TABLE 1.
QTLs identified from DC1 and BIM populations for the five grain size-related traits.
| QTL | Panel | Enva | Year | Chrb | Peak SNP | Posc | Allelesd | p-value | %PVEe | Effectf | Known gene |
| qGL3.1 | DC1 | Hainan | 2017 | 3 | AX-154083640 | 16806335 | A/C | 1.93E-09 | 54.73 | 0.3293 | GS3 |
| DC1 | Hainan | 2018 | 3 | AX-154083640 | 16806335 | A/C | 6.58E-09 | 55.28 | 0.0462 | GS3 | |
| BIM | IRRI | 2017 | 3 | rs3_16842769 | 16842769 | C/T | 3.80E-16 | 35.07 | 0.3425 | GS3 | |
| BIM | Hainan | 2018 | 3 | rs3_16842769 | 16842769 | C/T | 4.04E-10 | 21.60 | 0.0127 | GS3 | |
| BIM | Henan | 2018 | 3 | rs3_16729992 | 16729992 | G/C | 5.37E-10 | 21.56 | 0.2809 | GS3 | |
| qGL3.2 | DC1 | Hainan | 2017 | 3 | AX-165099081 | 21547035 | C/T | 8.71E-06 | 54.73 | 0.2209 | – |
| DC1 | Hainan | 2018 | 3 | AX-115865890 | 21602538 | C/T | 1.19E-06 | 55.28 | 0.0330 | – | |
| BIM | IRRI | 2017 | 3 | rs3_20691702 | 20691702 | G/T | 1.01E-07 | 35.07 | −0.1906 | – | |
| BIM | Hainan | 2018 | 3 | rs3_20691702 | 20691702 | G/T | 1.73E-06 | 21.60 | −0.0154 | – | |
| BIM | Henan | 2018 | 3 | rs3_20691702 | 20691702 | G/T | 1.66E-06 | 17.74 | −0.2016 | – | |
| qGL7 | BIM | IRRI | 2017 | 7 | rs7_24645555 | 24645555 | A/G | 6.82E-06 | 35.07 | 0.2911 | GL7/GW7/SLG7 |
| BIM | Hainan | 2018 | 7 | rs7_24669663 | 24669663 | C/G | 6.69E-06 | 21.60 | −0.0117 | GL7/GW7/SLG7 | |
| qGW5 | DC1 | Hainan | 2017 | 5 | AX-165092179 | 5364311 | G/T | 3.08E-15 | 59.78 | −0.1506 | GW5/qSW5 |
| DC1 | Hainan | 2018 | 5 | AX-165092179 | 5364311 | G/T | 1.03E-12 | 24.88 | −0.0021 | GW5/qSW5 | |
| BIM | IRRI | 2017 | 5 | rs5_4753775 | 4753775 | A/G | 4.54E-09 | 22.78 | 0.1164 | – | |
| BIM | Hainan | 2018 | 5 | rs5_4882721 | 4882721 | A/T | 4.08E-07 | 17.96 | −0.0231 | – | |
| BIM | Henan | 2018 | 5 | rs5_4685451 | 4685451 | C/G | 1.37E-05 | 10.42 | −0.0983 | – | |
| qGW7 | BIM | IRRI | 2017 | 7 | rs7_24380529 | 24380529 | A/G | 1.83E-07 | 22.78 | 0.1016 | GL7/GW7/SLG7 |
| BIM | Hainan | 2018 | 7 | rs7_24279896 | 24279896 | C/G | 5.46E-07 | 17.96 | −0.0061 | GL7/GW7/SLG7 | |
| BIM | Henan | 2018 | 7 | rs7_24505268 | 24505268 | A/T | 1.03E-05 | 10.42 | −0.0740 | – | |
| qGW8 | BIM | IRRI | 2017 | 8 | rs8_26573952 | 26573952 | A/C | 3.47E-09 | 22.78 | 0.0933 | GW8/OsSPL16 |
| BIM | Hainan | 2018 | 8 | rs8_26573952 | 26573952 | A/C | 6.04E-08 | 17.96 | 0.0831 | GW8/OsSPL16 | |
| BIM | Henan | 2018 | 8 | rs8_26351058 | 26351058 | C/G | 5.61E-05 | 10.42 | −0.0549 | – | |
| qGLWR3 | DC1 | Hainan | 2017 | 3 | AX-154083640 | 16806335 | A/C | 1.55E-06 | 63.35 | 0.1340 | GS3 |
| DC1 | Hainan | 2018 | 3 | AX-154083640 | 16806335 | A/C | 1.11E-06 | 59.60 | 0.0593 | GS3 | |
| BIM | IRRI | 2017 | 3 | rs3_16842769 | 16842769 | C/T | 5.96E-10 | 29.52 | 0.1453 | GS3 | |
| BIM | Hainan | 2018 | 3 | rs3_16842769 | 16842769 | C/T | 3.04E-08 | 17.95 | 0.0272 | GS3 | |
| BIM | Henan | 2018 | 3 | rs3_16842769 | 16842769 | C/T | 1.27E-05 | 11.98 | 0.1624 | GS3 | |
| qGLWR5 | DC1 | Hainan | 2017 | 5 | AX-165092179 | 5364311 | G/T | 2.31E-09 | 63.35 | 0.1667 | GW5/qSW5 |
| DC1 | Hainan | 2018 | 5 | AX-165085603 | 5368362 | C/T | 8.29E-08 | 59.60 | 0.0046 | GW5/qSW5 | |
| BIM | IRRI | 2017 | 5 | rs5_4685451 | 4685451 | C/G | 1.04E-07 | 29.52 | 0.2049 | – | |
| BIM | Hainan | 2018 | 5 | rs5_4685451 | 4685451 | C/G | 2.40E-07 | 17.95 | 0.0125 | – | |
| qGLWR7 | BIM | IRRI | 2017 | 7 | rs7_24686632 | 24686632 | A/G | 7.88E-10 | 29.52 | 0.2320 | GL7/GW7/SLG7 |
| BIM | Hainan | 2018 | 7 | rs7_24279896 | 24279896 | C/G | 6.46E-10 | 17.95 | −0.0297 | GL7/GW7/SLG7 | |
| BIM | Henan | 2018 | 7 | rs7_24505268 | 24505268 | A/T | 4.29E-07 | 19.23 | 0.1819 | GL7/GW7/SLG7 | |
| qGLWR8 | BIM | IRRI | 2017 | 8 | rs8_26573952 | 26573952 | A/C | 1.22E-07 | 29.52 | −0.1599 | GW8 |
| BIM | Hainan | 2018 | 8 | rs8_26573952 | 26573952 | A/C | 3.09E-07 | 17.95 | 0.0237 | GW8 | |
| qGT1 | BIM | IRRI | 2017 | 1 | rs1_6640911 | 6640911 | C/T | 3.54E-06 | 22.47 | −0.0311 | – |
| qGT3 | BIM | Henan | 2018 | 3 | rs3_17044632 | 17044632 | A/G | 8.04E-05 | 6.43 | −0.0231 | – |
| qGT5 | DC1 | Hainan | 2017 | 5 | AX-155076620 | 5420315 | A/C | 1.01E-05 | 30.87 | −0.0367 | GW5/qSW5 |
| DC1 | Hainan | 2018 | 5 | AX-165092179 | 5364311 | G/T | 2.35E-06 | 33.68 | −0.0009 | GW5/qSW5 | |
| BIM | Hainan | 2018 | 5 | rs5_5391586 | 5391586 | A/C | 8.39E-06 | 21.79 | −0.0004 | – | |
| qTGW3.1 | DC1 | Hainan | 2017 | 3 | AX-154017324 | 3310128 | A/G | 9.51E-06 | 40.47 | – | – |
| qTGW3.2 | BIM | IRRI | 2017 | 3 | rs3_16996623 | 16996623 | G/T | 6.79E-09 | 31.31 | 1.0800 | GS3 |
| BIM | Hainan | 2018 | 3 | rs3_16736681 | 16736681 | G/T | 4.71E-06 | 21.19 | 0.1362 | GS3 | |
| BIM | Henan | 2018 | 3 | rs3_16729992 | 16729992 | G/C | 4.78E-08 | 19.94 | 1.4490 | GS3 | |
| qTGW5 | DC1 | Hainan | 2017 | 5 | AX-165092179 | 5364311 | A/G | 2.14E-06 | 40.49 | −1.1514 | GW5/qSW5 |
| DC1 | Hainan | 2018 | 5 | AX-165092179 | 5364311 | A/G | 6.23E-06 | 40.80 | −0.0938 | GW5/qSW5 | |
| qTGW8.1 | DC1 | Hainan | 2018 | 8 | AX-115754523 | 861108 | C/T | 9.21E-05 | 40.47 | 0.1782 | – |
| qTGW8.2 | BIM | Henan | 2018 | 8 | rs8_26349349 | 26349349 | G/T | 1.94E-05 | 11.38 | 0.7771 | – |
aEnvironment where the trial was conducted, bChromosome number, cPhysical position (bp), dMajor/minor allele, ePercent phenotypic variance explained by the marker, fAllele effect with respect to minor allele.