Table 3 The list of MTAs and SNP markers significant with main agronomic traits
From: GWAS of agronomic traits in soybean collection included in breeding pool in Kazakhstan
Traits | Chr. | Position | P value | R2(%) | MAF | Allele | Effect |
|---|---|---|---|---|---|---|---|
VER2 | 06 | 20,370,075 | 5.8011E-5 | 24.6 | 0.179 | C/T | 5.77 |
19 | 49,964,637 | 7.2399E-6 | 21.2 | 0.152 | C/T | 5.73 | |
R2R4 | 2 | 45,940,601 | 2.4647E-5 | 24.0 | 0.232 | C/T | −10.18 |
10 | 3,066,211 | 1.2186E-5 | 23.5 | 0.268 | C/T | −1.84 | |
17 | 14,418,215 | 5.4006E-5 | 18.9 | 0.116 | A/G | −5.13 | |
20 | 3,020,597 | 1.0172E-5 | 23.3 | 0.313 | C/T | −3.43 | |
20 | 14,721,991 | 4.6494E-6 | 20.5 | 0.156 | A/G | 12.37 | |
20 | 23,536,158 | 2.6634E-5 | 17.1 | 0.344 | A/G | −7.95 | |
R2R8 | 5 | 8,597,246 | 4.0476E-5 | 14.7 | 0.063 | C/T | 17.73 |
20 | 3,020,597 | 1.0172E-5 | 23.3 | 0.313 | C/T | −3.43 | |
20 | 8,185,857 | 4.1578E-6 | 13.9 | 0.085 | C/T | −6.03 | |
R4R8 | 5 | 8,597,246 | 4.0476E-5 | 14.7 | 0.063 | C/T | 17.73 |
14 | 9,803,364 | 8.8788E-5 | 19.5 | 0.219 | C/T | −12.50 | |
14 | 28,158,698 | 1.9669E-5 | 18.4 | 0.290 | C/T | 4.85 | |
19 | 27,283,886 | 3.1538E-5 | 21.2 | 0.321 | C/T | 4.92 | |
VER8 | 10 | 48,586,134 | 5.5824E-5 | 24.9 | 0.259 | A/C | 3.32 |
14 | 7,151,265 | 8.5988E-5 | 17.3 | 0.446 | A/G | −10.63 | |
19 | 48,168,077 | 1.0025E-5 | 30.7 | 0.201 | A/G | −6.81 | |
20 | 3,020,597 | 1.0172E-5 | 23.3 | 0.313 | C/T | −3.43 | |
20 | 8,185,857 | 4.1578E-6 | 13.9 | 0.085 | C/T | −6.03 | |
20 | 14,721,991 | 4.6494E-6 | 20.5 | 0.156 | A/G | 12.37 | |
20 | 23,536,158 | 2.6634E-5 | 17.1 | 0.344 | A/G | −7.95 | |
PH | 9 | 42,241,644 | 4.7641E-5 | 15.9 | 0.487 | A/G | −14.94 |
20 | 8,185,857 | 4.1578E-6 | 13.9 | 0.085 | C/T | −6.03 | |
HFB | 9 | 42,578,079 | 4.1561E-5 | 17.2 | 0.112 | A/G | 4.20 |
20 | 40,765,691 | 3.8709E-5 | 18.5 | 0.299 | A/G | 5.46 | |
NFN | 14 | 9,803,364 | 8.8788E-5 | 19.5 | 0.219 | C/T | −12.50 |
19 | 30,103,637 | 8.2608E-5 | 17.3 | 0.317 | G/T | −5.17 | |
NSP | 8 | 14,431,777 | 1.6689E-5 | 31.0 | 0.152 | A/C | 5.04 |
10 | 981,062 | 1.7273E-5 | 30.5 | 0.156 | A/G | −7.73 | |
20 | 8,185,857 | 4.1578E-6 | 13.9 | 0.085 | C/T | −6.03 | |
20 | 30,417,244 | 4.7329E-5 | 15.7 | 0.094 | C/T | −13.06 | |
TSW | 2 | 12,244,605 | 6.6226E-5 | 22.9 | 0.496 | A/G | −31.82 |
4 | 516,796 | 8.8647E-5 | 21.7 | 0.335 | A/G | −33.08 | |
5 | 3,859,212 | 1.1104E-5 | 24.8 | 0.357 | C/T | −32.22 | |
7 | 16,031,010 | 6.2361E-5 | 18.8 | 0.161 | C/T | −22.28 | |
17 | 10,106,704 | 2.7099E-5 | 24.7 | 0.107 | C/T | −49.48 | |
20 | 14,721,991 | 4.6494E-6 | 20.5 | 0.156 | A/G | 12.37 | |
YP | 14 | 27,937,142 | 3.9461E-5 | 15.4 | 0.094 | C/T | −4.66 |
17 | 14,418,215 | 5.4006E-5 | 18.9 | 0.116 | A/G | −5.13 | |
20 | 8,185,857 | 4.1578E-6 | 13.9 | 0.085 | C/T | −6.03 | |
20 | 30,417,244 | 4.7329E-5 | 15.7 | 0.094 | C/T | −13.06 |