Traits / QTL / Chromosome / Environments / Position(cM) / Flanking marker / LOD threshold / LOD score / Additive / r2 (%) / Origin
LP / qLP-A4-1 / A4 / E2 / 6.51 / NAU3379-DPL0562 / 3.33 / 4.6 / 1.5438 / 9.66 / 86-1
qLP-A3-1 / A3 / E3 / 44.81 / NAU7656-SHIN-0659 / 2.94 / 4.14 / 1.5846 / 10.03 / 86-1
qLP-A5-1 / A5 / E8 / 1.01 / Gh243-NAU2140 / 3.41 / 4.8 / -1.3703 / 11.3 / Prema
qLP-A5-2 / A5 / E4 / 30.61 / Gh260-DPL0022 / 3.17 / 3.23 / -1.4557 / 7.52 / Prema
qLP-A5-2 / A5 / E8 / 11.91 / NAU2210-NAU1375 / 3.41 / 5.48 / -1.5111 / 14.87 / Prema
qLP-A8-1 / A8 / E3 / 2.01 / DPL0152-MUSB0175 / 2.94 / 3.39 / 1.9489 / 11.08 / 86-1
qLP-D10-1 / D10 / E3 / 32.91 / NAU5262-NAU7144 / 2.94 / 4.73 / -1.3952 / 10.88 / Prema
qLP-D11-1 / D11 / E3 / 36.31 / NAU4934-NAU2919 / 2.94 / 3.53 / 1.6655 / 11.93 / 86-1
qLP-D9-1 / D9 / E2 / 0.01 / NAU2954-DPL0530 / 3.33 / 4.2 / -1.5809 / 8.84 / Prema
SY / qSY-D3-1 / D3 / E2 / 12.01 / NAU530-NAU7157 / 2.83 / 3.42 / 13.2704 / 15.66 / 86-1
qSY-A1-1 / A1 / E3 / 4.01 / NAU4891-Gh215 / 2.92 / 4.59 / 8.8886 / 15.39 / 86-1
qSY-A13-1 / A13 / E4 / 0.01 / NAU1211-NAU3388 / 2.84 / 2.91 / -10.0381 / 5.86 / Prema
qSY-A3-1 / A3 / E5 / 37.91 / MUSS492-NAU1167 / 3.17 / 3.82 / -6.6858 / 7.81 / Prema
qSY-A7-1 / A7 / E3 / 8.51 / JESPR-12-CGR6061 / 2.92 / 5.43 / 6.3741 / 10.88 / 86-1
qSY-A7-1 / A7 / E4 / 14.51 / JESPR-12-CGR6061 / 2.84 / 6.54 / 23.9961 / 17.9 / 86-1
qSY-A7-2 / A7 / E3 / 2.01 / DPL0852-Gh527 / 2.92 / 3.78 / 6.4176 / 9.59 / 86-1
qSY-A9-1 / A9 / E4 / 8.91 / MUSS316-NAU3669 / 2.84 / 7.83 / -25.3922 / 16.78 / Prema
qSY-A9-1 / A9 / E8 / 9.91 / MUSS316-NAU3669 / 3.5 / 4.84 / -5.3394 / 11.96 / Prema
qSY-D13-1 / D13 / E4 / 0.01 / DPL0375-NAU6191 / 2.84 / 4.62 / -15.348 / 10.06 / Prema
qSY-D4-1 / D4 / E3 / 14.61 / BNL448- NAU5099 / 2.92 / 3.91 / -5.8926 / 9.39 / Prema
qSY-D4-1 / D4 / E4 / 18.01 / BNL448- NAU5099 / 2.84 / 3.13 / 27.9423 / 30.61 / 86-1
qSY-D4-2 / D4 / E4 / 28.61 / NAU3546-NAU7579 / 2.84 / 3.35 / 23.4691 / 21.55 / 86-1
SI / qSIA3-1 / A3 / E2 / 18.21 / NAU7572-MUSS162 / 3.03 / 3.3 / -0.4399 / 8.66 / 86-1
qSIA5-1† / A5 / E1 / 0.01 / CGR5667-NAU6966 / 3.44 / 3.6 / -0.2429 / 6.1 / 86-1
qSIA5-1† / A5 / E2 / 0.01 / CGR5667-NAU6966 / 3.03 / 4.75 / -0.3292 / 9.19 / 86-1
qSIA5-1† / A5 / E5 / 0.01 / CGR5667-NAU6966 / 3.23 / 3.28 / -0.3645 / 6.06 / 86-1
qSIA5-1† / A5 / E8 / 0.01 / CGR5667-NAU6966 / 3.04 / 3.06 / -0.2204 / 5.53 / 86-1
qSIA6-1 / A6 / E2 / 38.71 / NAU6973-NAU3859 / 3.03 / 3.93 / 0.4352 / 12.03 / Prema
qSIA7-1† / A7 / E1 / 12.51 / CGR6061-NAU1362 / 3.44 / 6.4 / 0.4672 / 15.56 / Prema
qSIA7-1† / A7 / E2 / 10.51 / NAU3634-NAU1362 / 3.03 / 3.03 / 0.4684 / 7.89 / Prema
qSIA7-1† / A7 / E3 / 12.51 / CGR6061-NAU1362 / 2.84 / 3.75 / 0.7631 / 12.49 / Prema
qSIA7-1† / A7 / E8 / 13.51 / CGR6061-NAU1362 / 3.07 / 3.08 / 0.3329 / 7.98 / Prema
qSIA7-2 / A7 / E1 / 0.01 / DPL0852-Gh527 / 3.44 / 6.92 / 0.4683 / 12.59 / Prema
qSIA7-2 / A7 / E2 / 0.01 / DPL0852-Gh527 / 3.03 / 4.15 / 0.4432 / 7.93 / Prema
qSIA7-2 / A7 / E3 / 2.01 / NAU3634-NAU1362 / 2.84 / 3.41 / 0.7183 / 8.63 / Prema
qSIA7-3 / A7 / E3 / 8.51 / NAU3634-NAU1362 / 2.84 / 3.56 / 0.7212 / 7.4 / Prema
qSIA8-1 / A8 / E2 / 0.01 / DPL0152-MUSB0175 / 3.03 / 3.29 / -0.4319 / 6.46 / 86-1
qSID10-1 / D10 / E3 / 2.01 / DPL0149-DPL0108 / 2.84 / 4.18 / -0.8206 / 8.75 / 86-1
qSID11-1 / D11 / E2 / 17.31 / CIR035-89-IN-550 / 3.03 / 4.75 / -0.5923 / 10.25 / 86-1
qSID11-1 / D11 / E3 / 26.21 / HAU3303-NAU4934 / 2.84 / 3.43 / -0.7844 / 8.85 / 86-1
qSID13-1 / D13 / E5 / 8.01 / NAU2697-NAU3948 / 3.23 / 3.68 / 0.6577 / 9.17 / Prema
qSID2-2 / D2 / E5 / 7.71 / CGR5034-NAU4022 / 3.23 / 3.95 / -0.648 / 7.46 / 86-1
qSID7-1 / D7 / E8 / 25.71 / HAU2681-NAU3053 / 3.07 / 3.74 / -0.3409 / 6.89 / 86-1
BW / qBW-A10-1 / A10 / E2 / 22.31 / HAU2147-MUCS439 / 3.1 / 5.43 / -0.5493 / 17.66 / 86-1
qBW-A10-2 / A10 / E2 / 28.61 / MUCS439-NAU3467 / 3.1 / 5.41 / -0.5483 / 15.03 / 86-1
qBW-A11-1 / A11 / E4 / 7.21 / NAU1014-NAU5192 / 3.06 / 3.83 / -0.4161 / 7.82 / 86-1
qBW-A12-1 / A12 / E3 / 14.21 / DPL0057-Gh273 / 3.15 / 4.64 / 0.3641 / 13.16 / Prema
qBW-A12-2 / A12 / E3 / 19.61 / DPL0057-DPL0917 / 3.15 / 5.02 / 0.401 / 14.43 / Prema
qBW-D11-1 / D11 / E2 / 22.21 / HAU3303-89-IN-550 / 3.1 / 3.88 / -0.7408 / 19.57 / 86-1
qBW-D11-1 / D11 / E1 / 22.21 / CIR035-89-IN-550 / 2.97 / 5.22 / -0.3704 / 17.64 / 86-1
qBW-D11-2 / D11 / E2 / 38.31 / NAU4934-NAU2919 / 3.1 / 3.24 / 0.4558 / 10.87 / Prema
qBW-D13-1† / D13 / E1 / 0.01 / NAU2697-NAU3948 / 2.97 / 8.17 / 0.3175 / 15.94 / Prema
qBW-D13-1† / D13 / E8 / 2.01 / NAU2697-NAU3948 / 3.01 / 3.38 / 0.3751 / 11.06 / Prema
qBW-D13-1† / D13 / E2 / 4.01 / NAU2697-NAU3948 / 3.1 / 3.53 / 0.4863 / 12.71 / Prema
qBW-D3-1 / D3 / E4 / 0.01 / DPL0375-HAU1355 / 3.06 / 3.81 / 0.4187 / 7.94 / Prema
qBW-D4-1 / D4 / E2 / 2.01 / HAU0558-CGR6409 / 3.1 / 4.45 / -0.4517 / 10.75 / 86-1
qBW-D4-2 / D4 / E3 / 12.61 / CGR6409-CGR6410 / 3.15 / 3.64 / -0.3285 / 7.35 / 86-1
qBW-D7-1 / D7 / E1 / 32.61 / HAU2681-NAU3053 / 2.97 / 3.29 / 0.2112 / 5.95 / Prema
FE / qFE-A1-1 / A1 / E3 / 7.81 / NAU4891-Gh215 / 3.1 / 4.59 / -0.7312 / 10.48 / Prema
qFE-A5-1 / A5 / E4 / 6.21 / Gh243-NAU1375 / 3.1 / 3.9 / -0.1009 / 7.99 / Prema
qFE-A7-1 / A7 / E4 / 3.11 / DPL0852-JESPR-12 / 3.1 / 4.89 / -0.1123 / 10.67 / Prema
qFE-A7-1 / A7 / E2 / 4.91 / Gh527-JESPR-12 / 3.21 / 4.36 / -0.5929 / 6.08 / Prema
qFE-A9-1† / A9 / E8 / 14.81 / CGR6252-NAU2354 / 2.91 / 3.59 / -0.2583 / 5.28 / Prema
qFE-D2-1 / D2 / E3 / 6.01 / HAU1455-HAU3236 / 3.1 / 3.81 / 0.447 / 6.83 / 86-1
qFE-D2-1 / D2 / E8 / 9.01 / HAU1455-HAU3236 / 2.91 / 3.48 / 0.2473 / 6.61 / 86-1
FL / qFL-A7-1† / A7 / E3 / 4.91 / Gh527-JESPR-12 / 3.07 / 8.51 / 0.9949 / 16.33 / Prema
qFL-A7-1† / A7 / E8 / 4.91 / Gh527-JESPR-12 / 2.93 / 3.32 / 0.4629 / 5.42 / Prema
qFL-A7-2 / A7 / E3 / 10.51 / CGR6061-NAU1362 / 3.07 / 5.21 / 0.7236 / 13.86 / Prema
qFL-A7-3 / A7 / E4 / 12.21 / NAU2710-CGR5108 / 3.05 / 3.61 / -0.7027 / 6.92 / 86-1
qFL-D10-1 / D10 / E5 / 12.01 / DPL0108-NAU5262 / 2.71 / 3.91 / 0.6925 / 12.29 / Prema
qFL-D11-1† / D11 / E1 / 22.21 / HAU3303-NAU2919 / 3.25 / 6.58 / -1.02 / 25.34 / 86-1
qFL-D11-1† / D11 / E2 / 15.31 / CIR035-HAU3303 / 3.21 / 6.58 / -1.1295 / 18.33 / 86-1
qFL-D11-1† / D11 / E3 / 20.21 / CIR035-89-IN-550 / 3.07 / 5.42 / -0.8065 / 15.86 / 86-1
qFL-D11-1† / D11 / E5 / 18.21 / CIR035-89-IN-550 / 2.71 / 5.45 / -0.6764 / 10.02 / 86-1
qFL-D11-1† / D11 / E4 / 17.31 / CIR035-89-IN-550 / 3.05 / 3.67 / -1.0292 / 10.05 / 86-1
qFL-D11-1† / D11 / E8 / 18.21 / CIR035-89-IN-550 / 2.93 / 10.18 / -0.7801 / 18.22 / 86-1
qFL-D3-1† / D3 / E1 / 14.01 / BNL2496-CIR261 / 3.25 / 4.83 / 0.6007 / 9.78 / Prema
qFL-D3-1† / D3 / E2 / 14.11 / BNL2496-CIR261 / 3.21 / 5.05 / 0.8925 / 9.77 / Prema
qFL-D8-1 / D8 / E5 / 46.01 / NAU1590-HAU1533 / 2.71 / 2.91 / 0.4666 / 5.22 / Prema
FS / qFS-A9-1 / A9 / E4 / 16.81 / CGR6252-NAU2354 / 2.83 / 6 / 1.1517 / 11.37 / Prema
qFS-A1-1 / A1 / E3 / 4.01 / NAU4891-SHIN-1397 / 3.4 / 5.14 / 1.5474 / 12.53 / Prema
qFS-A12-1 / A12 / E2 / 19.61 / DPL0057-DPL0917 / 3.09 / 4.31 / 1.6305 / 10.93 / Prema
qFS-A3-1 / A3 / E5 / 37.11 / CGR5258-NAU1167 / 3.49 / 3.64 / 1.5108 / 6.68 / Prema
qFS-A6-1 / A6 / E7 / 6.01 / TMD02-NAU5226 / 3.06 / 4.6 / 2.6315 / 6.41 / Prema
qFS-A7-1† / A7 / E6 / 4.91 / Gh527-JESPR-12 / 3.12 / 3.3 / 1.8639 / 4.1 / Prema
qFS-A7-1† / A7 / E3 / 3.11 / DPL0852-JESPR-12 / 3.4 / 3.97 / 1.1058 / 7.63 / Prema
qFS-A7-1† / A7 / E2 / 2.01 / DPL0852-Gh527 / 3.09 / 3.82 / 1.3882 / 7.44 / Prema
qFS-A7-1† / A7 / E8 / 2.01 / DPL0852-NAU3634 / 2.8 / 3.6 / 0.7686 / 5.06 / Prema
qFS-A9-1 / A9 / E6 / 18.81 / NAU3669-NAU2354 / 3.12 / 7.08 / 2.7715 / 14.54 / Prema
qFS-A9-1 / A9 / E7 / 18.81 / NAU3669-NAU2354 / 3.06 / 3.32 / 2.3122 / 7.46 / Prema
qFS-A9-1 / A9 / E8 / 14.81 / CGR6252-NAU2354 / 2.8 / 5.28 / 0.8693 / 6.07 / Prema
qFS-D13-1 / D13 / E8 / 9.01 / NAU2697-NAU3948 / 2.8 / 3.46 / 0.7592 / 6.25 / Prema
qFS-D3-1† / D3 / E4 / 14.41 / JESPR-101-CIR261 / 2.83 / 6.2 / 1.0656 / 8.15 / Prema
qFS-D3-1† / D3 / E6 / 14.11 / BNL2496-CIR261 / 3.12 / 3.23 / 1.851 / 4.51 / Prema
qFS-D3-1† / D3 / E7 / 14.41 / BNL2496-CIR261 / 3.06 / 3.99 / 1.9246 / 4.54 / Prema
qFS-D3-1† / D3 / E2 / 12.01 / BNL2496-CIR261 / 3.09 / 7.09 / 2.2994 / 17.55 / Prema
qFS-D3-1† / D3 / E1 / 14.01 / BNL2496-CIR261 / 3.4 / 4.11 / 1.3878 / 7.15 / Prema
qFS-D3-1† / D3 / E8 / 11.01 / BNL2496-JESPR-101 / 2.8 / 3.37 / 0.8386 / 8.74 / Prema
qFS-D3-1† / D3 / E8 / 16.41 / JESPR-101-CIR261 / 2.8 / 2.83 / 0.74 / 6.10 / Prema
qFS-D3-2 / D3 / E2 / 0.01 / NAU1086-NAU2215 / 3.09 / 3.14 / -1.5301 / 4.82 / 86-1
qFS-D4-1† / D4 / E4 / 18.51 / NAU3591-NAU5099 / 2.83 / 3.31 / 0.9239 / 7.12 / Prema
qFS-D5-1 / D5 / E4 / 0.01 / cot130-7844F-Y3350-800 / 2.83 / 2.86 / -0.4339 / 3.73 / 86-1
qFS-D5-1 / D5 / E3 / 0.01 / NAU927-CGR5022 / 3.4 / 4.28 / -1.051 / 8.27 / 86-1
FU / qFU-A12-1 / A12 / E2 / 16.21 / DPL0057-DPL0917 / 2.97 / 3.35 / 0.7331 / 8.32 / Prema
qFU-A5-1 / A5 / E2 / 57.51 / DPL0022-NAU2894 / 2.97 / 4.52 / 0.7149 / 11.07 / Prema
qFU-D10-1 / D10 / E2 / 16.41 / NAU1169-CGR6701 / 2.97 / 3.7 / -0.5175 / 7.25 / Jan-86
qFU-D3-1 / D3 / E4 / 14.01 / BNL2496-CIR261 / 3.43 / 5.02 / 0.6383 / 10.54 / Prema
qFU-D4-1 / D4 / E2 / 24.61 / JESPR-65-NAU7579 / 2.97 / 4.52 / -0.6922 / 9.27 / 86-1
qFU-D5-1 / D5 / E3 / 0.01 / NAU7549-NAU3525 / 3.58 / 4.51 / 0.7817 / 9.56 / Prema
qFU-D5-2 / D5 / E3 / 0.01 / NAU927-CGR5022 / 3.58 / 4.62 / -0.567 / 9.61 / 86-1
FSCI / qFSCI-D3-1 / D3 / E1 / 14.01 / BNL2496-CIR261 / 2.99 / 3.13 / 8.4885 / 5.73 / Prema
qFSCI-D3-1 / D3 / E2 / 14.01 / BNL2496-CIR261 / 3.4 / 5.04 / 13.5961 / 9.49 / Prema
qFSCI-D3-2 / D3 / E2 / 0.11 / NAU1086-NAU1186 / 3.4 / 3.84 / -11.9914 / 6.98 / 86-1
qFSCI-D6-1 / D6 / E3 / 4.41 / HAU0975-NAU2035 / 3.56 / 3.99 / 4.5087 / 7.77 / Prema
FMic / qFMic-A13-1 / A13 / E4 / 0.01 / NAU1211-NAU3388 / 3.18 / 3.51 / -0.1155 / 6.97 / Prema
qFMic-A3-1 / A3 / E2 / 0.01 / NAU997-CIR332 / 2.5 / 2.85 / -0.1364 / 6.1 / Prema
qFMic-A4-1 / A4 / E2 / 6.51 / NAU3379-DPL0562 / 2.5 / 3.45 / 0.1996 / 7.47 / 86-1
qFMic-A6-1 / A6 / E4 / 4.01 / TMD02-NAU2710 / 3.18 / 3.7 / 0.2195 / 11.04 / 86-1
qFMic-D10-1 / D10 / E1 / 0.01 / cot119-MUCS254 / 3.06 / 3.81 / -0.1955 / 8.01 / Prema
qFMic-D1-1 / D1 / E3 / 23.91 / DPL0504-NAU1536 / 3.49 / 4.11 / 0.2851 / 10.59 / 86-1
qFMic-D4-1 / D4 / E1 / 24.61 / JESPR-65-NAU7579 / 3.06 / 3.35 / 0.2102 / 7.07 / 86-1
FBN / qFBN-A1-1 / A1 / E2 / 25.91 / SHIN-1397-NAU2741 / 3.26 / 3.38 / -0.6554 / 8.56 / 86-1
qFBN-A1-2 / A1 / E2 / 34.11 / NAU5411-DC40052 / 3.26 / 3.98 / -0.6232 / 8.16 / 86-1
qFBN-A2-1 / A2 / E1 / 10.01 / CGR5250-NAU7087 / 3.47 / 4.15 / -0.8188 / 14.761 / 86-1
qFBN-A2-1 / A2 / E5 / 14.31 / CGR5250-NAU2277 / 2.96 / 5.59 / -0.792 / 10.02 / 86-1
qFBN-A9-1 / A9 / E4 / 14.81 / CGR6252-NAU2354 / 3.08 / 6.53 / -0.8231 / 14.29 / 86-1
qFBN-D5-1 / D5 / E2 / 5.91 / NAU3525-SHIN-0256 / 3.26 / 3.49 / 0.5582 / 6.49 / Prema
qFBN-D8-1 / D8 / E4 / 0.01 / DPL0064-NAU808 / 3.08 / 3.09 / 0.404 / 6.68 / Prema
qFBN-A1-1 / A1 / E2 / 25.91 / SHIN-1397-NAU2741 / 3.26 / 3.38 / -0.6554 / 8.56 / 86-1
Note: Environments for RILs were indicated as “E” respectively: E1, E1; E2, E2; E3, E3; E4, Akasu 2010; E5, E5; E6, E6; E7, E7; E8, combined analysis using means of E1～E5.
Seed-cotton yield (SY, g/plant),Boll weight (BW, g), Lint percentage (LP, %), and seed index (SI, g). Fiber quality traits included Fiber length (FL), Fiber strength (FS), Fiber elongation (FE), Fiber Uniform (FU),Spinning consistency index(FSCI),Micronaire (FMIC), Fruit branch number(FBN).
“†” Indicates that the QTLs were simultaneously found in the interaction between the QTL and environments detected in RILs
LOD threshold: The significant LOD threshold for the trait at P = 0.05 determined by 1,000 permutation test