Table 1.
Main effect additive QTLs for GPC and SGPC in rice in two environments (Env.1 and Env.2).
| Trait/QTL | Environment | Chromosome | Left marker | Right marker | Start (Mb) | End (Mb) | Peak marker | LOD | PVE (%) | Add | Position (Mb) | Type of SNP | Gene function |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| qGPC1.1 | Env.1 | 1 | Affx-93237905 | Affx-93229368 | 0.61104 | 1.11104 | CSCWR_Os01g02590__61041 | 3.832 | 13.855 | −0.426 | 0.86104 | non-synonymous SNP, resides in gene | Receptor-like kinase, putative, expressed |
| qSGPC1.1 | Env.1 | 1 | Affx-93237905 | Affx-93229368 | 0.61104 | 1.11104 | CSCWR_Os01g02590__61041 | 2.897 | 10.37 | −0.083 | 0.86104 | non-synonymous SNP, resides in gene | Receptor-like kinase, putative, expressed |
| qSGPC2.1 | Env.1 | 2 | Affx-93260438 | Affx-93236905 | 5.16506 | 6.16506 | CSCWR_Os02g10740_65058 | 3.316 | 6.703 | 0.059 | 5.66506 | resides in gene, synonymous SNP | Calcium-binding mitochondrial carrier CBG00135, putative, expressed |
| qSGPC7.1 | Env.1 | 7 | Affx-93225742 | Affx-93256949 | 22.1975 | 22.2975 | SCR100_Os07g37440_17971 | 3.51 | 7.678 | 0.067 | 22.2475 | resides in gene, resides in intron | Hypothetical protein |
| qSGPC11.1 | Env.1 | 11 | Affx-93232878 | Affx-93212320 | 3.73772 | 3.83772 | SCR200_Os11g07480_87716 | 2.873 | 6.424 | 0.076 | 3.78772 | non-synonymous SNP, resides in gene | WD domain, G-beta repeat domain containing protein, expressed |
| qGPC1.1 | Env.2 | 1 | Affx-93237905 | Affx-93229368 | 0.81104 | 0.91104 | CSCWR_Os01g02590__61041 | 4.017 | 13.851 | −0.581 | 0.86104 | non-synonymous SNP, resides in gene | Receptor-like kinase, putative, expressed |
| qGPC2.1 | Env.2 | 2 | Affx-93221488 | Affx-93245529 | 9.47632 | 10.4763 | SCR200_Os02g17350_76316 | 3.186 | 17.353 | 0.923 | 9.97632 | resides in gene, synonymous SNP | VHS and GAT domain containing protein, expressed |
| qSGPC1.2 | Env.2 | 1 | Affx-93230672 | Affx-93212941 | 39.0164 | 39.1164 | SCR100_Os01g66690_66361 | 3.309 | 18.463 | 0.492 | 39.0664 | resides in gene, synonymous SNP | Gene encoding ZIP4/SPO22 |
| qSGPC1.3 | Env.2 | 1 | Affx-93228332 | Affx-93233227 | 8.30788 | 8.40788 | CSCWR_Os01g14920__57875 | 4.07 | 16.401 | 0.481 | 8.35788 | resides in 5′ UTR, resides in gene | Zinc knuckle family protein, putative, expressed |
| qSGPC2.1 | Env.2 | 2 | Affx-93256429 | Affx-93260438 | 5.61506 | 5.71506 | CSCWR_Os02g10740_65058 | 3.528 | 14.636 | 0.54 | 5.66506 | resides in gene, synonymous SNP | Calcium-binding mitochondrial carrier CBG00135, putative, expressed |
| qSGPC3.1 | Env.2 | 3 | Affx-93253793 | Affx-93260929 | 35.3227 | 37.3227 | CSCWR_Os03g64360_22659 | 4.115 | 14.653 | 0.542 | 36.3227 | resides in gene, resides in intron | Putative expressed gene |
| qSGPC7.1 | Env.2 | 7 | Affx-93225742 | Affx-93256949 | 22.1975 | 22.2975 | SCR100_Os07g37440_17971 | 3.328 | 7.813 | 0.091 | 22.2475 | resides in gene, resides in intron | Hypothetical protein |
| qSGPC8.1 | Env.2 | 8 | Affx-93259293 | Affx-93258892 | 0.90055 | 1.00055 | SCR200_Os08g02400_50552 | 4.548 | 23.547 | 0.336 | 0.95055 | resides in gene, resides in intron | 40 S ribosomal protein S13, putative, expressed |
| qSGPC12.1 | Env.2 | 12 | Affx-93257146 | Affx-93240174 | 2.27059 | 2.37059 | CSCWR_Os12g05230_20586 | 2.966 | 14.486 | 0.531 | 2.32059 | resides in 3′ UTR, resides in gene | ATP-dependent RNA helicase, putative, expressed |