Theme 1:

Comparative and Applied Genomics (CAG)

Rajeev Varshney

Theme Leader, GCP

QTL

*cp488892 *cp491181*cp678132 *cp680434*cp681425

0.0

*OG905182 *OG9054747.8*OG938507 *OG927619*CaESTContig3 *OG901015

8.1

*OG895899 *OG92038217.7*OG898024 *OG89505420.2*OG90095721.0*OG947627 *OG898532*OG894236 *AGL82*OG898468

21.4

*ICCeM05524.3*M59_MtmtGEN_59_03_1 *M93_MtmtGEN_93-02_126.3*CPCB227.4*M3185-MtmtEST_3185_01_128.4*CaM147731.0*OG90257836.2*cp680889 *cp682003*cp490579 *OG903590*cp677240 *cp322948*cp679721

36.6

*cp49097038.9*cp17126641.6*cp17332842.7*OG897728 *OG89723948.2*ACONa56.9*ACONb62.9*ISSR848167.9*PG7_PisGEN7_1_2_178.9*ISSR884180.6*TC7748885.5*OG897376 *OG91886487.3*cp323000 *cp677227*cp677381 *cp491173

89.4

*OG910457 *H3H02190.2*cp32581892.7*cp490024 *cp173046*cp350308 *cp491085*OG898978 *cp676494*cp490693

93.2

*C81 *ICCM024595.4*cp490797 *ICCM0297*cp490675 *cp350018*OG894619 *OG897323*OG903021 *OG899509*OG902765 *cp350537

98.2

*cp67962299.2*cp49032399.5*cp491438 *cp48893799.6*TC80236104.3*H2A08105.0*CaM0403 *CaM0720*AJ005043

105.6

*OG905379 *AGL112*CaM0486

106.0

*Gm2120918 *cp681088*OG897579

106.4

*CaM1451 *OG913108106.8*OG901047 *OG908473107.6*OG900394108.9*OG912303 *cp490301111.1*H1G16120.4*TR43 *TA1*TA8

126.2

*P82_PisPR82_1129.4*R2609-2 *R2609-3132.2*PR10_oben135.0*ISSR858136.6*ISSR8552142.3*APF4.4150.1*ISSR8801156.4*cp679048167.0*cp490477 *cp678734172.6*OG897499177.5*OG910796 *OG894192*cp171403 *cp350554*cp679353 *cp491412*cp491472

181.3

*OG898940181.7*cp679810 *cp678432*cp173071 *OG905290

183.8

*OG961504 *C32184.3*OG897333186.5*OG902569187.8*H1H24189.1*OG902030 *OG898304189.5*cp678442 *cp676401*OG897347 *cp679336*cp490906 *cp350226*cp350627 *cp171322

189.9

*cp489385190.1*OG895237 *OG894516190.3*OG905292 *cp678248*OG912880

191.5

*OG948105195.5*Mt106628195.7*OG898883195.9*ACCO199.3*ISSR8842203.0*APF4.2207.7*IC_unten211.5*XP-Ca-9640 *M859_MtmtGEN_859_06_2213.3*cp491035 *cp678137*cp323728 *cp678822*cp678546 *OG894864*cp491097

220.1

*OG930652220.9*ICCM0289 *Mt125375221.3*cp325921225.8*cp327812 *cp327873226.1*OG894483226.2*OG895173226.6*OG898575 *OG902800229.1*cp327943 *cp326018229.5*STMS21240.7*ISSR810260.0*ISSR8601263.0*M1118_MtmtGEN118_03_1 *P59_PisPR59_1265.6*TA5R-TR42L_197-193266.5*GA11266.9*OG896385273.2*OG924216 *OG906873*OG901542

273.9

*OG896074 *OG902716278.8*cp679779 *cp173541*cp323904 *cp324017*cp324081

285.9

*cp325093286.4*OG901896287.0*OG915738 *CaM0797288.2*DMI1290.6

1

*P141_PisPR141_10.0*ISSR82621.3*MSU393 *AJ4046403.7*AGL3 *OG895374*OG898285 *OG897694

4.8

*cp680621 *cp6823935.3*OG8940615.6*OG8942626.0*cp1722956.4*M3223_MtmtEST3223_02_03_1 *M3188_MtmtESt_3188_06_08_18.6*ICCM0166a17.2*AGL179 *OG924480*OG895747

17.7

*cp489318 *cp32280618.5*ISSR855335.3*CS2737.9*Foc4 *R2609-138.6*TA120R-TS19L-3_184-188 *APAR639.8*TA9640.7*M10_MtmtGEN10_03_140.8*Foc5 *TA2742.6*TA5943.1*AB025002 *AJ00504147.3*H1H011 *ICCM0030b48.6*H1P09248.7*H2B06148.8*H1F05 *OG912685*OG901841 *ICCM0247*OG895601

48.9

*AGL202 *OG915900*OG923111 *OG918275*OG897346 *AGL21*OG903853

49.3

*CaM023349.4*CS27ASAP49.8*OG896190 *OG89720950.7*CaM0173 *ICCM008252.6*cp32623353.8*cp326223 *cp325101*cp325045 *cp325508*cp326716

54.2

*OG899729 *OG915207*cp327714 *cp327716*cp325794 *cp325853*cp325969 *cp326060*OG919333 *CaM0726

54.6

*cp327859 *cp32604155.7*cp32521656.5*cp32564657.2*H1J0761.0*H1A1261.6*CaM033665.3*OG89541270.0*cp17216471.5*CaM164872.0*CaM206472.9*TS8280.5*TAA6080.8*TA19481.4*TRb5882.0*R2607-286.8*Gluc_a_unten103.1*CaM1135121.3*LN211140.8*TA37150.8*ISSR8571154.9*AGL52 *OG895274171.7*OG903882172.5*cp678796173.9*cp490097 *cp491092*OG896024 *cp490237

175.8

*cp676706 *cp680356*cp681533 *cp677297*cp682089 *cp679116

177.0

*DK242178.9*M05_MtmtGEN05_04_1184.2*TA110184.3*AJ004960188.4*RGA_DS192.1*ISSR8681194.5*ISSR864200.3*PGI222.8*M218_MtcaEST218_01_1227.9*M215_MtcaEST_215_06_1 *M83_MtmtGEN83_04-1228.6*TC87369233.6*cp323663238.5*cp489497 *cp681259241.8*cp677147 *cp489404*cp490744 *cp491088*cp491301 *cp490226*Mt6817377

242.6

*OG961222245.6*OG903783248.7*OG918855250.2*cp323936 *cp323690259.1*cp489129261.2*cp172961262.6*TC76606_dCAPS271.7*cp676219 *cp675667288.6

2

*OG9239030.0*Ct687446410.1*CISP02913.7*CISP04119.2*OG90007522.6*Ca1027326.0*ICCeM03930.4*OG89964034.6*OG89431437.6*CISP03639.2*CaM0085 *OG90862567.9*OG897973 *LG7372.4*cp681754 *cp677013*cp489629 *cp350573

73.2

*cp680528 *cp488664*cp489415

74.9

*DNABP80.1*OG917794 *OG89424883.2*PG10_PisGEN10_1_188.3*STMS1590.5*TA1492.6*TR44104.5*APFF2.3113.6*CaM1868125.8*cp171521128.6*H3A03 *cp681792*cp490380 *cp678597*cp677806 *cp490199*cp490316 *cp489132*cp171418 *cp681513

129.6

*OG894408 *OG899538*OG900871 *OG899062*OG902919

131.6

*cp489518 *cp322954*cp490337 *cp489881*cp681694 *cp681488*cp677717 *OG894921*OG903023 *OG902834*OG902901 *OG914910*OG898034 *OG903841*OG897351 *OG897956*OG898370 *OG916065

133.7

*H6G10133.9*ICCM0284b *CaM0620*CaM1125 *CaM1763*CaM0806 *CaM0421

134.1

*OG908356134.9*OG914210135.7*cp490788 *Pc1722835*OG897362 *cp679761

136.5

*cp678637140.5*CaM1377140.9*OG907934 *OG902560*OG901197

141.9

*OG901133143.3*cp675974143.7*OG896498 *OG910601*cp680556 *cp679140*cp678144 *cp676665*cp172068 *cp172153

144.1

*cp679625150.2*CISP5 *OG913329151.0*OG906936151.3*CaM2168168.0*CaM1084 *CaM0251170.4*H1L161170.7*CaM1402 *CaM0753*CaM0677

170.8

*ICCM0191171.1*CaM0743179.3*OG899728180.2*OG899657180.9*OG900222 *OG946804185.9*OG906599 *OG895029*OG922092 *OG896103

194.2

*OG901904195.9*OG894415 *cp679880*cp682745 *cp350006*cp488839

196.7

*cp682128196.8*cp682478196.9*OG909974197.2*OG919211 *OG903717197.6*CaM0063 *cp490069197.8*cp489647 *cp678839199.2*cp488971 *cp679928*cp682560 *cp682104

201.3

*OG898533201.7*cp679791 *H3B08*H5A04

204.3

*APE4.2 *A2ga2_R6GA1*ICCM0104 *TS19R_TA118L-1_152*PR10_mitte *APAR2

206.9

*ICCM0242b *ICCM0242a208.7*XP-Ca-11617 *TR1215.4*R2607-1 *STK25_B216.2*ps179_psatEST179_02_1218.2*TGDH219.9*TC79726223.5*M86_MtmtGEN86_03-1 *ps169_psatEST_169_03_3227.5*TA80 *TRa7*TA22 *TA176

227.7

*TA4L-TA199R-1_345 *TA3R-TS71L-1_95229.4*XP-Ca-42461 *M367_MtmtGEN367_05_1*TC88598

230.1

*M51_MtmtGEN51_02_1230.6*TRAL236.3*CaM0594251.5*ICCM0284a260.4*CaM0464264.9*CaM1101272.4*TC78756294.1*M24_MtmtGEN24_04_1309.9*cp676639 *cp172996*cp680216

313.4

*CaM0244 *cp675609314.2*OG894270 *OG896567315.0*cp173163 *cp681531315.8*cp324158 *cp172290317.9*OG896584320.4*cp323841 *cp680413*cp680836 *cp680100*OG916436

333.0

*OG906822333.8*cp172879335.8*OG894755336.2*cp489826 *CaM1239*cp679581 *cp323760*cp322640

341.2

*OG905619341.6*cp325105 *cp675405*cp676491 *OG906575*cp324065 *cp490454*cp680120 *cp324115*cp679989 *cp491442*cp675253

342.0

*cp325265 *cp325803*cp325141 *cp325151

342.4

*cp325981 *cp680288*cp322687 *cp679505*cp679770 *cp680400

345.4

*cp325873347.9*EST948348.9*MTU07351.4*ISSR8551366.9*GA9369.8*M241_Mtmt_GEN_00241_05_1372.3*TA106372.4*AGL76375.7*M361_MtmtGEN361-01_1 *M320_MtmtGEN320_01_1379.5*M3163_MtmtGEN_3163_01_03_1380.4*QOR *ps205_psmtEST205_01_1381.0*GA34385.6*M3186_MtmtEST_3186_02_1 *M866_MtmtGEN866_02_1399.2

3

*OG9084830.0*cp67963016.2*OG89492724.9*OG89859926.5*OG90793729.7*ICCeM02848.3*RGA_A54.1*CaM062961.2*CaM062461.6*OG894002 *OG89532965.4*cp681290 *cp17319266.2*AGL7466.7*OG89426567.7*OG905434 *cp680815*cp680932 *cp677464*cp350498 *cp676134*cp488955 *cp681256*cp675751

68.2

*OG89435168.6*cp489460 *OG894263*OG907978 *OG894920*Tp6849720 *OG895724*OG908343

69.4

*cp325639 *cp32627071.3*cp32646071.4*cp32652871.7*cp32656471.9*ICCM012478.1*cp491550 *cp490442*cp490101

86.9

*OG897016 *OG89887293.0*OG937303 *OG917728*OG897513 *OG896613*OG908192 *OG902630*OG910318 *OG903058

93.8

*cp171270 *cp490711*cp682845 *cp677288*cp172053 *cp172088*OG896253

95.0

*OG894791 *OG923107*cp173254 *cp172387*OG898975

95.7

*P131_PisPR131_198.8*H1H22108.6*CaM1129 *CaM1515114.7*CaM0717 *cp173050*cp172357 *cp490103*cp679895 *cp675788*cp489156 *OG896348*CaM0658 *CaM0475

114.8

*cp326014 *cp325716*OG905013 *OG899689*OG917730 *OG902906*cp325884

115.6

*H1H11116.3*H1E22120.4*H4F09126.5*CaM0886137.8*CaM1358156.2*OG905195 *OG895162166.3*cp323821166.7*OG897009 *Gm2123242167.1*cp676885 *OG960856*OG918946 *cp323880*cp324051 *cp324951

167.5

*cp677165 *cp350651*cp488767 *cp489055*cp489840 *cp489987

168.3

*cp490507 *cp677267*cp675299 *OG894098*Gm2077934 *OG903842*Ms6943512 *cp677979

168.7

*ICCM0093c169.5*H1F14 *H2I01F*H5E02 *ICCM0282c*CaM1354 *ICCM0185*ICCM0178 *CaM2085*CaM1750 *CaM1020*CaM0600

169.9

*CaM1132175.3*STMS10188.2*STMS14188.9*STMS28189.4*TA135189.6*PG9_PisGEN_9_3_1 *TR2*TR31 *TA34*STMS4

189.8

*TA3R-TS71L-2_170191.0*TA120R-TS19l-2_490191.2*TA4L-TS129R192.4*STMS23 *TR56193.1*R3608-3195.0*M3177_MtmtCON_3177_01_03_1 *M01_MtmtGEN_01_01_1195.5*APAR4 *APBR*APAR5

198.2

*PGMa200.2*PGD6200.7*C33202.1*ISSR8903203.7*TC88726208.9*MSU380 *AJ291816*TC88512

209.3

*ICCM0159 *ICCM0197a211.8*CaM1122 *ICCM0062212.7*TC84431218.7*APC41227.8*MSL591 *RNAH237.6*AJ004917 *TC76881241.0*M16_MtmtGEN_16_01_1 *PG6_PisGEN6_3_1243.2*AGT243.7*OG908776 *OG910656249.7*OG896261251.8*OG914613252.2*AGL23253.4*TC78638255.1*TA64262.9*OG906875279.8*OG903883 *OG908710*OG928551 *Ca21249

295.2

*cp676386 *cp676452*cp682642

296.5

*cp679455296.7*cp489463296.8*cp678587296.9*OG903989297.0*OG896159297.5*OG905504 *OG933879299.0*CaM1042299.4*ISSR807301.5*CaM0610303.6*cp488860 *OG929069*OG919458 *OG912320*CISP111 *AGL94*OG894612 *cp172155*OG918895

304.0

*cp677994 *cp676615*cp679902 *cp350337*cp678699

305.5

*cp682496 *cp173150*cp173167

307.3

*cp682494308.8*P69_PisPR69_1316.9*TC86212324.4*ENOL325.9*ICCM0045 *TA120R-TS19L-1_510*APF4.3

327.6

*CaM0799 *OG901858*OG896979

329.4

*OG898832 *OG899490*OG916035 *2009_3*cp173452

330.7

*OG901180333.3*OG903904 *OG914943*OG910683 *OG918991*OG896448

334.5

*TR26 *STMS5340.3*SAMS345.7*M213_mtca_EST_00213_11_2346.5*XP-Ca-7894351.6*CaM0862353.6*OG897486 *cp676571*OG902798

354.1

*cp491267 *cp171590*cp172237 *cp681358

354.5

*cp681608356.6*OG910860357.8*cp491231 *cp682291*cp682299 *cp322975

358.2

*OG901928360.7*cp488624 *cp677322*OG960456 *cp488939

361.1

*AJ012739369.5*GAA45381.9*M1027_MtmtGEN1027_04_1386.5*M32_MtmtGEN32_01_1387.6

4

*OG8948850.0*OG8996836.8*cp681671 *cp3241248.1*ICCeM03527.9*cp67770736.3*AGL163 *cp67745247.1*Gm211854353.2*ICCeM02961.2*ICCeM03469.8*M209_MtcaEST_209_04_177.9*APE4.185.2*Con_Pero *Pero87.4*STMS689.1*ISSR856291.5*ISSR859292.4*ISSR856196.6*ISSR859196.9*CPOX299.2*OG946834 *TC87800*OG902760 *cp677907

103.5

*OG905371103.9*OG899072104.3*TC86258106.0*H2E13106.4*H3H121106.8*M3183_MtmtEST_3183_04_06_1111.0*P206_Psmt_206_01_1 *APDR22*P191_psatEST_191_01_1

115.5

*OG914635 *cp325980*cp681101 *cp682312*cp323423 *cp488733

122.8

*cp678635 *cp679193*cp680081 *cp489357*cp491065

125.6

*cp326437 *ICCM0074b*OG903027 *cp173427*cp326442

127.4

*ICCM0074a129.8*FIS-1 *AJ276270142.1*OG901547 *OG905278146.9*OG896873147.2*AJ489614153.7*COAO154.8*OG896040 *cp491201*OG918556

157.4

*EST671161.2*cp488703 *cp677011163.9*cp491099 *cp489427*cp489903

166.3

*cp489931167.2*OG905443 *OG900261168.7*cp488731 *cp489293*cp679199 *cp679688*cp491512

169.5

*OG894196190.4*cp490885 *cp489326211.2*OG908268211.6*cp676152212.6*TA4L-TA199R-4_540219.2*TSa62227.4*TGAA44 *GAA44239.3*TA78262.6*TA5L-TS71R270.4*MSU82274.2*CaM0558275.9*CaM0622 *H1I18276.7*cp682113 *cp325968284.8*ICCM0196 *OG897618285.8*AGL178 *H1O12287.9*cp173377 *cp326427288.7*cp327923 *cp490690*cp679050 *cp488935*cp489344 *cp679693*cp489394

289.1

*cp677139 *cp682693*cp679896 *cp676498

289.7

*OG897306290.8*cp682222 *cp681271*cp677961 *CaM0034*cp682791 *cp350187*cp350325 *cp680065*cp677368 *cp675455*CaM1159 *OG908917*OG916106 *OG927781*CaM0661 *cp677192

291.2

*H5E11 *H1C22292.0*TA28298.3*TAb140 *TAA58*TAA59

300.1

*TA18300.2*CaM0286310.0*CaM0598312.1

5

*OG8973260.0*OG895956 *cp4915801.2*OG9158025.7*Ct687595121.0*cp326339 *cp326078*cp325757 *cp325769*cp324038

25.3

*cp324126 *cp32399228.3*cp32551029.5*cp32599431.2*OG901184 *cp326036*cp323850

33.3

*cp323648 *cp32397835.4*OG896976 *OG910567*AGL111 *OG901729*OG894321 *OG901743*OG930121

37.1

*OG89691138.3*cp32346741.3*PG3_PisGEN3_2_1 *Gluc_a_mitte48.8*TC86606 *SHMT51.3*cp325702 *cp327625*cp323466 *cp675973*cp327902 *cp327947

57.4

*cp489237 *cp67787859.5*OG91274961.6*HRIP *cp677636*cp326059 *PG25_Pis_GEN_25_2-3_1*OG908396

62.4

*OG899054 *OG89804662.8*cp675317 *cp49086765.0*TC7670067.2*PR10_unten73.7*CALTL82.3*OG904041 *cp679047*OG898075 *OG894357*OG922990 *OG896981

84.7

*cp322634 *cp322638*cp679524 *cp678616*cp678187

85.1

*OG900259 *OG916001*OG910388 *OG895846

85.9

*OG896936 *OG90005386.3*OG90650786.7*cp678950 *cp68238289.7*OG896495 *OG89606690.2*cp48960091.1*OG898887 *OG897003*OG910862

91.5

*cp327870 *cp327974*cp327881 *cp327936*cp327868

92.7

*M853_Mtmt_GEN_00853_01_196.7*DSI *TA4L-TA191R_291-28497.5*OG895877 *Gm2125123*cp676929

100.0

*cp327807 *OG908289*OG919460 *OG903969*cp680545

101.2

*cp678117 *cp678340*cp675768 *cp323461

102.9

*cp327623 *OG901549*OG896540 *OG900006

103.7

*cp678768104.5*cp677822 *cp675905*cp491458 *cp675277*cp350553 *cp491484

104.9

*cp676464 *cp327672105.3*cp327869 *ICCM0293106.5*STMS11107.2*GA24 *GAA47*LN5A

112.4

*REP113.6*M400_MtmtGEN400_07_1115.9*P32_PisPR32_1 *TA4L-TA199R-3_300118.1*RL3119.7*M12_MtmtGEN12_03_1 *OG895535123.5*OG919735 *LG99126.4*cp490593127.6*cp488743 *cp678437128.0*cp679062 *OG903593*OG896007

128.8

*ICCM0024129.2*cp326008131.4*cp327960 *OG895578132.0*OG897715 *OG901985*ICCM0003

132.5

*ICCM0004 *OG910718134.0*Ca12863169747399137.4*TA3L-TS62R137.8*TA130142.8*ICCM0063144.4*ICCM0249 *cp323738148.2*OG935579 *OG922957*OG899078 *OG922889

149.0

*OG906662162.9*OG913321164.4*CaM1529165.3*GA2173.1*M214_MtcaEST214_01-4185.4*M224_MtcaEST_224_02_1 *CaM0232192.7*OG896733197.7*OG902016 *OG901045*tk_515 *OG899516*OG908504

199.1

*CaESTSingleton16 *cp677080199.3*cp491502 *cp680494*cp350396 *cp681085*cp490330 *cp488869*ICCM0127

200.1

*CaM0480200.5*cp676824201.8*cp676868 *cp678296*CaM0436

202.2

*CaM1903 *H1H13*CaM0113 *H1G20*H1H15 *CaM1666*CaM2049 *CaM1637

202.6

*H1B17 *CaM0691204.3*OG900323204.6*CaM0446208.1*CaM0909208.8*OG903155 *OG895060*CaM0507 *CaM1502

210.2

*CaM0645210.6*CaM1551211.6*OG927609212.8*Gm2084815 *OG894171213.9*CaM1158214.3*ppPF214.7*TR20218.2*TA13 *TA146225.9*TA72 *TA2226.4*STMS26227.2*TA4R-TA191L229.5*TS72230.2*ISSR8401232.3*cp682025234.1*cp490406 *ICCM0068244.9*ISSR8902246.9*cp490039255.6*OG913370280.6*OG917721 *OG895229281.2*ICCM0212c281.6*OG897521 *OG903088*cp172089

284.2

*ps190_psatEST190_01_1 *cp679174*cp323966 *cp323611*ICCM0257

285.1

*OG895163289.5*OG946905 *LUP51_CAPS*CYSPR2

291.7

*OG902037292.7*cp678644294.3*cp172299294.7*cp350492 *cp488878*cp491565 *cp491143*cp489107 *cp489311*cp676816 *cp677363*OG896166

295.9

*STMS24296.5*TA46305.4*M477_MtmtGEN477_04-1307.3*M336_Mtmt_GEN_00336_11_1 *TC87270317.0*CDC2 *P124_PisPR124_2318.1*ISSR842319.1*M13_MtmtGEN13_07_1321.5*OG894099322.9*cp675523328.5*cp675919 *cp677611*cp350449 *OG897469

329.2

*OG899684334.7

6

*cp1721060.0*cp3260502.7*cp679337 *cp490088*cp490044

9.1

*AIGP *cp32668412.3*cp67866816.3*cp49079831.9*cp678833 *cp678909*cp677780

52.8

*cp326520 *cp327752*Ca14402 *cp325821*cp325845 *cp489478*Ca14402150174189 *OG901215*cp681450 *cp681910*OG895760

53.8

*cp68178554.2*ISSR868259.6*STMS862.5*OG89488067.5*OG90307967.9*cp675348 *cp67557168.3*OG90536368.7*cp489370 *OG916130*cp491408

69.5

*OG91837371.1*OG908250 *CaM012373.7*cp327997 *cp32769986.3*cp350618 *cp677599*cp681197 *cp324054*cp677621

94.4

*OG900269 *LG103*OG899751 *cp488668

104.5

*cp489795105.7*OG896702 *OG904656*OG895900 *OG894358*Gm2091985

107.8

*cp171271 *cp680797*cp172050 *cp172845

108.6

*OG894965109.4*cp491303 *cp491526110.6*OG899600 *P192_psatEST_192_02_1113.6*R3608-1117.8*CaM0881118.5*M3175_MtmtCON_3175_03_04_1 *M3244_MtmtEST3244_02_05_1*OG903928

122.3

*OG902476 *OG900987*CaM0880

134.8

*cp676716148.0*cp489464 *cp489069*cp489565

148.8

*cp490810 *cp490937*Ts35

150.0

*P110_PisPR110_1165.3*OG894669167.5*cp489257175.6*cp490515 *cp350038*cp679231 *cp491620*cp677260 *cp675429*OG895630 *OG903813

177.2

*cp680271177.6*cp678440 *cp676553*cp350039 *cp172924*ICCM0205 *cp680674

180.6

*cp681903 *OG898508181.4*OG903939 *cp677437*TC80362

182.2

*ICCM0120b182.6*cp678275186.6*cp679168 *OG913047*CaM0463 *cp327899*cp324146 *OG917719

187.3

*cp682536187.7*cp677049 *cp679041*cp491184 *OG906843

188.5

*cp489176 *cp682538*cp680662 *cp677055*cp491350 *cp350118*OG899130 *P106_1_PisPR106_1

188.9

*TA5L-TS38R-1_470 *OG918150*OG895545

193.2

*OG895816 *OG910676*OG902462 *OG896744*cp679202 *cp488779*cp350493

193.6

*cp682214 *cp678477*cp680535

198.9

*ICCM0120a209.7*RGA_C219.6*Ps198_psmtEST198_02_2223.8*cp172130 *cp172152*Tp6857294 *Mt133126

227.9

*cp350116 *cp350541228.3*cp324020 *cp327946*cp327739 *cp325842

229.1

*M3179_Mtmt_CON_03179_03-04-1230.7*M116_MtmtGEN116_02_1 *ps175_psatEST175_01_1233.4*cp677807234.5*OG925843 *OG927739234.7*OG915805 *TCMO234.9*cp491008 *cp489932*cp490282 *cp171274*cp680370 *cp172962*OG896285 *cp676692

235.3

*OG896967 *cp682554*cp490678

236.1

*OG900450 *OG894267236.5*CaM0258242.7*TA5248.8*TS43 *STMS19251.1*P93_PisPR93_1253.6*M50_MtmtGEN50_03_1 *BTF3b254.6*H2B202 *CaM0698256.7*H2L102 *H2J09*CaM1545 *H1H07*H1O01 *OG915278*OG897350 *OG895358*OG915293 *OG936005*OG896202 *OG895876*CaM0805 *OG900217*CaM1218

257.2

*H4H11 *CaM0740*CaM1228 *ICCM0123a

257.6

*cp327747258.0*ICCM0134259.6*TRPT261.5*RGA_B265.9*TS53 *TA179*TR59

266.9

*STMS7 *TA71267.6*TAASH268.8*TA39 *TR29271.4*ICCM0076 *OG903808*OG912629 *OG895467*OG903716 *ICCM0081

276.9

*ICCM0079 *cp323897*cp323608 *cp679996*cp678399 *cp327849

277.3

*cp172370 *H4F07*OG894043 *OG904027*OG907169

279.4

*cp350631 *cp491000280.6*cp490581 *cp490006*cp172234 *cp488709

283.0

*cp682445283.2*cp676840283.3*CaM1036 *cp489634*OG902902 *OG907096*OG894007 *OG897198*cp679277 *cp678520

284.1

*TA66R-TS68L-2_340 *TA5L-TS38R-2_450290.5*ISSR843295.5

7

*M992_MtmtGEN992_02-1 *MA225_MtcaESTA225_03_2*CYSS

0.0

*XP-Ca-29820.5*CYSK3.3*MSU894.9*S1E110.2*CStC110.8*ICCM007218.2*cp68075619.6*OG90206320.4*OG91958420.8*cp680255 *cp677086*cp490463

21.8

*OG895142 *OG92440524.5*cp678287 *cp678922*cp682300 *cp172945*cp681747 *cp677354

30.6

*OG91965531.0*OG904000 *OG89807831.4*ICCM0130a *cp679509*cp680549 *cp171561*cp172966 *cp677302*cp676753

34.5

*Ca22434 *OG89761935.7*OG90696936.1*OG90389838.2*cp489035 *cp173466*cp489222

39.4

*cp68164939.6*cp68192039.8*CaM078742.7*OG89823144.1*Ts4547.5*X60755 *U7148.8*FENR50.1*G6PD54.1*ACONc54.3*PGMb61.1*OG89569073.2*OG896172 *OG89587177.3*TA3R-TA23L82.2*OG901744 *OG901711112.9*Ca21567 *cp350602118.9*OG898271 *OG919502122.3*H1D24 *H1C092*CaM0539 *H5B04

125.2

8

Genetic map

Technology

intervention

Genetics

of trait Knowledge-based

breeding

Uses or develops genomic tools and technologies and evaluates

multidisciplinary approaches to better understand gene function

and interaction to improve knowledge of gene system across

crops for enabling knowledge-based breeding

Not technology driven;

Demand driven tech use

- Assembly of genomics and germplasm

resources

- Development of comparative maps and

framework genetic markers for target

crops

- Assignment of genes and pathways to

phenotypes

- Validation of genes and pathways

Four objectives

Large-scale molecular markers including SSR, SNP

and DArT markers for less-studied crops

Genetic maps with moderate marker density available

Cost-effective SNP genotyping platform i.e.

GoldenGate assays, KASPar assays for a number of

crops

Transcriptomic resources for chickpea, pigeonpea,

sweetpotato, cowpea, cassava

Physical maps for cassava, cowpea

Mutant collections in common bean, potatoes

Utilization of mutant collections in rice for function

analysis

Progress updates- i

Cloning of AltSB (SbMATE1) and Pup1 in sorghum and

rice and diagnostic markers

Molecular markers associated with traits of interest to

breeders in cowpea, chickpea

Gene expression analysis for drought tolerance in rice

Bioinformatic tools for comparative genomics

analysis

Gene expression analysis for selected transcription

factors in wheat for drought tolerance

Allele discovery for drought tolerance in sorghum and

rice

Bioinformatic tools for gene expression analysis

ISMU pipeline for analysis of NGS data…

Progress updates- ii

Comparative Genomics Challenge Initiative (PDC: Leon Kochian USDA/ARS & Cornell Uni)

• This CI takes advantage of previous GCP projects where two genes AltSB (SbMATE1) and Pup1 have either already been cloned.

Rice PUP1 Sorghum AltSB

Clone homologs

Clone homologs

Maize Sorghum Maize Rice

Verify role in P efficiency

Verify role in Al tolerance

P Efficient Maize

P Efficient Sorghum

Products for breeding programs in developing countries

Al Tolerant Maize

Al Tolerant Rice

Products for breeding programs in developing countries

Pyramid P Eff & Al Tol

• Rice: QTL mapping and GWAS for Al-tolerance (G7009.07, Susan McCouch);

cloning and characterization of Pup1 and dissemination of breeding linesto NARS partners (G7010.03.04, Sigrid Heuer)

• Maize: Cloning and characterization of Al-tolerance

(G7010.03.02, Claudia Guimaraes);

Cloning and characterization of Pup1 (G7010.03.01, Leon Kochian); breeding for Al-tolerance and P-efficiency (G7010.03.05, Sam Gudu)

• Sorghum: Cloning and characterization of P-efficiency (G7009.03, Jura Magalhaes)

breeding for Al-tolerance and P-efficiency (G7010.03.03, Eva Weltzein)

Comparative genomics RI

• Pup1 major tolerance gene is a constitutive enhancer of root growth

• Acts upstream of genes with key function in root growth and stress response

• Final set of Pup1 gene/allele specific markers available

• Development of Pup1-breeding lines by MABC completed

• First field data confirm beneficial effect of Pup1

• Seed increase ongoing at IRRI and ICABIOGRAD

• Mapping of Al-tolerance in rice is underway

Sigrid Heuer, IRRI

Genotyping and Phenotyping of

Sorghum Association Panel • Initially genotyped with Illumina 1536 SNP chip by M Hamblin

• Currently being genotyped by sequencing by Ed Buckler and

Sharon Mitchell as part of their NSF BREAD grant .

-Developed multiplexing approach to sequence multiple

samples in one lane of Illumina High-Seq.

- Developed a bioinformatics pipeline for SNP ID

- Hope to add 100,000 to 200,000 SNPs to each member of

association panel.

• Have phenotyped entire panel for Al tolerance – waiting for

genotyping to be completed to conduct GWAS on Al tolerance.

• Have phenotyped the IGD part of the panel (converted lines) for

P efficiency at Embrapa.

•Will soon phenotype panel for P efficiency and root architecture in

low P soils in greenhosse at Cornell

Leon Kochian, USDA/ARS & Cornell Uni

GWAS of Rice 3D Root Architecture Traits

• Have completed phenotyping rice for 3-D RSA traits under control conditions in gel-based media. Phenotyped the McCouch’s NSF-TV rice diversity panel (500 lines) and also bi-parental mapping population (168 lines).

• That involved phenotyping approximately 2000 individual plants in gellan gum cylinders.

• Roots imaged at 3, 6, 9, & 12 days after planting to include dynamic growth parameters. • Randy is in Taiwan for the summer where he as nearly completes 3D reconstructions and quantification of his 20 RSA traits. • GWAS analysis will be completed in Fall with 950k SNP chip.

Leon Kochian, USDA/ARS & Cornell Uni

Breeding value of AltSB

0.00

1.00

2.00

3.00

Control (-Al) TT tt

Yie

ld (

ton

s/h

a)

Allelic substitution effect:

100 RILs BR007 x SC283

r=0.28 (P=0.0047):

nutrient sol. vs. field

Drought x Al

tt TT 0.5 - 1 ton/ha

Chr 3

Map position (cM)

-lo

g1

0(p

)

0 50 100 150 200 250

02

46

810

12 Gy

Gy_floRnrg

AltSB

• Background SNP markers • Association pipeline for Al tolerance • Assessment of AltSB on acid soils (grain yield advantage)

Jura Magalhaes, EMBRAPA

Establish network for genomics community for

enhanced discussions in the area of

development and application of genomic tools

Develop user friendly portal that will present

information on tools, resources developed by

GCP or available in public domain to offer one-

stop shop solution to the breeding community

Broker-access to economically priced

genotyping and sequencing services

Agricultural Genomics Network

(AGN)

Consensus:

AGN is a GREAT initiative, it would encourage new

breeders also to have access and provide all help to

implement molecular breeding.

AGN will keep the existing GCP community vibrant and

active in post-GCP era!

Markers of choice for breeding applications:

SNPs (also SSRs in some cases!)

Genotyping through outsourcing is preferred and

accepted solution by NARS breeders

Discussions on AGN

Suggestions:

A broader survey about requirements of tools,

resources on portals may be conducted

Some basic information about molecular breeding

together with tutorials may be kept on portal

Helpdesk to respond on genomics related questions in

time is URGENTLY required.

Portal can be in wiki style

Sustainability is an important issue in post-GCP era.

Discussions on AGN

Comparative genomics

vs

species specific genomics research

Excellent for understanding the genome

evolution, gene function and trait mechanism

Applied aspects- few examples?

Cloning of one gene in one species- how useful

this is for the other species? Pup1 and Al-

tolerance in cereals?

Development of diploid genome physical map

for applications in 4x groundnuts?

Species specific genomic resource

development is no more an expensive and time

consuming task?

Challenges/ Opportunities

Data management and sharing (continuous discussions)

Analysis of large scale datasets especially NGS data

(working with international players/Theme 3)

Outsourcing vs. in-house work to generate data in cost-

effective and timely fashion (BGI collaboration)

Conversion of genomics research platform in breeding

application platforms (KASar assays in collaboration

with Theme 2/ IBP)

Capacity building – an important component of

Genomics Integrated Breeding Services

Utilization of developed genomic resources

Assemble large scale informative SNPs for breeding

applications

Accelerated activities of Comparative Genomics CI

towards identifying diagnostic markers for Al-tolerance

and P-uptake in targeted cereals

Publication of large scale datasets

Engage CGIAR community by implementing AGN under

GIBS

Perspectives

Thank you !