Table 2.
SNPs detected significantly associated with lint percentage at least in two environments or at least by two models.
| SNP | Chr | Pos. (bp) |
GAPIT | Tassel | ||||
|---|---|---|---|---|---|---|---|---|
| FaST-LMM | FarmCPU | BLINK | MLMM | MLM | TMLM | |||
| TM6245 | A3 | 6,000,457 | BLUP (4.90) | BLUP (4.90) | ||||
| TM6246 | A3 | 6,008,064 | BLUP (5.10) | BLUP (6.99) | BLUP (5.10) | |||
| TM6247 | A3 | 6,015,363 | BLUP (5.10) | BLUP (5.10) | ||||
| TM6248 | A3 | 6,020,227 | BLUP (4.90) | BLUP (4.90) | ||||
| TM8562 | A4 | 1,704,160 | E5 (6.37) | E5 (6.23) | ||||
| TM8787 | A4 | 5,125,340 | E1 (7.94) | E1 (10.43) | ||||
| TM10387 | A5 | 7,465,603 | E5 (4.71) | E5 (4.71) | ||||
| TM10953 | A5 | 21,122,062 | E3 (4.97) | E3 (9.45) | ||||
| TM13159 | A5 | 83,646,730 | E3 (6.75); E4 (6.30); E5 (6.66) | E3 (17.39); E4 (6.90); E5 (9.84) | ||||
| TM21439 | A7 | 73,820,001 | E2 (5.42) | E2 (5.42) | ||||
| TM22226 | A8 | 8,180,911 | E4 (15.51) | E4 (11.19); E5 (6.70) | ||||
| TM38921 | A11 | 65,498,934 | E2 (6.45) | E2 (7.92) | ||||
| TM39097 | A11 | 77,128,215 | E2 (5.41) | E2 (5.01) | ||||
| TM39105 | A11 | 77,162,385 | E2 (4.94) | E2 (5.23) | ||||
| TM39111 | A11 | 77,201,721 | E2 (4.85) | E2 (5.06) | ||||
| TM39118 | A11 | 77,245,152 | E2 (5.41) | E2 (4.73) | ||||
| TM39119 | A11 | 77,250,629 | E2 (6.57) | E2 (7.05) | E2 (4.99) | E2 (6.57) | E2 (5.48) | E2 (4.80) |
| TM39120 | A11 | 77,254,990 | E2 (5.35) | E2 (5.42) | ||||
| TM39121 | A11 | 77,259,287 | E2 (5.39) | E2 (4.72) | ||||
| TM39122 | A11 | 77,267,198 | E2 (5.33) | E2 (5.42) | ||||
| TM39136 | A11 | 77,356,582 | E3 (9.26); E5 (12.70) | E1 (5.59); E2 (4.84); E3 (14.49); E4 (5.33); E5 (13.96) | ||||
| TM42527 | A12 | 73,222,779 | E1 (5.91) | E1 (13.91) | ||||
| TM42563 | A12 | 73,856,986 | E2 (5.34) | E2 (7.14) | ||||
| TM46588 | A13 | 60,134,206 | E1 (6.86) | E1 (14.22) | ||||
| TM47373 | A13 | 72,835,782 | E3 (8.73) | E3 (7.06) | ||||
| TM52184 | D2 | 51,543,776 | E1 (4.89); E4 (10.43) | E4 (6.60) | ||||
| TM53197 | D2 | 64,206,361 | E1 (4.77) | E3 (6.30) | ||||
| TM53588 | D3 | 4,016,585 | E4 (15.33) | E1 (13.39); E4 (14.39); E5 (10.63) | ||||
| TM55461 | D4 | 2,087,134 | E2 (6.19) | E2 (9.29) | E2 (6.19) | E2 (5.23) | ||
| TM55484 | D4 | 2,902,882 | E5 (9.59) | E5 (13.00) | ||||
| TM55582 | D4 | 3,824,554 | E2 (6.80) | E2 (6.86) | ||||
| TM55817 | D4 | 7,622,861 | E2 (5.35) | E2 (5.35) | ||||
| TM55819 | D4 | 7,631,258 | E2 (5.35) | E2 (5.35) | ||||
| TM57002 | D5 | 6,810,289 | E1 (4.85); E3 (5.82) | |||||
| TM57478 | D5 | 19,820,229 | E4 (4.95) | E4 (22.33); E5 (4.79) | E4 (12.47) | E4 (4.95) | E4 (4.76) | |
| TM57486 | D5 | 20,068,395 | E2 (5.45) | E3 (4.87) | ||||
| TM58314 | D5 | 49,232,321 | E1 (4.90); E3 (4.77) | |||||
| TM69172 | D8 | 53,049,470 | E3 (13.74) | E3 (8.17) | ||||
| TM72587 | D9 | 43,752,600 | E3 (7.45) | E3 (7.83) | ||||
| TM73642 | D10 | 8,030,303 | E3 (5.42) | E3 (6.93) | ||||
| TM75017 | D10 | 58,300,092 | E4 (4.72) | E4 (13.12) | ||||
| TM76204 | D11 | 24,111,532 | E3 (8.00) | E3 (14.52) | ||||
| TM78526 | D12 | 34,893,826 | E2 (4.84) | E3 (5.16) | E2 (4.84) | |||
| TM80159 | D13 | 2,590,468 | E5 (5.39) | E5 (9.39) | ||||
| TM81325 | D13 | 42,144,468 | E1 (7.99); E2 (9.96) | E1 (6.54) | ||||
E1, E2, E3, E4, and E5 indicate the five environments 2014–2015 Yacheng, 2014–2015 Damao, 2015–2016 Yacheng, 2015–2016 Damao in the greenhouse, and 2015–2016 Damao, respectively; Fast-LMM, FarmCPU, BLINK, MLMM, and MLM were models used in GAPIT 3.6.0 software; TMLM 5 was the model used in Tassel 5 software. All the SNPs were also detected by GLM and SUPER in GAPIT 3.6.0 software and were also identified by GLM of Tassel 5 software.