Table 3.
QTNs for CP, CL, HC, NDF, and ADF in the four environments using six multi-locus GWAS methods.
| Trait | QTN | Chr | Pos (bp) | Environment | GWAS | |||
|---|---|---|---|---|---|---|---|---|
| Method | Effect | LOD | r2 (%) | |||||
| CP | RSS17673 | 2 | 60877961 | 2016hn | pKWmEB pLARmEB | −0.7575 −0.0014 | 5.11 5.11 | 10.89 2.87E-05 |
| RSS22092 | 2 | 74893615 | 2015fy | pKWmEB pLARmEB | −0.9453 −0.0014 | 4.17 3.31 | 9.37 1.28E-05 | |
| RSS48493 | 5 | 65128246 | 2016hn | FASTmrEMMA | 3.0389 | 4.56 | 5.82 | |
| RSS62628 | 7 | 56446694 | 2016hn | EM_BLASSO | −0.8022 | 3.95 | 4.53 | |
| RSS72060 | 9 | 564198 | 2015hn | pLARmEB | 0.002 | 3.63 | 3.61E-05 | |
| CL | RSS21890 | 2 | 74389054 | 2015hn | FASTmrMLM EM_BLASSO pKWmEB | 0.0259 0.026 0.026 | 3.99 4.49 4.75 | 10.58 10.62 14.85 |
| RSS50197 | 5 | 70141003 | 2015fy | FASTmrMLM pKWmEB | 3.05E-05 3.45E-05 | 3.17 3.17 | 5.77E-06 6.08 | |
| RSS68908 | 8 | 52710244 | 2016hn | pLARmEB | −0.0017 | 3.47 | 1.42E-02 | |
| HC | RSS1510 | 1 | 7334364 | 2015hn | FASTmrMLM EM_BLASSO pKWmEB | 0.0273 0.0265 0.0265 | 5.32 5.36 5.36 | 7.70 7.27 10.37 |
| RSS3431 | 1 | 16641334 | 2016hn | EM_BLASSO | −2.06E-05 | 3.14 | 3.55E-06 | |
| RSS76122 | 9 | 48549474 | 2016hn | FASTmrMLM pKWmEB | 0.025 0.026 | 4.93 3.33 | 5.24 7.74 | |
| NDF | RSS973 | 1 | 5021420 | 2015fy | pLARmEB | −0.0011 | 9.61 | 9.00E-04 |
| RSS2859 | 1 | 12968078 | 2015hn | pLARmEB | 0.0031 | 4.49 | 1.47E-02 | |
| RSS3945 | 1 | 19028439 | 2015hn | pLARmEB | −0.001 | 5.26 | 6.00E-04 | |
| RSS4300 | 1 | 21729035 | 2015fy | FASTmrMLM | −5.22E-05 | 3.91 | 5.72E-06 | |
| RSS7796 | 1 | 66643031 | 2015hn | EM_BLASSO | 0.0435 | 4.12 | 10.89 | |
| RSS14238 | 2 | 9529690 | 2015hn | pLARmEB | 0.0011 | 4.50 | 1.17E-03 | |
| RSS21890 | 2 | 74389054 | 2015hn | pKWmEB | 0.0419 | 4.80 | 15.72 | |
| RSS44026 | 5 | 4665028 | 2015fy | FASTmrMLM | −1.00E-04 | 3.70 | 2.00E-04 | |
| RSS50197 | 5 | 70141003 | 2015fy | pKWmEB | 0.0428 | 4.58 | 7.07 | |
| RSS54219 | 6 | 47408694 | 2015hn | pLARmEB | 0.0014 | 3.37 | 1.58E-03 | |
| RSS55031 | 6 | 49852623 | 2015hn | pLARmEB | −0.0013 | 4.35 | 1.24E-03 | |
| RSS58234 | 6 | 58636709 | 2015fy | pLARmEB | 0.002 | 3.80 | 1.89E-03 | |
| RSS61032 | 7 | 8098766 | 2015hn | pLARmEB | 0.0019 | 4.07 | 2.19E-03 | |
| RSS65142 | 7 | 65417969 | 2015hn | pLARmEB | 0.003 | 3.17 | 7.65E-03 | |
| RSS65800 | 8 | 2362643 | 2015hn | pLARmEB | 0.0012 | 3.64 | 1.15E-03 | |
| RSS65801 | 8 | 2362646 | 2015hn | pLARmEB | 0.0011 | 3.77 | 8.00E-04 | |
| RSS66600 | 8 | 5538354 | 2015hn | pLARmEB | 0.0017 | 3.28 | 2.12E-03 | |
| RSS68217 | 8 | 48827265 | 2015hn | pLARmEB | 0.0016 | 3.90 | 2.12E-03 | |
| RSS70856 | 8 | 60604340 | 2015fy | pKWmEB | 0.044 | 4.08 | 7.77 | |
| RSS72128 | 9 | 886296 | 2015hn | pLARmEB | 0.0013 | 3.46 | 5.00E-04 | |
| RSS72803 | 9 | 2831721 | 2015fy | pLARmEB | 0.002 | 3.61 | 4.72E-03 | |
| RSS76122 | 9 | 48549474 | 2016hn | pKWmEB | 0.0302 | 3.87 | 5.99 | |
| RSS79370 | 9 | 58586399 | 2015fy | pLARmEB | −0.0037 | 3.76 | 1.33E-02 | |
| RSS81889 | 10 | 12257429 | 2015hn | pLARmEB | −0.0012 | 3.15 | 2.21E-03 | |
| ADF | RSS29915 | 3 | 60813170 | 2015fy | mrMLM | 0.0763 | 4.41 | 20.24 |
| RSS35476 | 4 | 6415156 | 2015hn | EM_BLASSO pKWmEB | −0.0159 −9.00E-04 | 3.27 3.38 | 2.98 4.43 | |
| RSS40375 | 4 | 60973382 | 2015hn | EM_BLASSO | 0.0144 | 3.51 | 3.09 | |
| RSS50197 | 5 | 70141003 | 2015fy | FASTmrMLM EM_BLASSO pLARmEB | 0.0292 0.0292 0.0032 | 4.42 4.42 3.64 | 3.97 3.97 4.91E-02 | |
| RSS68908 | 8 | 52710244 | 2016hn | pLARmEB | −0.0018 | 3.44 | 1.41E-02 | |
| RSS79627 | 10 | 386174 | 2015fy | pLARmEB | 0.0047 | 3.10 | 0.28 | |
| RSS83457 | 10 | 50561994 | 2015hn | FASTmrMLM pKWmEB | 0.0178 0.0175 | 3.15 3.26 | 4.25 7.09 | |