cp678520 527.6 XP_Ca_96;AAMCTA15 268.9 RGA_DS 356.5 468.1 CaM0836 M859_Mtm 276.6 CaM1101 277.1 OG907937 cp675455;CaM1159;OG908917 306.4 ppPF 528.2 RGA_D 491.2 CaM0368;CaM1016 272.3 294.8 TC78756 OG903883;OG908710;OG928551 AAMCTT01 516.6 TA66R_TS cp491035;cp678137;cp323728 276.7 ISSR8681 277.4 OG916106;OG927781;CaM0661 311.9 OPG09_4 535.1 cp678822;cp678546;cp491097 308.8 M24_Mtmt Ca21249 314.5 Pyruvat_ 521.5 282.3 ISSR864 312.2 cp676639;cp172996;cp680216 cp676386;cp676452;cp682642 cp677192 318.5 ACMCAC03 525.3 OPB08_1 OG894864 525.9 TA5L_TS3 535.9 OG930652 288.5 HR_unten 313.0 CaM0244;cp675609 278.3 cp679455;cp489463;cp678587 357.3 H5E11;H1C22 321.2 TR20;TA13 526.8 OPB08_2 293.2 AAMCTA10 OG903989 363.6 TA28 321.7 TA146;TA72 532.6 ACMCAC02;CAMCTA05 536.3 ICCM0289;Mt125375 313.8 OG894270;OG896567 534.3 AAMCTA09 294.9 AAMCTA05 278.8 OG896159 323.0 TA2 540.6 cp325921 314.6 cp173163;cp681531 TAb140;TAA58;TAA59 535.8 CAMCAT09;CAMCAT03 296.5 AAMCTA03;AAMCTA04 280.3 OG905504;OG898599;OG933879 365.5 335.9 TS54 540.9 cp327812;cp327873;OG894483 316.6 cp324158;cp172290 539.4 ISSR843 541.3 OG895173 308.7 AAMCTT07 280.7 CaM1042 TA18 347.6 STMS26 563.3 CaM1238 319.0 OG896584 371.0 OPA12_3 349.5 ps189_ps 568.2 CaM1098 543.8 OG898575;OG902800 333.3 PGI 284.1 ISSR807 cp323841;cp680413;cp680836 349.6 TA4R_TA1 569.6 CaM1722 544.2 cp327943 338.8 M218_Mtc 330.4 cp680100;OG916436 284.3 CAMCAT11 371.2 CAMCAT04 350.4 TS72 571.3 CaM1360 544.4 cp326018 339.5 M215_Mtc;M83_Mtmt 287.7 CaM0610 CaM0286 579.3 CaM0358 331.2 OG906822 cp488860;OG929069;OG919458 378.3 350.8 ISSR8401 586.7 CaM0038 554.6 STMS21 341.7 M237_Mtm 354.0 OPS13_2 562.1 Apero 333.2 cp172879 288.2 OG912320;AGL94;OG894927 386.0 TA180 591.3 CaM1068 344.9 TC87369 360.3 OPT12_5 609.6 CaM0073 569.0 APFF2.2 347.1 cp489497;cp681259 333.6 OG894755 OG894612;cp172155;OG918895 399.1 CaM0598 372.1 cp682025;cp490406 611.8 CaM0848 584.0 ISSR810 cp489826;CaM1239;cp679581 cp677994;cp676615;cp679902 412.3 OPG09_2 374.1 ICCM0068 624.4 OPE32 cp489404;cp490744;cp491088 338.4 289.6 642.8 OPAC43 587.2 ISSR8601 347.9 cp323760;cp322640 cp350337;cp678699 378.9 OPD16_1 cp491301;cp490226;Mt681737 291.4 cp682496;cp173150;cp173167 421.7 HR_Oben 655.6 CaM1417;CaM0111 589.7 M1118_Mt;P59_PisP 338.8 OG905619 381.2 OPC14_2 664.6 H1N12;CaM1469 350.8 OG961222 293.0 cp682494 439.9 ISSR8112 ISSR8902 590.6 TA5R_TR4 cp325105;cp675405;cp676491 385.0 665.1 STMS25 353.8 OG903783 301.1 P69_PisP 479.0 CaM0277 397.6 OPS13_3 668.8 TA196 591.1 GA11 OG906575;cp324065;cp490454 355.5 OG918855 339.2 305.7 OPP06_1;OPP06_2 408.6 OPT12_3 688.8 TA125 597.2 OG896385 373.9 OPC14_1 cp680120;cp324115;cp679989 492.9 CaM0435 712.5 OG896348 597.9 OG924216;OG906873;OG901542 309.3 TC86212 430.8 cp490039;OG913370;OG917721 739.2 CaM0790 380.7 APFF2.1 cp491442;cp675253 310.8 ENOL 495.1 CaM0705 431.2 OG895229 740.5 CaM0260 602.6 OG896074;OG902716 cp679779;cp173541;cp323904 398.4 ISSR8661 cp325265;cp325803;cp325141 312.6 ICCM0045 511.5 CaM0864 ICCM0212;AAMCTT03;OG897521 743.4 CaM1079 609.3 339.6 cp325151 433.7 OG903088 750.4 CaM2045 cp324017;cp324081 418.4 IC_oben 313.9 OPL42;TA120R_T;APF4.3 524.8 CaM0958 CaM0751 cp325093 cp325981;cp680288;cp322687 317.5 CaM0799;OG901858;OG896979 cp172089;ps190_ps;cp679174 754.4 609.8 342.5 535.8 CaM1496 434.6 cp323966;OPC10_1;cp323611 754.9 CaM0466;CaM1007;CaM1542 CaM1668;CaM1149;CaM2155 610.4 OG901896 cp679505;cp679770;cp680400 OG898832;OG899490;OG916035 OG915738;CaM0797 318.8 Ca2009_3;cp173452 544.2 CaM1497;CaM1506;CaM1591 437.2 CAMCAG10 CaM1714 611.6 344.9 cp325873 439.4 ICCM0257;ACMCAC09 CaM1581;CaM1337;CaM0519 613.7 ACMCAC11 345.9 EST948 321.3 OG901180 563.8 CaM2060 755.0 CaM0632 441.9 OG895163;OG946905;LUP51_CA 613.9 DMI1 348.4 MTU07 322.5 OG903904;OG914943;OG910683 577.5 OPQ13_1 443.0 CYSPR2 769.2 CaM0656 OG918991;OG896448 781.7 CaM1658;CaM0340;CaM1975 640.2 CaM1301 ISSR8551 444.6 OG902037 362.5 328.2 TR26;STMS5 782.4 CaM2162 LG 2 647.0 CaM1326 445.0 cp678644 783.1 CaM0443 GA9 Nayak et al. 2009 671.0 CaM0955 364.6 332.7 SAMS CaM0795 cp172299;cp350492;cp488878 784.0 372.3 M241_Mtm ISSR8882 CaM0599;CaM0345 686.7 CaM1761 354.7 446.2 cp491565;cp491143;cp489107 784.5 CaM1827 690.6 CaM0284;CaM0686;CaM0076 372.4 M19_Mtmt 380.4 M213_mtc 792.3 cp489311;cp676816;cp677363 797.4 CaM2186 709.8 CaM0215 377.2 TA106 381.9 CAMCAG11 446.8 OG896166 809.2 CaM1620 711.4 CaM1543 381.1 AGL76 383.7 OPD03_5 455.0 STMS24 835.4 CaM0025 384.8 XP_Ca_78 858.0 CaM0578 711.8 CaM1770;CaM0870;CaM1298 385.5 M361_Mtm;M320_Mtm 456.9 TA46 872.7 CaM0997 734.2 CaM1978 386.4 M3163_Mt 386.8 CaM0862 628.7 AJ276275 465.9 M477_Mtm;M336_Mtm 873.7 CaM1207;CaM2016;CaM1493 759.2 CaM2101 387.0 QOR;ps205_ps OG897486;cp676571;cp491267 467.0 TC87270;CDC2 881.6 CaM0050 387.3 cp171590;cp172237;cp681358 468.0 P124_Pis 921.7 CaM1607 393.4 GA34 470.4 ISSR842 959.9 CaM1679 389.3 cp681608 400.2 RGA_Gv 390.5 OG910860 471.9 M13_Mtmt CaM2080;CaM0317;CaM1961 962.6 CaM1953;CaM1693;CaM1166 411.4 STMS2 cp491231;cp682291;cp682299 477.1 OG894099 CaM1247 440.6 CAMCAG08;CAMCAG09 390.9 cp322975 cp675523;cp675919;cp677611 963.4 CaM1257 477.8 LG 5 M1121_Mt cp350449 969.1 CaM1783 455.4 393.4 OG901928 1012.6 M578_Mtm 461.2 OPN06_5 cp488624;cp677322;OG960456 483.0 OG897469 1015.4 M1433P 393.8 483.8 OG899684 LG 1 470.2 M3186_Mt;M866_Mtm OG906875;cp488939 1020.7 OG897369;OG897884 510.9 ISSR8901 1024.0 AF457590 486.1 TR3 401.6 AJ012739 1027.6 MSU83 494.6 OG961744 412.4 GAA45 1029.2 STMS22 MSU40 416.9 M1027_Mt;M32_Mtmt 1041.9 STMS20 494.9 AIGP 421.1 TA76 1045.9 LG 3 502.3 TC88727 508.2 TS83;GA26 GA21;CaM0399;GAA41 508.7 GAA39 LG 4 LG 6 LG 7 512.3 OG897528 513.1 H1I16 537.2 RGA_D2r
    • Groundnut marker discovery and validation  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 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 agb04 117.3 cM  Over 300 F1-derived families with at least agb01 107.3 cM BM68 one gene for resistance to bruchids (arcelin), common bacterial blight (CBB), 7B BM171 7F BM199 ATA5 or bean common mosaic necrosis viruses BM140 Ph1.1, Ldg1.2 ATA2 BMd27 (BCMNV) were developed and screened 10Q ATA20 10O 11V Pp4.1,2, Sep4.1 7E with markers. Genetic crosses made with Dm1.2, Df1.1 10H 4N BMd10 10S Spo1 commercial seed types and drought- .1 10E ATA3 7N 10N tolerant genotypes. 69 families advanced 12F 12M 15F 15G in Malawi 15M Yld4.1 FIn 14K 7K BM201 11I BM53 BM149 Yldp1.1 BM200 BM195 Based on trials for the DOR364 x BAT477 6L RBCS  2B 4Q Dm1.1,3 9J Ldg 1.1, Ph 1.2 9C (DxB) population, a total of 24 yield QTL 3D Df1.2,3 1H 1C 14N 2C 13S 13B were identified in drought treatment and 10B 4L 7D 4J 13N 14B 11 under irrigation. Significant differences 14C 15E 4E 6F 14Q 13A were also found in the BAT881 x G21212 6I 4K 10J 14G 13L 4G 7S (BxG) population 1G 11C 14U 11H 6D BM161
    • 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 7 rosette segregating F2:3 populations involving 3 Phenotyping for Rosette at ICRISAT Malawi 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 • Development of Advanced Backcross populations across genepool boundaries SER16 = small red drought tolerance sources SER48 = 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 SEA5 = cream colored SEA15 = medium red seeded CAL96 = K132 (Ugandan release, high marketability) CAL143 = Napilira (Malawi release, low P tolerant) BRB191 = BCMNV resistance source
    • Chickpea pre-breeding Donors  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 Cultivars introgressing QTL for root traits in one desi (ICCV 93954; donor parent ICC 4958) and two kabuli cultivars (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
    • 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
    • Cross-species resources – Obj 5 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%
    • 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
    • Cowpea phase I  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)
    • Common bean 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  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.
    • Chickpea phase I 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
    • 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
    • Evolution TLI phase I to phase II  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
    • 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
    • The 7 Challenge Initiatives Following 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 Cereals: 1) Improving drought tolerance in rice for Africa 2) Improving drought tolerance in sorghum for Africa 3) improving drought tolerance in wheat for Asia Legumes: 4) Improving drought tolerance in chickpeas for Africa and Asia 5) 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
    • Molecular Breeding Platform A 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
    • Interaction of breeding workflow and platform elements LIMS MSL High density GRSS ST genotyping GeneticResources FDM TSL Phenotypic Key characterization Information System A&DS Choose parental material based on haplotype Sample Parental Material ST values, known genes, traits and adaptation Tracking Develop crossing scheme based on genotype Breeding Information system PIM Pedigree Information A&DS and phenotype compatibility Public Crop Information Laboratory LIMS Information Crossing Block Pedigree information updated PIM FDM Field Data High density Analysis & LIMS MSL genotyping A&DS Decision Nursery 1 ST Support FDM TSL Phenotypic Platform Services evaluation Genetic Selection of lines based on QTL analysis / Resource A&DS estimation of marker breeding values GRSS Service Nursery 2 Pedigree information updated PIM Marker MSL Service n cycles of selection Marker ST LIMS MSL and recombination genotyping Trait TSL Service Selection on index of marker values A&DS Evaluation Trials Multi-location GRSS ST FDM TSL testing Selection of improved lines based on trait Cultivars A&DS improvement and adaptation & Breeding Improved Lines Pedigree information updated PIM Lines
    • 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
    • Groundnut Cowpea Common bean Chickpea
    • National Program Partner Institutions Groundnut Cowpea Bean Chickpea Capacity Building East Africa Ethiopia SARI EIAR SARI; EIAR University of Egerton University of Nairobi, Kenya Nairobi University Egerton University Naliendele Naliendele Research Tanzania ECABREN Research Station Station; ECABREN West Africa Burkina Faso INERA INERA Senegal ISRA ISRA ISRA Southern Africa Chitedze Chitedze Research Station; Malawi Research Station, SABRN; DARS SABRN; DARS DARS Universidade Universidade Eduardo Mozambique Eduardo Mondlane Mondlane Zimbabwe DR&SS DR&SS
    • Other Partner Institutions Integration across crops: drought phenotyping, data Groundnut Cowpea Bean Chickpea and project management (Obj. 5) University of ICRISAT California– CIAT ICRISAT Riverside, USA Cornell University of North Carolina State University, CIRAD, France IITA University, California, Davis, USA USA USA University of Riken, Japan NCGR, USA CIAT Georgia, USA North Dakota Catholic University State IIPR, India ICRISAT of Brasilia, Brazil University, USA EMBRAPA, Brazil IITA West Africa Centre for Crop Improvement, Ghana
    • 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!