TABLE 1.
QTLs for pericarp color identified in this study.
| QTL | Environment† | Evaluation method* | Chromosome | The most significant SNP position (bp)# | p-value | Variation explained (%) | Co-location QTL/Candidate genes§ | References |
| Whole population | ||||||||
| qPC-1 | 2016GZ | PA | 1 | 28,560,888 | 2.68E-07 | 3.61 | ||
| DPC | 28,560,888 | 4.43E-07 | 3.69 | |||||
| 2018YJ | PA | 1 | 28,560,888 | 2.68E-07 | 3.61 | |||
| DPC | 28,560,888 | 3.87E-07 | 4.25 | |||||
| qPC-2 | 2016GZ | DPC | 2 | 20,137,220 | 3.41E-05 | 2.46 | ||
| qPC-3 | 2016GZ | PA | 3 | 7,256,887 | 3.49E-06 | 2.92 | ||
| 2018YJ | PA | 3 | 7,256,887 | 3.49E-06 | 2.92 | |||
| qPC-6 | 2016GZ | PA | 6 | 2,829,129 | 7.79E-05 | 2.10 | ||
| DPC | 2,829,129 | 2.63E-05 | 2.53 | |||||
| 2018YJ | PA | 6 | 2,829,129 | 7.79E-05 | 2.10 | |||
| DPC | 2,829,129 | 5.15E-05 | 2.67 | |||||
| qPC-7 | 2016GZ | PA | 7 | 6,105,212 | 1.19E-24 | 15.72 | Rc | Sweeney et al., 2006 |
| DPC | 6,105,212 | 1.25E-24 | 16.66 | |||||
| 2018YJ | PA | 7 | 6,105,212 | 1.19E-24 | 15.72 | |||
| DPC | 6,218,264 | 1.17E-22 | 17.19 | |||||
| qPC-8a | 2016GZ | PA | 8 | 6,095,179 | 1.47E-06 | 3.15 | ||
| DPC | 6,095,179 | 5.63E-06 | 2.96 | |||||
| 2018YJ | PA | 8 | 6,095,179 | 1.47E-06 | 3.15 | |||
| DPC | 6,095,179 | 1.51E-06 | 3.8 | |||||
| qPC-8b | 2016GZ | PA | 8 | 9,415,989 | 2.05E-05 | 2.45 | ||
| DPC | 9,526,822 | 2.08E-05 | 2.6 | |||||
| 2018YJ | PA | 8 | 9,415,989 | 2.05E-05 | 2.45 | |||
| DPC | 9,526,822 | 1.38E-05 | 3.09 | |||||
| qPC-8c | 2016GZ | PA | 8 | 12,397,795 | 1.70E-09 | 5.01 | Os08g0301500 | Huang et al., 2010 |
| DPC | 12,396,756 | 4.47E-10 | 5.71 | |||||
| 2018YJ | PA | 8 | 12,397,795 | 1.70E-09 | 5.01 | |||
| DPC | 12,397,795 | 7.29E-09 | 5.57 | |||||
| qPC-8d | 2018YJ | DPC | 8 | 17,842,687 | 1.87E-05 | 2.99 | RM339 ⋇ | Shao et al., 2011 |
| qPC-9 | 2016GZ | PA | 9 | 16,851,795 | 2.30E-05 | 2.42 | ||
| DPC | 16,851,795 | 1.44E-05 | 2.70 | |||||
| 2018YJ | PA | 9 | 16,851,795 | 2.30E-05 | 2.42 | |||
| DPC | 16,851,795 | 3.81E-05 | 2.77 | |||||
| qPC-11 | 2016GZ | PA | 11 | 4,082,549 | 1.84E-05 | 2.48 | ||
| DPC | 4,082,549 | 1.64E-06 | 3.31 | |||||
| 2018YJ | PA | 11 | 4,082,549 | 1.84E-05 | 2.48 | |||
| DPC | 4,236,188 | 9.38E-06 | 3.21 | |||||
| Colored population | ||||||||
| qPC_C-3 | 2016GZ | DPC | 3 | 14,087,316 | 2.30E-07 | 25.24 | ||
| 2018YJ | DPC | 3 | 14,032,259 | 6.13E-06 | 16.53 | |||
| qPC_C-6 | 2016GZ | DPC | 6 | 5,129,068 | 3.63E-05 | 15.43 | OsC1 | Gao et al., 2011; Hu et al., 2020 |
| qPC_C-9 | 2016GZ | DPC | 9 | 5,331,163 | 1.42E-06 | 21.6 | qDRC-9 | Dong et al., 2008 |
| qPC_C-10 | 2016GZ | DPC | 10 | 13,761,244 | 9.45E-06 | 17.94 | ||
†The experimental bases of Guangzhou in 2016 (2016GZ) and Yangjiang in 2018 (2018YJ).
*Evaluation of pericarp color based on the presence and absence of pigmentation in the pericarp (PA) and degree of pericarp color (DPC).
#Position of the most significant SNP at the QTL region.
§ QTLs or candidate genes for PC identified by the previous studies.
⋇Simple sequence repeat marker associated with grain color and flavonoid content.