This document appears to be a list of genes or genetic markers from the Medicago truncatula genome arranged in order with their physical position on chromosomes indicated in the left column. There are over 500 entries included in the list with various identifiers like "cp", "OG", "CaM", and others potentially representing different genes or markers. The document provides a dense listing of genetic data from M. truncatula but does not include any additional context or explanation.

1. Theme 1:
Comparative and
Applied Genomics (CAG)
Rajeev Varshney
Theme Leader, GCP

2. QTL
*cp488892 *cp491181
*cp678132 *cp680434
*cp681425
0.0
*OG905182 *OG9054747.8
*OG938507 *OG927619
*CaESTContig3 *OG9010158.1
*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 *cp49117389.4
*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
*AJ005043105.6
*OG905379 *AGL112
*CaM0486106.0
*Gm2120918 *cp681088
*OG897579106.4
*CaM1451 *OG913108106.8
*OG901047 *OG908473107.6
*OG900394108.9
*OG912303 *cp490301111.1
*H1G16120.4
*TR43 *TA1
*TA8126.2
*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 *OG905290183.8
*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
*OG912880191.5
*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
*OG901542273.9
*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 *OG8976944.8
*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
*OG89574717.7
*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 *cp490237175.8
*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 *cp35057373.2
*cp680528 *cp488664
*cp48941574.9
*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 *cp679761136.5
*cp678637140.5
*CaM1377140.9
*OG907934 *OG902560
*OG901197141.9
*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
*CaM0677170.8
*ICCM0191171.1
*CaM0743179.3
*OG899728180.2
*OG899657180.9
*OG900222 *OG946804185.9
*OG906599 *OG895029
*OG922092 *OG896103194.2
*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 *cp682104201.3
*OG898533201.7
*cp679791 *H3B08
*H5A04204.3
*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 *TA176227.7
*TA4L-TA199R-1_345 *TA3R-TS71L-1_95229.4
*XP-Ca-42461 *M367_MtmtGEN367_05_1
*TC88598230.1
*M51_MtmtGEN51_02_1230.6
*TRAL236.3
*CaM0594251.5
*ICCM0284a260.4
*CaM0464264.9
*CaM1101272.4
*TC78756294.1
*M24_MtmtGEN24_04_1309.9
*cp676639 *cp172996
*cp680216313.4
*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 *cp325151342.4
*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
*cp49010186.9
*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
*APAR5198.2
*PGMa200.2
*PGD6200.7
*C33202.1
*ISSR8903203.7
*TC88726208.9
*MSU380 *AJ291816
*TC88512209.3
*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 *Ca21249295.2
*cp676386 *cp676452
*cp682642296.5
*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
*cp173167307.3
*cp682494308.8
*P69_PisPR69_1316.9
*TC86212324.4
*ENOL325.9
*ICCM0045 *TA120R-TS19L-1_510
*APF4.3327.6
*CaM0799 *OG901858
*OG896979329.4
*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
*OG902798354.1
*cp491267 *cp171590
*cp172237 *cp681358354.5
*cp681608356.6
*OG910860357.8
*cp491231 *cp682291
*cp682299 *cp322975358.2
*OG901928360.7
*cp488624 *cp677322
*OG960456 *cp488939361.1
*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 *cp677907103.5
*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_1115.5
*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
*OG918556157.4
*EST671161.2
*cp488703 *cp677011163.9
*cp491099 *cp489427
*cp489903166.3
*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 *cp676498289.7
*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
*TAA59300.1
*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
*cp32385033.3
*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
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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

3. - 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

4.  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

5.  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

6. 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

7. • 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

8. • 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

9. 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

10. 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

11. Breeding value of AltSB
0.00
1.00
2.00
3.00
Control (-Al) TT tt
Yield(tons/ha)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)
-log10(p)
0 50 100 150 200 250
024681012
Gy
Gy_flo
Rnrg
Alt
SB
• Background SNP markers
• Association pipeline for Al
tolerance
• Assessment of AltSB on
acid soils (grain yield
advantage)
Jura Magalhaes, EMBRAPA

12.  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)

13. 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

14. 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

15. 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?

16. 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

17.  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 !