Ssq1(L)

transcript

Ssq1(L)

Tsw1(G

ec3b40.0

e43m50h1555.0At3g079507.7

e46m59h25513.2

At3g0242019.7

e39m50v13124.8e54t69v15028.2At2g2393032.3

e31m60h32536.9

e47t74v45042.5At3g1676046.4e45m34v16248.9At3g2224051.6

e31m61h9856.7e44m38v45259.8Na14-G06a63.1e50t70h7666.8

p33m38v31371.7p87m38v91174.7

e34m50v15580.1p53m33v16784.0

e45t66v71488.7At2g24765b92.4

At4g31720b98.3

At4g34140b103.2

e62m33v765112.4

At4g37280a117.6At4g39690121.0At4g39350a125.0

At3g024200.0e43m50h1551.1At3g086903.0At3g079507.9e46m59h2558.6e54t69v1509.4At3g1081016.2At2g2393019.4

At3g1676025.9e47t74d40026.4e44m38v45229.8e31m61h9830.6At4g2416035.4p79t78t27039.4

At4g2015045.7At4g1840047.7

At4g3015055.3

At4g3348066.1

e34m49d7073.7

p48t67v2800.0e31m50t3451.1At5g082803.2At5g107805.4At5g122906.4At5g131908.5e31m42v22516.6At5g2018017.9At5g1915020.0e31m61d14529.3At2g4080032.2e44m38h21234.8At4g2684036.2p62t78v27839.5e51t78v8940.9p53t82t35043.0At1g6831046.1At1g7309047.4At1g7035048.0At1g7289049.0At1g7464050.5e35t63v30153.6e42m32v23254.5e47t71v13255.5e51t78v37857.7At2g0164058.8e31m49h31059.6e51t78t20061.5e43m50v15262.9

Sbr1(D)

Msl1(L)

Sqms1(L)

p58m71h1540.0p48t67v2802.2At5g082806.4p33m71v1397.2At5g1229011.7

e31m42v22516.2

At5g1915022.9

e46t65h72327.2e44m38h21230.4At4g2684033.1

p62t78v27837.4At1g6831041.5e34m43h45044.3At1g7309046.1e35t63v30148.8e42m32v23251.7e31m49h31053.3p33m32h41057.6e43m50v15260.6

At1g7193066.5p33t83h17169.9

p65m32v29575.3

e34m43v26079.7At5g6197082.8

Supplementary Fig. S3 The framework TD and VH maps showing distribution of QTL for 12 yield associated traits. Linkage groups of the TD and VH maps have been suffixed with TD and VH respectively. Common markers among the two maps have been underlined. QTL were designated using the trait name initials followed by the number identifying the QTL number for the trait (Supplementary Table S6). The allele that increased the trait value is indicated by red bars (TM-4 in TD and Varuna in VH map) and the blue bars (Donskaja-IV in TD and Heera in VH map). The alphabet in the parenthesis indicates the environment (D - Delhi, B - Bharatpur, G – Gwalior, L – Leh) where the QTL were detected. Plant height (Plht), Primary branches (Pbr), Secondary branches (Sbr), Main shoot length (Msl), Siliqua per main shoot (Sqms), Siliqua per plant (Sqp), Siliqua length (Sql), Seeds per siliqua (Ssq), Thousand seed weight (Tsw), Siliqua density (Sqdy), Days to flower (Df), Seed oil content (Oil)

e31m61d340

At4g251400.0Ra3-D02B3.7At4g262404.4e31m42v2506.1At4g2110510.0Na14-G0211.7At4g1790012.6e31m50h8713.4BRMS-05015.3p32t77v33019.2p48t67h39025.0p37t64t19826.1At3g2140027.3At3g1312033.9At3g1259036.2e39m50h18137.2

At4g0258048.653.9

At2g2339054.5At2g4268056.6At2g3991060.7At2g3888062.7e51t78v32563.4At2g3149068.8BN12A71.0

At5g1880076.5At5g1756080.3

A3-TDSql1(D)

Sql2(B)

Tsw1(D)

Sqdy1(D,B)

Oil1(L)

e32t70v7180.0At4g00585b1.7

At4g303107.6At4g2624012.0At4g2444015.4Na14-G0217.6At4g2015019.1At4g1790021.5At3g5230024.2BRMS-05026.9p32t77v33031.7

p48t67h39037.0

At3g2140041.6

p62m45v18446.6e39m50h18148.9

At3g0396057.8e62t65h39060.3p53m33v18064.2

At2g23090b69.2At2g2339072.7At2g2852075.3

Ra2-F1181.4e51t78v32583.7At2g3149086.1BN12A90.4

At3g4618096.2Ra2-E11100.2

p33m38h274104.5At5g15230108.4

e34m62h290116.5

At5g06240b126.0

Tsw3(L)

Tsw2(D

Sqp1(D)

Msl2(L) Sbr1(G

At2g440500.0

p63t78v4006.1At2g430807.3

At2g4089012.7

e31m47v11117.3

At2g3577024.2

At2g2264046.5e50t67d13849.4At5g4156050.7At5g3748053.7p62t78d12056.0At3g5413058.0e35t63d20059.2

Df1(D)

At2g445200.0

p63t78v40013.5

At2g4204019.1At2g4069022.1p58t68v45525.4e31m47v11129.4At2g36530c33.3

e48m39v10038.1

At2g3252044.5At2g31490a47.8

At2g3013052.2At2g28880b55.3

p33t65h25961.2At2g2264065.6At5g4156068.0At5g3748071.0Ni2-F11(N73)74.7At3g63420b77.1At5g15840a80.9

DF1(L)

Tsw4(D

Msl3(D

Plht1(L)

Sql3(D)

Df2(D)

Oil2(D)

e35t63v2400.0At5g173101.8e34m62d2504.0At2g263205.9

At3g0992512.8p32t77h31013.5

e31m50t9826.7

e31m49v29536.2e31m61v13637.5Na10-B0838.4e31m42v14438.9At2g3292041.8e47t70v25844.3At2g3636049.5

At2g4579056.5

At2g4639071.5

A5-TDe35t63v2400.0e50t66h4603.9e50m32v2208.8e50t66v47010.0

p32t77h31018.9

p32t77v30124.1

At2g23930a28.9

e62m35h19036.6At3g12120a37.5Ra3-H1039.4At3g1631043.5p53t76h29245.3Na10-B0852.9e31m49v29553.6e34m62v15755.5At2g3292060.7

e43m59h9965.0

At2g4497075.7

BRMS-03480.9

At2g4639088.4p80m48h28090.1

Tsw2(D)

e31m50d1050.0

At1g085806.6At1g1223010.4

At1g1578014.8e31m50d33017.8

At1g1873024.4e31m61h11527.2At1g2083030.1e47t74t28032.3At2g1742035.9At2g1891036.5At5g2774041.9e34m49h16044.1

At2g0135057.7

e39m32t17567.7At5g4285068.9

A6-TDSql1(G

Ssq2(G)

Tsw5(G

Sqdy1(L)

p40m82h1780.0At1g51740a4.1

p33m71v1599.0

At1g4858015.5

e43m59v12821.5

At1g12840a25.6

p32t77v10530.4At1g1223032.1At1g1652036.1

At5g2576040.3

e31m61h11545.6

At5g2409050.5e39m32v20353.1

e34m49h16059.4At3g2637063.7e31m604h33066.4Ra2-F0469.4e60m42v16570.0

At2g0135076.3

At5g4704081.9At1g7245083.9At5g4067087.4e47t70h12491.4

Plht2(D)

Pbr1(D)

Sbr2(B)

Sql4(L)

Tsw3(L)

At1g756900.0At1g741403.0At1g732405.3

At1g6831012.5p62t78v21115.4e31m42h17319.1

At1g7904025.8

e32t66h8834.7At2g2749039.1e34m50v13742.7At2g2667044.0e39m50h45046.4

e39m32h15352.6At1g7735053.2e50t66h13958.9e45m34h10261.6At2g1890064.4e39m50v36067.0At2g1956069.0

p48t67t22077.3

p48t67d42181.5

Plht1(D,G,L)

Pbr1(D,G)

Sbr2(D)

Sql2(L)

Ssq3(L)Tsw

Sqdy2(D) DF3(D

Oil1(D

At1g765400.0

At1g708004.8

e60t65v2538.9

p53m42h15318.3

At1g6831023.2At1g6837026.0p62t78v21129.1

At1g7904036.0

Ra2-A01a41.6At3g55005c44.7

e32t66h8848.9

At2g28880a55.7At2g2749059.1

e39m50h45063.3At1g2344066.0e50t66h13971.8At3g2480073.5At2g1686075.3At2g1890076.4At1g7080079.4

Plht3(D)

Plht4(L)

Sbr3(D) M

sl1(L)

Sqms1(L)

Tsw4(D,L)

Oil3(D,L)

At4g145700.0e31m60t1153.4

At3g1395019.0At1g5346023.0At1g5024025.3e31m60h9226.6At4g1551027.5e32t66v19130.4At4g3172031.3At4g2996033.0p58t83t37335.1At4g3146037.3At4g3847041.8At1g2853044.8At1g2554048.9At1g7667053.4e39m50v47054.2

e60t65v14862.6

At1g1188068.1

At1g0976074.4At1g0848078.6e48t78v40080.7

Plht2(L)Sbr3(G

Sqp2(G)

Sql3(D)

DF4(L)

Oil2(D

Oil3(G

At4g317200.0

e32t70v7208.6At1g295809.5e31m60h9211.8At4g1551014.9e32t66v19120.2At4g3146023.6

At4g2820027.9

e48m34h18232.4

At1g2853038.9At1g2431043.5At1g2554046.9e39m50v47048.4At1g18340a51.1

At1g7031059.5e60t65v14863.8At1g1188066.3At1g1124070.0

e48t78v40075.7p53m48v16477.2p48t87v29581.8

Pbr2(L)

Sbr4(L)

Sbr5(L)

Tsw5(L)

Sqdy2(L)

At4g025800.0

At1g2810021.7At2g1417025.5

At2g1926032.1e50t66v25135.6e31m50t34039.0e31m58v28941.8p87t77h28244.9e55t63v11848.4At4g0553049.0p32t77h40050.8At3g5126056.3e44m38v21459.0At3g5543059.7e34m62v39063.3

e46m59h13272.2At3g4352074.6e44m39h21477.9At2g2237079.5At2g2112082.4At2g2049085.6p63t71h21389.5At1g1188092.0e62t65d18594.7p48t94h26198.8At1g0520599.3

At2g38380108.4

Sbr4(G)

Sqp3(G)

Sqp4(D)

Sql4(G)

Sql5(L)Tsw

7(G,L)

Sqdy3(D,L)

GSl-odd0.0

GA-R212.3At4g0258013.6

At5g2721019.0At5g25610b22.0

e34m43h36026.8

e31m58v25032.1

At5g6759040.8

At2g1417047.5At2g1742050.4At1g29990b53.8At2g1926056.5p53m62v34559.1e50t66v25163.4At4g0553068.5At1g6264070.6e31m58v28973.0p87t77h28276.7At4g0976077.7At4g0906078.5p32t77h40080.5p48t94h39081.3p48t67h31884.7e48t78h14086.1At3g5126091.3p58m71v95296.2e44m38v21498.9At3g55430101.4e34m62v390105.0At2g25740b109.7At3g43520113.6At2g20490117.2At2g20760120.8At1g16190123.1p63t71h213126.8e46m59v304128.8e43m59h106130.2At1g11880133.4

At1g05205140.9At2g22370142.9e50t67h113147.8p48t94h261148.4

Plht5(D,B,L)

Pbr3(D,B)

Sbr6(B)

Msl2(D,B)

Msl3(L) Sqms2(D,L)

(D,B,L)

Sql5(L)

Sql6(D,B)

(D,B) Ts

Sqdy3(D,B,L)

Df3(D,B)

Oil4(D,B)

At1g028700.0e50t66h3721.9e62t65v5204.1e45m34v2254.9At5g591409.2e39m50v41511.6e60t65v27513.3p79t78d6716.4

At5g1628027.3

p63t78d23935.2

e34m62t17044.4

At5g0931049.5

A10-TD

Plht3(D,G,L)

Pbr2(D,G)

Sbr5(D)

Sbr6(G)

Sqms2(D

Sqms3(L)

Sqms4(D

Sqp5(D,G,L)

Sql6(D,G)

Ssq4(D,G)

Tsw8(D

Sqdy4(D,G,L)

Oil4(D

e34m43h1190.0At1g028700.7e50t66h3722.4e62t65v5205.9e50m32h8410.0At5g5914013.1e60t65v27513.9e58t75v16015.1At5g2025017.8At5g1867020.3At5g1727025.7At5g1633028.1At1g7255030.5At5g15400a32.6At5g1492034.5At5g13190b37.8wg8g741.2Ni4-A0344.1At5g0931049.9p48m67v15052.9At5g06240a56.4At5g05920a58.9ec5a762.8At5g07690b65.6At5g0116068.7p62m66v93170.0

A10-VH

Sqms3(D)

e34m49v1010.0e31m50h1150.9p58t68h3802.3e50t67v1203.5e62t65h2584.9At3g105725.4e43m50v2706.1At3g116208.7At3g1664014.1At3g1730016.3e44m38v42017.3At3g2092019.9e39m32v8522.7e62t65v12627.0At5g2875028.5At5g2508031.7e31m50t43036.6e34m50v29440.8At1g5822044.5At2g4184046.8e44m39h13148.0e47t74t39449.1At3g1990053.0At3g5126054.7e35t63v14455.5e43m50d8063.0p48t94t12864.1

At3g0869075.2

p87t77h15782.5e31m60t25083.7

Sql7(D)

Tsw9(L)

Tsw10(D

At1g705600.0e34t74h7193.1

e34m49v10111.7e31m50h11512.6e58m40h24715.4e34m62v18416.2e34m47h19819.7At3g1057222.3p32m66v90127.0At3g1730030.5At3g1860031.5At3g2092033.9p62t73h22835.5p33m71v92038.7Ni2-A0740.8e45m34h10144.7e39m32v8547.8e62t65v12649.0At5g2875051.6At5g2508053.2e34m50v29455.3At1g5822060.1At5g2006064.1e32t70h74568.1e35t63v14469.3p53m42h18873.8At3g1485078.5

At3g12260b89.4

At3g0869095.2p87t77h15798.5p87m38h152100.6

At5g15650105.9

At3g13062117.3

Plht6(L)

Sqms4(D)

e31m58v1950.0At4g372802.1At4g369605.3

e34m62v21914.1At4g3414016.1e39m50v39017.0At4g3310020.5At2g2464023.2At4g3079026.6At4g2966030.4e35t63h32831.1

p63t71h26041.8At4g2386044.3At4g2468046.6At4g2041050.1e31m62h34553.8At4g1553055.6e44m39h28556.6e44m38h10358.9At5g1649060.6

Ni2-D1072.8At3g4510074.1e47t71t21076.1e31m47v13280.1e60t77h36082.8e34m49t42087.3e31m62v19990.0p37t64h17993.6Ni2-A1294.4e45m34h34595.1At1g6591097.4e55t73h10299.2e44m50v120101.5p32t77v313103.1e32t66h340104.4At1g72740110.7e34m49v340111.7e62t65h420113.8At1g75980115.8e62t65h147116.9e44m39h184121.9

B2-TDPlht4(G

e35t69h7360.0

e31m58v1956.4p37t64h4009.0At4g3728012.2p61m57h19615.2

e34m62v21920.9At4g3446021.6

e39m50v39029.0At4g3414030.6At4g3392534.2At4g3310036.9

p33t65v19942.1At4g3113044.9At4g3079046.7At4g2966052.4At4g2749056.0Na14-G06b60.2p63t71h26062.3Ni2-D1065.0e31m47v13267.2At4g17050b70.9e34m43h35073.7At5g2001076.0e31m62v19977.3p63t71h16379.8Ni2-A1281.6p63t71v15883.5Ni2-A1187.2

e55t73h10294.0e44m50v12096.5p32t77v313100.5

e32t66h340104.9

e34m50v99110.6e34m49v340114.8e62t65h442117.1e62t65h420119.6At1g75980122.8e62t65h147124.6p61m57h298126.0At1g78040129.5e44m39h184134.0

Oil5(D)

Oil6(B)

At3g608100.0At3g591103.2

At3g5629017.3

At3g5500527.6At3g5467028.2At3g5413029.8At3g5299032.3e34m49t29035.3At4g3269040.8Ni4-F1142.4p58t68h19243.8At3g4562044.7e51t78t38046.7At4g0058550.5At4g0131055.7At2g2659058.4e31m50v25560.1e42m32h22563.6e42m32d30067.1e42m32h19669.9p63t78h42576.1e35t63v21577.1At5g5914081.6e31m42h10885.0

At5g1575090.5p87t77v40093.1

At5g1303098.9

e34m62t210103.1At5g09310106.6

e31m42t165115.9p53t82h195118.0

Pbr3(G)

Msl4(L)

Sqms5(G

s6(L)Sqm

Sqp6(L)

Sql8(G,L)

Tsw11(G

12(D,L)

Sqdy5(L)Sqdy6(G

)Sqdy7(L)

e47m43h2580.0

e35t63h2105.0

e31m47v23515.8At3g5500516.5At3g5413018.3e55t63h13723.6At3g51130a28.6At4g0419030.0e45m34h30832.7At3g4562036.5p58t68h19237.8Ni4-F1139.0p33m71h28639.8Ni3-G0543.9At4g0131046.9At4g01897b50.0Ni4-C1153.2At4g1018057.1At2g2659059.1At2g45690b61.7e44t66v74565.6e42m32h22568.0e62m33v8371.8At2g3881075.3At2g36530a77.7e42m32h19681.2e47t71v34286.7Ni2-A0889.3p63t78h42593.2e35t63v21595.7At5g5914097.6e44m38v22699.1e31m42h108102.7At5g17410105.0At5g15750109.0At5g13030112.3

p65t71h400123.1At5g09310125.0e47m33h155127.7At5g01220129.8

Pbr4(B)

Sbr7(L)

Sqms5(B)

Tsw7(B)

Oil7(L)

e31m47v960.0

At3g529905.0

p63t78t8736.4At1g8046041.0At1g7969044.2At1g7939045.2

p48t67h42050.5

p79t78t18064.0

At2g2819071.6

e31m50t33488.5

p53t91t335105.9

At2g38130112.3

e60t77d250118.4At2g45790121.3

At2g44610127.4

At2g40765131.5

B4-TDSbr7(D

Sqp7(L)Sqp8(D

Sql9(D)

Tsw13(D

e31m60v1710.0At1g804601.2At4g141104.2At1g682207.2At3g529909.2e31m47v9613.1

At3g63420a20.6

At3g53190b26.4Ra2-A01b30.8e51t78v10632.8

At1g7969038.5p48t67h42042.4

p61m44v31548.9p33t65h27552.5At2g21620b56.4

At1g1674060.6

Ni4-A1064.9At2g3208068.3

e31m62v18874.2

At5g6522078.4

p53t91v19083.1

At1g5826089.8

At1g4757099.7At2g38130103.8At2g37560105.4

e47m33v212114.2At2g36930b116.8

wg6d7b127.6

Plht7(B)

Sqdy4(L)

Df4(B)

e39m50h1340.0e55t73d2003.2

e42m32v19811.9At5g4709013.3

p53t82t13823.8p53t82d14524.6At1g1084026.7At1g1058527.6

At1g6398041.9e44m39h17543.7e31m58v21846.4At2g0351048.6

e31m61t10564.4At2g0140066.1At3g2734067.9At2g0250070.3

Sqms8(G

) Df6(D

At1g49340b0.0

e47t71v1855.6Ni2-E058.5e34m50v8811.4p58m35h40015.9e39m50h13417.2e55t63v22419.6e42m32v19822.9At1g2041024.7p62t78v26527.2At1g1924031.2e45m34v20534.7

e62m33h14640.3At1g1084044.2At2g15430a46.2e31m49v24549.7p53m62h28251.2p33m67v14553.6e44m39h17558.0e31m58v21860.0e62m32h7763.4At2g0194066.7e49m35h21168.8e50t66h28772.0e31m62h28875.7

GE-N187.5

Oil8(D)

At3g028600.0

e31m61t3106.3

e60t65d40013.7

At3g1162037.9

e39m32t20052.7

At3g1619060.3At3g2032063.7e31m62d21066.4p32t93t28069.6

e31m60h39073.7e39m32t11077.6

p32t77d39086.1

At2g3104090.1e54t71v25894.4e45m34v27396.4e47t71t17097.4At2g38290At2g40340At2g42430At2g43430At2g43920

Msl5(G

Oil5(G

At3g02420b0.0p87m38v9124.0

p61m44v9458.3p58m35v10811.7e48m34v83814.8At3g12260a19.9At3g12120b21.7At3g15190a23.5

At2g2808032.2

e60t65h39039.7

e31m60h39047.1At2g2819051.5At2g29980b53.1e48m32v28757.3e54t71v25861.2e45m34v27363.4p65m47v32064.9

At1g78560b69.9e62m33h10773.9

103.5105.6107.4108.5111.5

Plht8(L)

Plht9(D)

Pbr5(D)

Msl4(L)

Msl5(D)

Sqms6(B)

Sqms7(L)

Sql7(D,B) Ss

q6(D,B)

Tsw8(D)

Tsw9(B)

Sqdy5(D,B)

Df5(D,B)

Oil9(D)

p63t78t1980.0

e39m32h22512.4e31m50v20813.0e31m47h23215.0e39m32h7516.7

e44m38d19024.1

e46m59t12029.7

e51t78d21038.7At1g6717040.1e39m50v11242.3At1g6866043.6At1g7353044.4p79t78v12745.8e39m50v20949.4e31m42d38550.1e39m50h44656.2e51t78h34057.2e46m59h27858.4e51t78v49062.1At4g2015066.4e48t78v20568.6e31m49v16069.9At1g2618071.2At1g0209077.2e44m50t28084.3At4g3172085.8

At1g08780106.1At1g09760107.0At1g04950111.6p58t68t350113.1

Plht5(D)

Pbr4(D)

Sqp9(D)

Sql10(D)

Sql11(G)

Ssq5(L)Df7(L)

Oil6(G

Oil7(D

At2g299200.0At2g20320a3.2e31m50v2085.6e39m32h757.2e44m39v1139.6At1g7414013.3At1g72380b17.5Na12-A0219.7

At1g6717025.3

At1g6866030.5e39m50v11232.7At1g7353034.7At1g7384038.3e46t65v70842.6e39m50v20945.6e46t65v70648.6At1g7098050.5e50m32h20954.1e39m50h44657.3Ni4-F0960.8e51t78v49065.3At4g2015067.7p53t76h36870.4At4g3452074.9e48t78v20578.5e31m49v16080.1At1g23180b81.8At1g2618085.0At1g28560a89.6e44t75v23590.3

At1g76670104.7

e46t65h726109.9p32t77v268113.1p62m59h400117.4At1g09760119.2At1g08780121.6At1g05055124.9At1g05850126.5At1g02410a128.9

At1g052050.0At1g057200.6

e34m50h13314.9At4g1552015.5e32t66h14718.5e50t66v9619.5e31m50h33524.5

At2g2309030.2

At5g5873037.9At5g2264038.9e35t63h28039.8At5g1820045.0

At5g1007053.3e44m39v30055.9e31m58h50057.9At1g2344059.1

At5g0828079.4

e31m50h20285.5

At5g2875092.8p37t64v12894.1

p53t82h210100.8At4g16060103.9

At5g24490110.3

At5g24314120.0

At5g27380126.9e50t66v323127.6At4g25140131.2At4g26240133.4

p63t78h267143.3

Sbr8(B)

Sqms8(L)

Sql8(L)

Tsw10(L)

Plht6(D,L)

Plht7(G)

Sql12(L) Ssq6(L)

)Oil8(D

At1g057200.0

At1g6172015.9p33t66v20016.5e34m50h13320.3e32t66h14724.0At2g0769027.9p53m48v34530.0At2g2076032.7At2g2309036.0e31m50h33539.2At5g5873042.5At5g2264046.1

At5g1993052.2

At5g1820056.8

At5g15400b64.1e55t63v14368.4At5g15840b70.0At5g09310b74.9At5g1007075.4e50t66v9677.2e31m58h50079.0e47t71h34083.0

p33m38v26097.9e31m50h202100.4At5g28750102.6p53t82h210104.2At3g51240b109.4

p48m67h295114.9At4g07666a117.8At5g24314119.9e62m32v179123.8At5g27380126.1e50t66v323128.0

At4g25140135.2At4g26240136.5

p63t78h267146.8

Ssq1(L)

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