Table 1.
QTL identified by GWAS for AC, GC, GT and PC in SY and SZ.
| QTL | Env | Peak | Allelesa | MAFb | p | Effectc | R2 (%)d | Gene/QTL |
|---|---|---|---|---|---|---|---|---|
| qAC1 | SZ | S1_10888508 | C/T | 0.47 | 4.10E-05 | −3.5 | 8.8 | qAC1b |
| qAC2.1 | SZ | S2_12269764 | C/T | 0.24 | 7.50E-05 | −7.1 | 8.5 | |
| qAC2.2 | SY | S2_19252894 | T/G | 0.07 | 9.90E-05 | −3.6 | 6.5 | OsBEIIb |
| qAC3 | SY | S3_33525313 | G/A | 0.08 | 5.90E-08 | −5.6 | 12.9 | qAC3 |
| qAC4 | SY | S4_28862203 | C/T | 0.14 | 5.40E-06 | −5.4 | 8.9 | |
| qAC5 | SY | S5_27617633 | G/T | 0.05 | 6.20E-05 | −4.1 | 7.0 | |
| qAC6 | SY | S6_1746440 | G/A | 0.23 | 1.10E-15 | −8.1 | 31.6 | Wx |
| SZ | S6_1746440 | G/A | 0.24 | 5.90E-08 | −6.9 | 16.3 | ||
| qAC9 | SZ | S9_20798975 | C/T | 0.25 | 7.30E-05 | −6.9 | 8.3 | qAC-9b (9) |
| qGC2 | SZ | S2_6132333 | C/A | 0.05 | 5.70E-05 | 19.3 | 8.2 | qGC-2a |
| qGC4 | SY | S4_28862203 | C/T | 0.14 | 7.50E-06 | 22.4 | 8.7 | |
| qGC6 | SY | S6_1662107 | C/T | 0.23 | 7.00E-14 | 29.4 | 26.2 | Wx |
| SZ | S6_1616444 | G/A | 0.24 | 2.90E-07 | 20.0 | 14.3 | ||
| qGC11 | SY | S11_24266777 | A/T | 0.13 | 7.80E-05 | 16.6 | 6.7 | |
| qGC12 | SY | S12_25629093 | A/G | 0.08 | 8.50E-05 | 15.3 | 6.9 | |
| qGT3 | SZ | S3_29474609 | T/C | 0.49 | 8.70E-05 | −0.8 | 11.9 | |
| qGT6 | SY | S6_6752888 | C/T | 0.31 | 2.56E-16 | 2.8 | 41.0 | ALK |
| SZ | S6_6752888 | C/T | 0.32 | 6.43E-10 | 1.2 | 16.5 | ||
| qGT7 | SY | S7_27788464 | C/G | 0.12 | 3.60E-05 | −1.5 | 7.5 | |
| qPC2 | SZ | S2_24197424 | G/C | 0.07 | 3.00E-06 | 1.6 | 7.6 | |
| qPC10.1 | SY | S10_7659738 | C/T | 0.07 | 2.90E-05 | −2.3 | 8.1 | qPC10 |
| qPC10.2 | SY | S10_17723490 | T/C | 0.29 | 1.00E-04 | −1.4 | 6.7 |
aMajor/Minor allele.
bMAF: Minor allele frequency.
cEffect: Allele effect with respect to the minor allele.
dR2 (%): Phenotypic variance explained.