Post on 25-Dec-2014
description
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 !