Terminal drought is one of the major limitations to chickpea production, which results up to 50% of yield losses. Based on extensive genotyping and phenotyping data on ICC 4958 × ICC 1882 recombinant inbred line (RIL) population, a genomic region (~35cM) harbouring several QTLs for drought tolerance related traits was identified on linkage group 04 (LG 04). This region contained only four markers (TAA170, ICCM0249, STMS11 and GA24). 8 Jan 2013

1. Financial support from Generation Challenge program (GCP), Australia-India Strategic Research Fund (AISRF)
and technical assistance from M Aziz and Vinay kumar are greatly appreciated.
Using GBS approach, 828 SNP markers were identified. A high density genetic map of 1031 loci which is 723.64cM
in length with the average marker interval of 126 and average inter loci distance is 0.71cM has developed. The QTL region (~35cM)
has narrow down to ~14cM. This will be further reduced for the candidate gene identification and QTL cloning.
Terminal drought is one of the major limitations to chickpea production, which results up to 50% of yield losses. Based on
extensive genotyping and phenotyping data on ICC 4958 × ICC 1882 recombinant inbred line (RIL) population, a genomic region (~35cM)
harbouring several QTLs for drought tolerance related traits was identified on linkage group 04 (LG 04). This region contained only four
markers (TAA170, ICCM0249, STMS11 and GA24). Recently six markers were mapped in this region using targeted marker development and
medicago – chickpea synteny approach. For enhancing the marker density in this region genotyping by sequencing (GBS) approach was
used. In this context, GBS approach (with Apek I enzyme) with the coverage of 5x and 0.2x were employed on parental lines and 232 RILs
respectively. By using stringent criteria genotyping data was assembled for 828 SNPs on the population. A comprehensive genetic map
was developed comprising a total of 1,013 marker loci (including 746 SNPs), spanning a distance of 723.64 cM. By using GBS approach 49
SNP markers were integrated on to the QTL region. As a result, the QTL interval is reduced from 35 cM to 14 cM. Thus fine mapping of this
region will help in enhancing drought tolerance in chickpea through MAS, identification of candidate genes and map-based cloning.
Abstract
Towards fine mapping of drought tolerance related QTL
region in chickpea using genotyping-by-sequencing
(GBS) approach
Deepa Jaganathan1, Mahendar Thudi1, Sarwar Azam1, Pooran Gaur1, Henry Nguyen2,
Tim Sutton3, Rajeev Varshney1,4*
1International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India
2University of Missouri, Columbia, USA
3Australian Centre for Plant Functional Genomics Pty , Adelaide, Australia
4Generation Challenge Programme (GCP), c/o CIMMYT, Mexico DF, Mexico
*Corresponding author : r.k.varshney@cgiar.org
Acknowledgements
SNP discovery through GBS
Enrichment of QTL hot spot region with SNP markers
Summary
Approaches for fine mapping
Synteny based marker
development
Targeted marker
development
43 markers selected
from published
chickpea genetic maps
Three approaches were adopted for fine mapping
1.Targeted marker development
2. Synteny based marker development
3. Marker development through Genotyping-by-Sequencing (GBS)
 A set of 208 RILs were used for restriction site associated DNA (RAD)
sequencing along with the parental lines ICC 4958 and ICC 1882
High density genetic map of chickpea (ICC 4958 ×ICC 1882)
49 SNP markers (in red) integrated in QTL region through GBS approach
19 polymorphic SSR markers and 3 CAPS were
used for integration into genetic map
LG01 LG02 LG03 LG06ALG04A LG07 LG08
LG06B
LG04B
NCPGR23654.4
TR2054.6
NCPGR23154.8
NCPGR3055.5
H4G1156.0
H1A1956.5
Ca4_1592593658.8
CaM190359.0
Ca4_1594238859.3
Ca4_1565180459.4
Ca4_1627860059.7
Ca4_1593490159.8
TR860.2
Ca4_1627867160.3
Ca4_1593460760.7
Ca4_1592616061.1
Ca4_1595707061.2
Ca4_16149998 Ca4_1604692861.3
ICCM024964.5
ICCM006566.3
Ca4_1255854167.7
Ca4_1372466668.5
Ca4_13588956 Ca4_1369966368.7
Ca4_13840484 Ca4_1384025168.8
Ca4_1127622569.5
Ca4_1139888969.6
NCPGR12769.8
Ca4_11276413 Ca4_1123413070.0
Ca4_11441735 Ca4_11435380 Ca4_1143565170.1
Ca4_11343257 Ca4_11343230 Ca4_11547141
Ca4_11246164 Ca4_11398699 Ca4_11334350
Ca4_11246093 Ca4_11273405
70.2
Ca4_11398682 Ca4_11517582 Ca4_11246173
Ca4_11517517 Ca4_11277574 Ca4_11491864
Ca4_11273328 Ca4_11490100 Ca4_11334343
Ca4_11490496 Ca4_11274281 Ca4_11244334
Ca4_11244395 Ca4_11276484 Ca4_11275171
Ca4_11465075
70.3
Ca4_11465057 Ca4_11441604 Ca4_1144167370.4
Ca4_1298242072.4
Ca4_13787649 Ca4_1378744872.8
Ca4_1384134072.9
Ca4_1384022773.0
Ca4_1383879673.1
Ca4_13839288 Ca4_13839294 Ca4_1368745673.2
TAA17077.4
NCPGR2178.3
STMS1178.8
cpPb-68055279.6
CaM061582.6
CaM084583.8
CaM085684.0
Tp68496486.3
TA640.0
CaM061519.3
NCPGR12127.8
H1H1336.3
H1N1240.2
H2I0145.2
TA7851.7
CISR11754.6
STMS956.8
CaM064560.3
CaM050761.3
NCPGR2762.2
NCPGR762.5
ICCM006962.6
ICCM006862.7
ICCM025063.0
H1B1763.3
NCPGR24563.8
TR2064.5
NCPGR23165.2
H1A1965.7
H4G1165.9
TA1866.7
NCPGR23667.1
CaM090668.2
H1A1272.0
CaM204973.6
TA4676.9
ICCM024978.8
ICCM025783.8
NCPGR12788.1
TAA17094.2
NCPGR2197.3
CpPb-680552102.8
CpPb-490776CpPb-678284105.4
GA24108.2
STMS11111.2
CaM0446123.4
Tp684964131.7
NCPGR91148.3
ICCM0249
STMS11
14 cM
Chromosome No of SNPs
identified
Markers
mapped
Chromosome/ pseudo molecule1 84 77
Chromosome/ pseudo molecule2 80 69
Chromosome/ pseudo molecule3 45 39
Chromosome/ pseudo molecule4 292 290
Chromosome/ pseudo molecule5 10 9
Chromosome/pseudo molecule6 127 122
Chromosome1/pseudo molecule7 78 33
Chromosome/ pseudo molecule8 48 46
Chromosome 0 64 61
Total 828 746
Readsinmillion
1.0
0.5
2.0
1.5
2.5
ICCeM00480.0
ICCM01203.1
Ca1_330955919.4
Ca1_3309557710.0
Ca1_1166979410.1
TA3010.9
Ca1_1401575714.4
Ca1_1233744515.0
Ca1_1596527826.8
Ca1_1637925828.8
TS7129.2
ICCM029732.0
TA134.6
TA30s34.9
CaM069435.3
Ca1_19572408Ca1_1957249437.6
Ca1_4033906538.3
Ca1_40366866Ca1_40366858
Ca1_40366862
38.5
Ca1_40358747Ca1_27745471
Ca1_37690465
38.7
Ca1_40358693Ca1_38877670
Ca1_39436291Ca1_37722095
Ca1_37722143
38.8
Ca1_37880995Ca1_40346280
Ca1_30232233Ca1_30262124
Ca1_28082758Ca1_40190230
Ca1_34727251
38.9
Ca1_40343216Ca1_34272001
Ca1_40190093Ca1_31393408
Ca1_34161921Ca1_26129961
Ca1_40367940
39.0
Ca1_32686814Ca1_3966343239.1
Ca1_3845158839.2
CaM010240.6
CaM170241.6
CaM040341.8
CaM001541.9
CaM174242.1
CaM004642.2
NCPGR26342.9
NCPGR13643.5
Ca1_1655275144.3
CaM014445.3
H2A0848.2
CaM039349.9
Ca1_654003564.5
Ca1_654001364.7
Ca1_632981465.0
Ca1_6390541Ca1_643392565.6
Ca1_6491008Ca1_649101765.8
Ca1_6512349Ca1_6478736
Ca1_6486446
65.9
Ca1_6470708Ca1_6521670
Ca1_6521673Ca1_6553107
66.0
Ca1_652185666.1
Ca1_652185966.2
cpPb68210671.3
cpPb679216cpPb679915
cpPb677690
71.4
Ca1_524986874.8
Ca1_418933376.6
Ca1_509360777.6
Ca1_280760480.4
Ca1_288581781.0
Ca1_285592781.3
Ca1_285600381.4
Ca1_304763481.8
Ca1_1859914Ca1_1858608
Ca1_1858509Ca1_1858600
83.0
Ca1_186183783.1
Ca1_2002844Ca1_1987101
Ca1_1987366
83.3
Ca1_1986964Ca1_197363283.5
cpPb-171485cpPb-49096287.8
cpPb-677798cpPb-679323
cpPb-677672cpPb-677038
87.9
ICCM0009aICCM0009b91.1
Ca1_109887492.3
Ca1_109870392.4
Ca1_1083388Ca1_108340392.7
NCPGR184101.3
CaM08610.0
CaM029320.5
H2B06123.6
TA20024.3
TA11027.2
TA20629.8
TA3731.5
TA9634.0
H1P092 TA2734.7
H1H01134.8
ICCM008235.2
ICCM024735.9
CaM014236.6
TAA19437.6
Ca2_32629763 Ca2_32481983
Ca2_32415809 Ca2_32416166
47.2
Ca2_32058591 Ca2_32061054
Ca2_32545320
47.4
Ca2_3206105347.5
Ca2_3200353647.6
Ca2_32351839 Ca2_32140939
Ca2_32140948
47.7
Ca2_31428279 Ca2_3142813247.8
Ca2_31428405 Ca2_31908857
Ca2_31908845
47.9
Ca2_30921092 Ca2_31109358
Ca2_31109311 Ca2_31188355
Ca2_31109436 Ca2_31201859
Ca2_30951724 Ca2_31109435
Ca2_30880243 Ca2_31201872
Ca2_30954317 Ca2_31005845
Ca2_30880246 Ca2_31005847
Ca2_30954305 Ca2_31005670
48.2
Ca2_30925784 Ca2_31203154
Ca2_30925755
48.3
Ca2_3108877848.4
Ca2_31427902 Ca2_3142802448.5
Ca2_3142842948.6
Ca2_32129272 Ca2_3190869448.7
Ca2_3235182148.9
Ca2_32119331 Ca2_3211926849.0
scaffold80_41266950.5
CISR251.4
cpPb-48931852.0
NCPGR14457.1
Ca2_3544118060.0
Ca2_3567047861.9
Ca2_35709129 Ca2_3567326262.1
Ca2_35593797 Ca2_35593824
Ca2_35593827 Ca2_35612587
Ca2_35612895 Ca2_35759932
Ca2_35754287 Ca2_35754350
Ca2_35754617 Ca2_35612644
Ca2_35759940 Ca2_35754557
Ca2_35759981
62.3
Ca2_35709004 Ca2_3570903262.4
Ca2_35676127 Ca2_3567616062.5
Ca2_35704069 Ca2_3570401862.6
Ca2_3565853762.7
GA1667.7
GA2092.2
TR20.0
TS58s2.4
STMS143.3
CaM03913.9
CaM19054.2
CaM05204.4
ICCeM0507.8
TA69.7
CaM10899.8
TS17X10.4
H3F0810.8
ICCeM005911.2
TA7811.5
TR5612.0
CaM005112.5
GA11913.8
NCPGR17314.0
Ca3_361755514.5
Ca3_922387514.6
Ca3_625824014.8
CaM197315.0
scaffold9_3224915.2
scaffold8210_145115.3
NCPGR10015.5
NCPGR4915.9
CaM183516.5
CaM218116.6
CaM130616.7
TA34 H2I0116.9
CaM032617.0
CaM000317.1
CaM041017.2
CaM012017.4
CaM1843 CaM071317.6
CaM015717.8
CaM102417.9
ICCM016018.3
CaM020418.5
CaM176519.0
NCPGR27319.3
NCPGR27819.7
CaM185120.3
NCPGR25520.8
scaffold420_4337221.4
NCPGR26822.7
CaM203123.8
CaM123225.1
CaM156825.5
H3C0627.0
NCPGR1027.8
CaM198831.4
Ca3_2514524732.4
CaM137632.7
CaM099836.2
Ca3_2701087537.5
Ca3_2789084941.1
Ca3_2993250446.3
Ca3_3083728447.6
Ca3_31478882 Ca3_3152114249.2
Ca3_31521155 Ca3_31631534
Ca3_31268143 Ca3_31631561
Ca3_31321725 Ca3_31520190
Ca3_31321778 Ca3_31520119
Ca3_31520198 Ca3_31520225
Ca3_31321850 Ca3_31431216
Ca3_31630195
49.3
Ca3_31341335 Ca3_31279605
Ca3_31279606 Ca3_31279616
Ca3_31302060 Ca3_31516662
Ca3_31516766 Ca3_31517201
Ca3_31517136
49.4
Ca3_3161882949.6
Ca3_3126803853.5
Ca3_3449698255.8
TA6456.7
Ca3_36447364 Ca3_36447520
Ca3_36447525 Ca3_3644727469.1
cpPb6823280.0
H3A078.6
NCPGR2289.3
NCPGR4010.7
TAA13712.0
H2L10213.3
TA11613.5
TA4214.0
CaM003814.4
CaM063915.7
CaM080515.9
CaM043616.0
NCPGR23316.6
TA516.8
ICCM0202 H4H02
H2J0916.9
CaM122817.1
CaM209817.3
CaM202617.9
NCPGR10518.8
CaM084819.2
NCPGR17620.1
TR1820.4
H1H0722.4
TR2923.5
CaM215824.9
NCPGR18930.9
NCPGR25435.4
Ca5_4550137935.9
Ca5_38092606 Ca5_38064661
Ca5_38064631 Ca5_38110219
Ca5_38018552 Ca5_38018558
Ca5_38080349 Ca5_38062576
45.3
CaM127859.4
H4H060.0
NCPGR874.2
CaM05005.2
H6G106.1
H1F217.1
CaM11258.3
NCPGR20310.9
NCPGR13911.6
ICCM010412.0
ICCM024212.1
H5A0412.3
CaM153013.0
CaM075313.7
CaM1431 CaM089913.9
CaM182614.2
CaM042114.7
CaM063615.3
CaM179016.2
TR717.1
ICCeM0051 ICCeM05117.7
scaffold96_27773519.0
Ca6_4955294619.5
scaffold134_22331819.9
CaM038921.2
TA12023.4
Ca6_2220809328.6
CaM176028.8
Ca6_2222289828.9
Ca6_2225214929.3
cpPb-48918733.0
NCPGR10735.3
Ca6_5415615836.5
NCPGR20037.2
Ca6_2670321537.6
STMS238.9
NCPGR9339.8
Ca6_1802739143.6
TA1445.2
Ca6_1712957446.0
Ca6_1709621446.4
Ca6_5798665849.1
Ca6_5798670049.2
Ca6_5794858749.5
Ca6_1334001251.4
Ca6_1362538851.6
Ca6_1372964951.7
Ca6_1362229251.8
Ca6_1359159052.0
Ca6_1341384852.1
Ca6_13827484 Ca6_1382745252.2
NCPGR20254.6
Ca6_5890802456.8
Ca6_10670368 Ca6_10215262
Ca6_10670582 Ca6_10682221
Ca6_10671444 Ca6_10671458
Ca6_10670482 Ca6_10677469
Ca6_10677501
58.5
Ca6_10259614 Ca6_10456774
Ca6_10588030 Ca6_1026027458.6
Ca6_10495747 Ca6_10231092
Ca6_10231095 Ca6_1045685458.7
Ca6_10567518 Ca6_10613546
Ca6_10442148 Ca6_10445274
Ca6_10574535 Ca6_10192017
58.8
Ca6_10192015 Ca6_10192247
Ca6_1019229658.9
Ca6_10670773 Ca6_1015197359.0
Ca6_9872988 Ca6_1015885059.2
Ca6_1001365159.3
Ca6_10111488 Ca6_10116608
Ca6_983372559.4
Ca6_10088984 Ca6_10100863
Ca6_1004564459.5
Ca6_10020177 Ca6_1002018759.6
Ca6_817017065.9
Ca6_809105066.0
Ca6_816631766.1
Ca6_816633966.2
Ca6_8052987 Ca6_817981566.3
Ca6_7929647 Ca6_809073966.4
Ca6_7829627 Ca6_8094879
Ca6_799473266.5
Ca6_7851000 Ca6_7835738
Ca6_808180066.6
Ca6_7852481 Ca6_7939281
Ca6_7834895 Ca6_7834922
Ca6_7939465
66.7
Ca6_7554101 Ca6_7554094
Ca6_7600817 Ca6_7929607
Ca6_7929628
66.8
Ca6_7667328 Ca6_7667301
Ca6_7929263 Ca6_7661924
Ca6_7661930 Ca6_7829485
Ca6_7834595 Ca6_7835427
Ca6_7647907 Ca6_7647931
66.9
Ca6_8070427 Ca6_7832023
Ca6_7832029 Ca6_7831899
Ca6_7831874
67.0
Ca6_7744730 Ca6_7835984
Ca6_758272667.1
Ca6_7747254 Ca6_813438167.2
Ca6_7581799 Ca6_758195667.3
Ca6_802922667.4
Ca6_757179267.5
Ca6_687135069.7
NCPGR470.2
TA10677.0
Ca6_499487677.8
H1I1682.1
Ca6_2540711 Ca6_254103286.4
Ca6_2541088 Ca6_2540749
Ca6_2542942 Ca6_2542981
Ca6_2543062 Ca6_2543096
86.5
Ca6_254999186.6
Ca6_252776886.7
Ca6_221417888.3
GA2689.3
Ca6_15893894.9
CaM0399104.4
CaM21870.0
CaM05396.5
ICCeM00549.5
H3C1112.8
TS5715.1
Ca8_1602243215.8
Ca8_16028064
Ca8_1602806216.0
TR517.4
TA318.4
TA2518.7
TA12719.2
CaM127420.3
CaM139920.4
H5B04H3E05220.5
NCPGR26420.6
NCPGR20920.8
H1H1421.4
Ca8_1165656223.2
Ca8_1265545423.4
Ca8_1140380523.6
Ca8_11087250
Ca8_1106709623.7
Ca8_1108714323.8
Ca8_1110288423.9
Ca8_1106664424.0
Ca8_1048646125.7
scaffold1219_8501526.1
NCPGR8927.6
NCPGR14628.1
NCPGR11828.4
NCPGR17028.6
Ca8_915172232.8
Ca8_910011133.0
Ca8_9097297
Ca8_909730033.1
Ca8_909758533.2
Ca8_890434633.4
Ca8_885360233.5
Ca8_827050335.3
CaM191837.7
CaM008140.3
CaM081248.4
Ca8_461762356.1
NCPGR16457.2
Ca8_410664458.9
Ca8_305045264.6
CISR8072.4
Ca8_71497478.0
Ca8_706614
Ca8_709094
Ca8_701837
Ca8_701803
Ca8_706793
Ca8_706514
78.1
Ca8_116920781.5
NCPGR4888.6
CaM21310.0
NCPGR196.6
Ca7_30060299 Ca7_30004767
Ca7_30026039 Ca7_30026017
Ca7_30029820
12.1
Ca7_3119247414.9
Ca7_1239077418.8
Ca7_3287579925.2
Ca7_3302615025.5
Ca7_3336432927.3
Ca7_33461168 Ca7_3346091827.5
Ca7_3346330027.6
Ca7_3338072027.7
Ca7_33267485 Ca7_33267496
Ca7_3336435427.8
Ca7_3341174627.9
cpPb-49087429.0
CISR11729.9
Ca7_1447054930.7
ICCeM001832.4
Ca7_34277010 Ca7_3427701432.9
Ca7_33867334 Ca7_3386814833.0
Ca7_3386767433.1
STMS1234.6
Ca7_4648593435.2
Ca7_4142504935.3
Ca7_38283909 Ca7_35274680
Ca7_35274828 Ca7_3534227135.4
Ca7_35274859 Ca7_3527485835.5
Ca7_2505801335.6
TA18037.0
ICCM16037.4
NCPGR9937.6
CaM011137.9
H1O1238.4
CaM059838.6
CaM215538.8
CaM044339.0
CaM194239.3
CaM146940.1
STMS2542.8
ICCM197a44.1
CaM156746.2
ICCM0199c ICCM199c48.1
NCPGR17152.7
NCPGR14153.3
CaM141754.4
CaM204162.9
TA14263.0
TR2482.3
NCPGR1296.6
Ca4_482691380.0
Ca4_48263603 Ca4_48275016 Ca4_483225020.4
Ca4_48228061 Ca4_482281100.5
Ca4_48355358 Ca4_48355468 Ca4_48498331
Ca4_48498334 Ca4_48501662 Ca4_48465107
Ca4_48467653 Ca4_48498181 Ca4_48485263
Ca4_48478018 Ca4_48478303 Ca4_48475461
0.6
Ca4_48345604 Ca4_483456080.8
Ca4_484578761.1
Ca4_4759245510.0
cpPb-490776 cpPb-678284 GA13712.9
Ca4_3757657813.6
Ca4_4661306815.4
CaM082123.7
ICCM025725.1
Ca4_4522506326.2
Ca4_4503558927.4
Ca4_4501976427.8
Ca4_4497910827.9
Ca4_44590678 Ca4_4459065230.1
Ca4_4459069730.4
Ca4_3534641735.8
ICCeM005837.3
Ca4_4169838238.2
Ca4_4103259940.8
Ca4_4094128341.1
Ca4_41032590 Ca4_41032564 Ca4_4079506041.2
Ca4_4072321241.3
Ca4_41142290 Ca4_40723208 Ca4_41142288
Ca4_41142299 Ca4_40807053 Ca4_40839967
Ca4_40839949
41.4
Ca4_40795085 Ca4_4080699541.6
Ca4_41144277 Ca4_4035718241.7
Ca4_4109455441.8
Ca4_4073476541.9
Ca4_40668451 Ca4_40668481 Ca4_4066848742.1
Ca4_4059753442.3
Ca4_40203462 Ca4_40203399 Ca4_40203432
Ca4_40429386 Ca4_40267713 Ca4_4042932842.4
Ca4_4018570242.5
Ca4_41145875 Ca4_4015436142.6
Ca4_40368765 Ca4_4006203142.8
Ca4_4006223342.9
Ca4_4005988043.1
Ca4_3971960644.0
Ca4_3745359044.4
Ca4_24261779 Ca4_38370926 Ca4_3837094144.8
Ca4_3892968144.9
Ca4_39081951 Ca4_39086269 Ca4_39086017
Ca4_39031823 Ca4_3904293845.0
Ca4_38215267 Ca4_3883142745.1
Ca4_38659377 Ca4_38179583 Ca4_38420093
Ca4_38157210 Ca4_38153183 Ca4_38153198
Ca4_38194220 Ca4_38918430 Ca4_38153216
Ca4_38181292
45.2
Ca4_38194159 Ca4_38834383 Ca4_38918394
Ca4_38918424 Ca4_38918628 Ca4_38834423
Ca4_38834431 Ca4_38362132 Ca4_38475310
Ca4_38425720 Ca4_38289066 Ca4_38343633
Ca4_38288823 Ca4_38288997 Ca4_38289052
Ca4_38770348 Ca4_38405153 Ca4_38770450
Ca4_38540247 Ca4_38770510 Ca4_38540201
Ca4_38358067 Ca4_38770606 Ca4_38834405
Ca4_38358398 Ca4_38475547 Ca4_38370848
Ca4_38370902 Ca4_38833304
45.3
Ca4_3875964045.4
Ca4_38039251 scaffold40_1053215
Ca4_38039046 Ca4_38039076 Ca4_38039088
scaffold40_1049594 scaffold40_1050164
45.5
Ca4_37364980 scaffold40_1052983
Ca4_38918547 Ca4_38029208 Ca4_38029215
Ca4_38029358 Ca4_38029380 scaffold40_968798
Ca4_38039289 Ca4_37550122 Ca4_37286632
Ca4_38029136 Ca4_37633044
45.6
Ca4_37454296 scaffold40_871346 Ca4_38008062
Ca4_38008227 Ca4_38008082 Ca4_37576730
Ca4_37897351 Ca4_37897261 scaffold306_19215
Ca4_38008205 scaffold40_911602 Ca4_37349212
Ca4_37630404 scaffold40_1053247
Ca4_37630445 Ca4_43319846 Ca4_37630527
Ca4_43324547 Ca4_38038959 Ca4_37450294
Ca4_37450326 Ca4_37450206 scaffold157_100364
Ca4_37316738
45.7
Ca4_38833415 Ca4_37293773 Ca4_38833333
Ca4_3646798045.8
scaffold157_106331 scaffold2763_49700 Ca4_30300334
Ca4_35231891 scaffold157_325857 scaffold953_42329
Ca4_36979879 Ca4_36844149
45.9
scaffold2763_104549 Ca4_36979926 Ca4_30599188
scaffold38_520311 scaffold2763_108763 Ca4_36468053
Ca4_36468003 Ca4_35171719 scaffold2763_49533
Ca4_30260485 Ca4_35171506 scaffold157_100529
scaffold2763_107486 scaffold2763_107488 Ca4_26002991
scaffold157_142843 Ca4_30258484 scaffold157_352747
scaffold157_352712 Ca4_30153505 Ca4_29958113
scaffold157_100228 Ca4_29958122
46.0
Ca4_29923380 Ca4_36639382 Ca4_36955706
Ca4_31218647 Ca4_36984795 Ca4_36984727
scaffold2763_107033 scaffold2763_107087 scaffold2763_106920
scaffold2763_106936 scaffold2763_106974 scaffold598_161754
Ca4_24857501 scaffold2763_107376 scaffold2763_107437
scaffold2763_100874 scaffold2763_100928 scaffold2763_107180
scaffold2763_82342 scaffold2763_82369 scaffold2763_101084
scaffold2763_125716 Ca4_30668893 Ca4_29671606
Ca4_35311815 scaffold1128_341416 Ca4_35229966
scaffold2763_82319 scaffold2763_82328 scaffold2763_99364
scaffold1448_74434 scaffold1448_74436 Ca4_22865390
46.1
Ca4_22865436 Ca4_29323082 Ca4_36709731
Ca4_22904152 Ca4_37806689 Ca4_22904166
Ca4_36673677 scaffold290_824993
46.2
Ca4_34916032 Ca4_35393643 scaffold157_355222
Ca4_36977194 scaffold157_213477 scaffold157_213487
scaffold157_213404
46.3
Ca4_3491598646.4
Ca4_38976822 Ca4_3897683546.5
Ca4_22908360 Ca4_3745358646.6
Ca4_3757563647.4
Ca4_2016160150.2
CaM209350.4
CaM050750.6
cpPb-49040650.7
CaM132850.8
Ca4_1822372150.9
cpPb-67686851.0
TA13251.1
cpPb-68202551.3
ICCM006951.5
NCPGR2751.7
ICCM006852.0
NCPGR752.2
ICCM025052.4
H1B1752.6
cpPb-32292152.7
NCPGR3153.2
CaM092353.5
CaM168454.0
NCPGR23654.4
TR2054.6
NCPGR23154.8
NCPGR3055.5
H4G1156.0
H1A1956.5
Ca4_1592593658.8
CaM190359.0
Ca4_1594238859.3
Ca4_1565180459.4
Ca4_1627860059.7
Ca4_1593490159.8
TR860.2
Ca4_1627867160.3
Ca4_1593460760.7
Ca4_1592616061.1
Ca4_1595707061.2
Ca4_16149998 Ca4_1604692861.3
ICCM024964.5
ICCM006566.3
Ca4_1255854167.7
Ca4_1372466668.5
Ca4_13588956 Ca4_1369966368.7
Ca4_13840484 Ca4_1384025168.8
Ca4_1127622569.5
Ca4_1139888969.6
NCPGR12769.8
Ca4_11276413 Ca4_1123413070.0
Ca4_11441735 Ca4_11435380 Ca4_1143565170.1
Ca4_11343257 Ca4_11343230 Ca4_11547141
Ca4_11246164 Ca4_11398699 Ca4_11334350
Ca4_11246093 Ca4_11273405
70.2
Ca4_11398682 Ca4_11517582 Ca4_11246173
Ca4_11517517 Ca4_11277574 Ca4_11491864
Ca4_11273328 Ca4_11490100 Ca4_11334343
Ca4_11490496 Ca4_11274281 Ca4_11244334
Ca4_11244395 Ca4_11276484 Ca4_11275171
Ca4_11465075
70.3
Ca4_11465057 Ca4_11441604 Ca4_1144167370.4
Ca4_1298242072.4
Ca4_13787649 Ca4_1378744872.8
Ca4_1384134072.9
Ca4_1384022773.0
Ca4_1383879673.1
Ca4_13839288 Ca4_13839294 Ca4_1368745673.2
TAA17077.4
NCPGR2178.3
STMS1178.8
cpPb-68055279.6
CaM061582.6
CaM084583.8
CaM085684.0
Tp68496486.3
Ca4_539031794.3
Ca4_490785995.0
Ca4_491108395.7
Ca4_491113095.8
Ca4_317131797.3
Ca4_4578674 Ca4_4628243 Ca4_453631098.1
Ca4_4536286 Ca4_4535728 Ca4_4452018
Ca4_457883698.2
Ca4_4468394 Ca4_4454305 Ca4_4454464
Ca4_445238098.3
Ca4_414825099.4
Ca4_402782999.6
Ca4_4097989 Ca4_4097935 Ca4_399033499.9
LG05
Markers highlighted in
green are novel SNP
markers
LG No of
markers
mapped
No of
SNP
markers
mapped
Length
(cM)
LG01 109 77 101.27
LG02 90 70 92.16
LG03 94 44 69.13
LG04 386 342 112.1
LG05 39 9 59.41
LG06 161 124 104.36
LG07 61 33 96.59
LG08 73 47 88.62
Total 1013 746 723.64
Barcoded DNA samples
• No of reads generated – 701.049 millions; No of base generated – 59030.7Mbp
• Polymorphic SNP identified – 828; Coverage - 0.38X
Genotyping by
Sequencing
828 novel SNPs
identified
1013 loci map developed using these markers and 55 markers integrated in
the QTL region (49 SNP + 6 SSR)
75 SNPs identified
and 32 converted
to CAPS
317 markers (Published earlier)
RAD sequencing
using ApeKI enzyme
with 0.2x coverage
Marker distribution on each LGs
Markers identified on eight pseudo molecules
Fig:2 Graphical representation of SNP identification
Fine mapping approaches
Fig:1 GBS reads per sample
• Of 828 SNPs,
746 SNPs were
integrated on
the genetic
map and 49
SNPs were
integrated in
the QTL hot
spot
• As a result QTL
interval is
reduced from
35 cM to 14 cM