Table 2 QTNs consistently identified for grain weight and grain shape in at least two years by GWAS
Trait a | QTN b | Chr. | Lead SNP c | Allele d | P-value | Population/Subgroup | Year of QTN detected | Known gene |
|---|---|---|---|---|---|---|---|---|
TGW (g) | qTGW3.1 | 3 | rs3_4504988 | C/T | 2.59E-08 | Whole | 2015, 2016 | Â |
qTGW3.2 | 3 | rs3_16733441 | T/G | 2.25E-08 | Whole | 2015–2017 | GS3 [33] | |
|  | 3 | rs3_16733441 | T/G | 1.78E-11 | Xian | 2015–2017 |  | |
qTGW5 | 5 | rs5_5371529 | C/A | 7.22E-10 | Whole | 2015–2017 | qSW5/GW5 [34] | |
|  | 5 | rs5_5361877 | T/A | 1.38E-10 | Xian | 2015–2017 |  | |
qTGW7 | 7 | rs7_28305040 | A/G | 8.12E-18 | Whole | 2015–2017 | FZP [35] | |
|  | 7 | rs7_28362557 | G/A | 7.37E-08 | Xian | 2015–2017 |  | |
|  | 7 | rs7_28322588 | T/C | 1.04E-09 | Basmati | 2015–2017 |  | |
|  | 7 | rs7_28287280 | A/G | 9.14E-12 | Aus | 2015–2017 |  | |
qTGW9 | 9 | rs9_21404841 | C/T | 2.47E-08 | Whole | 2015, 2017 | Â | |
qTGW11 | 11 | rs11_3019935 | T/C | 5.17E-07 | Xian | 2016, 2017 | Â | |
GL (mm) | qGL3 | 3 | rs3_16733441 | T/G | 1.97E-73 | Whole | 2015–2017 | GS3 [33] |
|  | 3 | rs3_16733441 | T/G | 8.65E-59 | Xian | 2015–2017 |  | |
| Â | 3 | rs3_16733441 | T/G | 2.54E-15 | Temperate geng | 2016, 2017 | Â | |
|  | 3 | rs3_16733441 | T/G | 5.16E-09 | Tropical geng | 2015–2017 |  | |
| Â | 3 | rs3_16728308 | C/T | 4.75E-09 | Aus | 2016, 2017 | Â | |
qGL4 | 4 | rs4_29308534 | C/T | 1.79E-06 | Whole | 2015, 2017 | Â | |
qGL5 | 5 | rs5_5373491 | A/G | 2.49E-21 | Whole | 2015–2017 | qSW5/GW5 [34] | |
|  | 5 | rs5_5361894 | A/G | 2.09E-18 | Xian | 2015–2017 |  | |
| Â | 5 | rs5_5351264 | T/A | 3.44E-08 | Tropical geng | 2016, 2017 | Â | |
|  | 5 | rs5_5288638 | G/A | 2.58E-07 | Aus | 2015–2017 |  | |
qGL7 | 7 | rs7_28289869 | T/C | 4.62E-19 | Whole | 2015–2017 | FZP [35] | |
| Â | 7 | rs7_28287400 | C/G | 7.12E-07 | Xian | 2016, 2017 | Â | |
|  | 7 | rs7_28290297 | G/A | 1.40E-10 | Tropical geng | 2015–2017 |  | |
| Â | 7 | rs7_28287280 | A/G | 7.82E-08 | Basmati | 2016, 2017 | Â | |
qGL10 | 10 | rs10_13616240 | A/C | 1.19E-07 | Whole | 2015–2017 |  | |
GW (mm) | qGW3 | 3 | rs3_16733441 | T/G | 6.82E-09 | Whole | 2015–2017 | GS3 [33] |
|  | 3 | rs3_16717406 | G/A | 2.21E-08 | Xian | 2015–2017 |  | |
qGW5 | 5 | rs5_5371772 | G/A | 1.84E-77 | Whole | 2015–2017 | qSW5/GW5 [34] | |
|  | 5 | rs5_5361894 | A/G | 1.96E-71 | Xian | 2015–2017 |  | |
|  | 5 | rs5_5364791 | T/C | 3.73E-10 | Temperate geng | 2015–2017 |  | |
|  | 5 | rs5_5375786 | G/A | 2.07E-25 | Tropical geng | 2015–2017 |  | |
|  | 5 | rs5_5346606 | T/A | 2.16E-19 | Aus | 2015–2017 |  | |
qGW7 | 7 | rs7_24898274 | A/T | 2.59E-16 | Whole | 2015–2017 | ||
|  | 7 | rs7_24902815 | A/G | 3.17E-07 | Tropical geng | 2015–2017 |  | |
qGW8 | 8 | rs8_26504638 | A/G | 3.58E-10 | Aus | 2016, 2017 | GW8 [13] | |
RLW | qRLW1 | 1 | rs1_3657795 | A/G | 1.42E-07 | Aus | 2015, 2017 | Â |
qRLW3 | 3 | rs3_16733441 | T/G | 2.50E-55 | Whole | 2015–2017 | GS3 [33] | |
|  | 3 | rs3_16733441 | T/G | 4.00E-43 | Xian | 2015–2017 |  | |
|  | 3 | rs3_16733441 | T/G | 4.11E-07 | Temperate geng | 2015–2017 |  | |
| Â | 3 | rs3_16728485 | G/C | 6.65E-11 | Tropical geng | 2016, 2017 | Â | |
|  | 3 | rs3_16686074 | G/A | 7.33E-08 | Basmati | 2015–2017 |  | |
qRLW4 | 4 | rs4_29317460 | C/A | 3.68E-09 | Whole | 2015–2017 |  | |
|  | 4 | rs4_29309086 | C/G | 1.14E-08 | Aus | 2015–2017 |  | |
qRLW5 | 5 | rs5_5371609 | A/G | 3.59E-69 | Whole | 2015–2017 | qSW5/GW5 [34] | |
|  | 5 | rs5_5361894 | A/G | 1.25E-67 | Xian | 2015–2017 |  | |
|  | 5 | rs5_5364791 | T/C | 9.49E-12 | Temperate geng | 2015–2017 |  | |
| Â | 5 | rs5_5375793 | G/A | 5.48E-25 | Tropical geng | 2016, 2017 | Â | |
|  | 5 | rs5_5375764 | A/G | 5.56E-15 | Aus | 2015–2017 |  | |
qRLW7 | 7 | rs7_24533303 | T/C | 4.89E-13 | Whole | 2015–2017 | ||
|  | 7 | rs7_24537476 | C/T | 3.67E-07 | Xian | 2015–2017 |  | |
| Â | 7 | rs7_24902815 | A/G | 8.02E-07 | Tropical geng | 2016, 2017 | Â | |
qRLW8 | 8 | rs8_26504638 | A/G | 1.17E-14 | Aus | 2015–2017 | GW8 [13] |