Table 2.
QTL identified for nine traits in two environments.
| QTL | Env | Peak SNP | Allelesa | MAF | p | Effectb | R2(%)c |
|---|---|---|---|---|---|---|---|
| qGL2 | SZ | S2_7684141 | C/T | 0.12 | 2.5E-05 | −0.59 | 8.2 |
| qGL3.1 | SY | S3_1249933 | T/C | 0.13 | 1.7E-05 | −0.52 | 7.8 |
| SZ | S3_1249933 | T/C | 0.14 | 7.2E-05 | −0.49 | 7.2 | |
| qGL3.2 | SY | S3_5043816 | G/A | 0.11 | 6.1E-05 | 0.74 | 6.8 |
| qGL3.3 | SY | S3_15049416 | A/G | 0.12 | 3.4E-05 | −0.80 | 7.2 |
| SZ | S3_15434503 | C/T | 0.12 | 5.1E-06 | −0.90 | 9.5 | |
| qGL3.4 | SY | S3_15745213 | C/T | 0.13 | 3.0E-06 | −0.77 | 9.2 |
| SZ | S3_15745213 | C/T | 0.13 | 3.0E-05 | −0.71 | 8.1 | |
| qGL3.5 | SY | S3_16883926 | G/A | 0.49 | 2.4E-06 | 0.66 | 9.6 |
| SZ | S3_16785761 | A/G | 0.47 | 2.3E-05 | −0.61 | 8.5 | |
| qGL4.1 | SZ | S4_17471146 | T/C | 0.35 | 3.1E-05 | 0.45 | 8.5 |
| qGL4.2 | SZ | S4_18248441 | T/C | 0.12 | 5.2E-05 | 0.63 | 7.5 |
| qGL4.3 | SY | S4_20297417 | G/A | 0.15 | 2.8E-05 | 0.74 | 8.0 |
| SZ | S4_20137296 | T/A | 0.08 | 8.7E-05 | 0.61 | 7.0 | |
| qGL6.1 | SY | S6_3562109 | C/T | 0.13 | 9.2E-05 | 0.49 | 6.5 |
| qGL6.2 | SZ | S6_8736179 | C/T | 0.09 | 3.5E-05 | −0.67 | 7.7 |
| qGL7 | SY | S7_22569856 | A/T | 0.20 | 1.7E-05 | −0.62 | 7.8 |
| SZ | S7_22569856 | A/T | 0.22 | 1.0E-04 | −0.57 | 6.6 | |
| qGL8 | SZ | S8_2849446 | A/T | 0.11 | 3.6E-06 | −0.67 | 11.1 |
| qGL9 | SZ | S9_8688246 | C/T | 0.32 | 8.1E-06 | −0.49 | 9.5 |
| qGW1.1 | SY | S1_10935666 | C/A | 0.13 | 3.8E-05 | −0.20 | 7.2 |
| SZ | S1_10935666 | C/A | 0.13 | 3.2E-05 | −0.19 | 8.0 | |
| qGW1.2 | SZ | S1_35120676 | G/A | 0.18 | 1.1E-05 | −0.30 | 8.9 |
| qGW3.1 | SZ | S3_7012384 | T/C | 0.21 | 5.7E-05 | −0.51 | 7.4 |
| qGW3.2 | SY | S3_15203521 | G/A | 0.16 | 2.7E-05 | 0.22 | 7.4 |
| SZ | S3_15049416 | A/G | 0.14 | 3.7E-05 | 0.29 | 7.7 | |
| qGW4.1 | SZ | S4_20331973 | T/C | 0.06 | 4.8E-05 | 0.29 | 7.6 |
| qGW4.2 | SZ | S4_31788543 | G/A | 0.04 | 9.2E-05 | 0.31 | 7.1 |
| qGW5 | SY | S5_5369802 | G/A | 0.36 | 8.9E-07 | 0.17 | 10.4 |
| SZ | S5_5459847 | A/G | 0.32 | 1.0E-04 | 0.14 | 6.5 | |
| qGW6 | SZ | S6_24696098 | C/T | 0.07 | 9.2E-05 | 0.19 | 7.3 |
| qGW7.1 | SZ | S7_19709162 | G/A | 0.10 | 5.2E-05 | −0.24 | 7.8 |
| qGW7.2 | SY | S7_20971202 | C/T | 0.07 | 3.5E-05 | −0.29 | 7.8 |
| qGW7.3 | SY | S7_22569856 | A/T | 0.20 | 6.4E-05 | 0.21 | 6.7 |
| qGW7.4 | SY | S7_23080276 | G/T | 0.13 | 6.2E-05 | 0.19 | 6.7 |
| SZ | S7_22980051 | G/A | 0.06 | 2.6E-05 | −0.34 | 8.1 | |
| qGW8.1 | SZ | S8_21536949 | G/A | 0.18 | 6.8E-05 | 0.34 | 7.5 |
| qGW8.2 | SZ | S8_27055234 | G/A | 0.19 | 7.0E-06 | −0.29 | 9.5 |
| qGW9 | SZ | S9_20389437 | A/T | 0.06 | 9.2E-05 | 0.21 | 7.1 |
| qGW10.1 | SZ | S10_13811940 | C/T | 0.09 | 8.2E-05 | 0.22 | 7.2 |
| qGW10.2 | SY | S10_19624722 | T/C | 0.25 | 1.7E-05 | 0.20 | 7.8 |
| SZ | S10_19624722 | T/C | 0.27 | 1.6E-05 | 0.21 | 8.5 | |
| qGW11 | SZ | S11_5752053 | C/A | 0.16 | 1.3E-05 | 0.19 | 8.8 |
| qGLWR1 | SZ | S1_2698492 | C/T | 0.23 | 9.5E-05 | 0.29 | 7.6 |
| qGLWR2 | SY | S2_34856918 | C/T | 0.14 | 8.7E-05 | 0.42 | 6.4 |
| qGLWR3.1 | SZ | S3_14988992 | C/A | 0.12 | 2.1E-06 | −0.66 | 10.3 |
| qGLWR3.2 | SY | S3_16785761 | A/G | 0.47 | 9.9E-05 | −0.37 | 6.4 |
| SZ | S3_16785761 | A/G | 0.47 | 5.6E-05 | −0.38 | 7.5 | |
| qGLWR4.1 | SZ | S4_17267620 | G/T | 0.08 | 8.1E-05 | 0.37 | 7.3 |
| qGLWR4.2 | SZ | S4_18248441 | T/C | 0.12 | 6.6E-05 | 0.41 | 7.3 |
| qGLWR5 | SY | S5_5369802 | G/A | 0.36 | 1.8E-05 | −0.31 | 7.8 |
| SZ | S5_5369802 | G/A | 0.35 | 9.0E-05 | −0.29 | 6.9 | |
| qGLWR7 | SY | S7_22569856 | A/T | 0.20 | 9.0E-05 | −0.49 | 9.7 |
| SZ | S7_22569856 | A/T | 0.22 | 1.2E-05 | −0.44 | 8.7 | |
| qGLWR9 | SZ | S9_8714326 | G/A | 0.11 | 2.7E-05 | 0.40 | 8.0 |
| qGLWR10 | SZ | S10_19552708 | T/C | 0.38 | 6.3E-05 | −0.32 | 7.8 |
| qGLWR11.1 | SZ | S11_5752053 | C/A | 0.16 | 3.8E-05 | −0.32 | 7.8 |
| qGLWR11.2 | SY | S11_17039961 | C/G | 0.23 | 4.8E-05 | −0.55 | 6.9 |
| qGLWR12 | SZ | S12_26246050 | C/T | 0.06 | 3.8E-05 | 0.42 | 7.6 |
| qDEC1 | SZ | S1_5420348 | G/A | 0.23 | 7.3E-05 | −29.8 | 7.3 |
| qDEC3 | SZ | S3_7302378 | C/T | 0.10 | 8.7E-06 | 14.7 | 9.3 |
| qDEC7 | SY | S7_24749850 | C/T | 0.05 | 1.1E-05 | 12.3 | 8.2 |
| qDEC8 | SZ | S8_27055234 | G/A | 0.19 | 6.2E-05 | −16.9 | 7.5 |
| qPGWC3 | SZ | S3_7489318 | C/T | 0.20 | 1.2E-05 | −48.2 | 8.9 |
| qPGWC5 | SY | S5_5369802 | G/A | 0.36 | 1.9E-05 | 19.6 | 7.9 |
| SZ | S5_5369802 | G/A | 0.35 | 9.3E-06 | 23.2 | 9.6 | |
| qPGWC8 | SZ | S8_27055234 | G/A | 0.19 | 2.2E-05 | −39.5 | 8.4 |
| qPGWC10 | SZ | S10_13811940 | C/T | 0.09 | 7.4E-05 | 31.4 | 7.4 |
| qTr1 | SY | S1_29263696 | A/T | 0.06 | 1.7E-05 | 1.4 | 7.8 |
| qTr2 | SZ | S2_18924283 | C/T | 0.30 | 3.4E-05 | 1.1 | 8.1 |
| qTr4 | SY | S4_923547 | C/A | 0.23 | 5.6E-05 | 0.8 | 8.8 |
| qTr7.1 | SY | S7_6134470 | A/C | 0.05 | 1.2E-06 | 1.4 | 10.6 |
| qTr7.2 | SY | S7_24749850 | C/T | 0.05 | 4.5E-05 | 1.2 | 7.0 |
| qTr7.3 | SY | S7_25428951 | T/C | 0.29 | 9.9E-05 | 1.2 | 6.5 |
| qBRR1.1 | SZ | S1_40365293 | T/A | 0.23 | 2.8E-05 | −2.8 | 7.9 |
| qBRR1.2 | SZ | S1_42736913 | C/T | 0.23 | 7.5E-05 | −1.6 | 7.1 |
| qBRR3 | SY | S3_34735871 | G/A | 0.08 | 5.4E-05 | −3.9 | 6.9 |
| qBRR7 | SZ | S7_8452759 | C/T | 0.06 | 5.3E-05 | −2.9 | 7.3 |
| qBRR9 | SY | S9_9144846 | T/C | 0.28 | 3.8E-05 | −3.7 | 7.2 |
| qBRR11 | SY | S11_23855546 | C/T | 0.25 | 2.9E-06 | 3.0 | 9.3 |
| qMRR3 | SY | S3_34735871 | G/A | 0.08 | 5.2E-07 | −5.0 | 11.1 |
| qMRR9 | SY | S9_10381563 | G/C | 0.24 | 3.6E-05 | −5.6 | 7.5 |
| qMRR10 | SY | S10_15603572 | A/T | 0.20 | 5.8E-05 | 6.8 | 6.8 |
| qMRR11.1 | SY | S11_23855546 | C/T | 0.25 | 2.0E-05 | 2.9 | 8.1 |
| qMRR11.2 | SY | S11_27415368 | G/A | 0.19 | 7.2E-05 | −2.8 | 6.7 |
| qHMRR3 | SZ | S3_15745213 | C/T | 0.14 | 7.9E-05 | 13.4 | 7.1 |
| qHMRR9 | SY | S9_10381563 | G/C | 0.24 | 8.4E-05 | −7.4 | 6.8 |
a
Major/Minor allele.
b
Effect: Allele effect with respect to the minor allele.
c
R2 (%): Phenotypic variance explained.