Table 3 Genes of interest with HIGH impact SNPs (annotated with snpEff28 with their respective position, that overlap with eating quality QTLs (EA) and seed-related QTLs (SR). Full table available at supplementary material 1.
From: Whole-genome polymorphisms and relatedness of rice varieties circulating in the Mediterranean market
Gene ID | Chr: Position | Modification | EA QTLs | SR QTLs | Total QTLs |
|---|---|---|---|---|---|
Os8Tak2 | 1: 858,021 | Stop gained | QTAROqtl-987, QTAROqtl-989, qST3-2, qAC-6 | yd1a, gy12 | 6 |
PAO1 | 1: 29,513,400 | Stop gained | QTAROqtl-623, QTAROqtl-1048, QTAROqtl-1049, QTAROqtl-288 | QTAROqtl-362, gpp4, QTAROqtl-705 | 6 |
OsYUCCA12 | 2: 9,878,862 | Stop gained | qOE3-1, qTA3, amy6-1, asv6-1, QTAROqtl-5, qAC9, qPC9, elr11-1, QTAROqtl-294 | qGW3, qGY-3, gwt4a, gwt4a, QKw5, qTHJ-5, qGY6-1, gw-6, QTAROqtl-154, QTAROqtl-449 | 19 |
GS3 | 3: 16,733,441 | Stop gained | qGL3-1, amy6-1, asv6-1, QTAROqtl-5, elr11-1 | gw3.1, qGL-3, qLWR-3, gwt4a, gwt4a, QKw5, qGY6-1, gw-6, QTAROqtl-154, QTAROqtl-449 | 15 |
OsbHLH148 | 3: 30,406,910 | Start lost | QTAROqtl-623, qER-2a | QTAROqtl-362, gpp4 | 4 |
WX1 | 6: 1,765,761 | Splice donor & intron variant | QTAROqtl-987, QTAROqtl-989, qST3-2, qAC-6, hr6, alk6-1, qGC-6, qAC9, qPC9, QTAROqtl-157 | yd1a, gy12 | 12 |
OsPol lambda | 6: 7,131,087 | Splice donor & intron variant | qOE3-1, qTA3, amy6-1, asv6-1, QTAROqtl-5, QTAROqtl-157, QTAROqtl-294, qGT-6, qAC9, qPC9, elr11-1 | qEML-2, QKw5, tns6, sd6, qGY6-1, nfb8, QTAROqtl-154, QTAROqtl-449, gy12 | 20 |
