From: Genome-Wide Association Study of Rice Rooting Ability at the Seedling Stage
Trait | marker | population-identyfied | allele | Chr | Pos | p-value | candidate genes | functional annotations |
---|---|---|---|---|---|---|---|---|
RN | seq3_1727891 | full, Pop2 | C/T | 3 | 1727891 | 6.54E-06 | CDPK13 (Ho et al., 2013) | gibberellin biosynthesis |
 |  |  |  |  |  |  |  | drought stress |
MRL,RGA,RL | seq4_5315034 | full, Pop2 | A/G | 4 | 5315034 | 9.69E-07 | OsCyc1 (Otomo et al., 2004); | allelopathy |
 |  |  |  |  |  |  | OsDTS2 (Wilderman et al., 2004) | allelopathy |
MRL,RGA,RL | seq4_15403602 | full, Pop2 | T/C | 4 | 15403602 | 8.52E-10 | Â | Â |
MRL | seq4_18740406 | Pop1 | C/G | 4 | 18740406 | 1.84E-08 | SLL1/OsSAD5 (Shelley et al., 2013) | lateral root length |
 |  |  |  |  |  |  |  | ,fatty acid denatures |
RGA | seq5_6882162 | Pop2 | T/C | 5 | 6882162 | 2.88E-05 | OsPYL (Kim et al., 2014); | abscisic acid receptor |
 |  |  |  |  |  |  | OsGA2ox10 (Lo et al., 2008) | gibberellin 2-oxidases |
RGA | seq5_6884530 | Pop2 | C/A | 5 | 6884530 | 2.88E-05 | Â | Â |
RGA | seq5_6890004 | Pop2 | G/A | 5 | 6890004 | 2.88E-05 | Â | Â |
RGA | seq5_6908893 | Pop2 | T/C | 5 | 6908893 | 2.88E-05 | Â | Â |
RGA | seq5_6935074 | Pop2 | T/G | 5 | 6935074 | 2.88E-05 | Â | Â |
RGA | seq5_6945,054 | full, Pop2 | T/C | 5 | 6945054 | 5.54E-06 | Â | Â |
RGA | seq5_6959356 | Pop2 | G/A | 5 | 6959356 | 2.88E-05 | Â | Â |
RGA | seq5_6981293 | Pop2 | T/C | 5 | 6981293 | 2.88E-05 | Â | Â |
MRL,RL | seq6_12537542 | full, Pop2 | T/C | 6 | 12537542 | 3.73E-06 | OsPT9 (Wang et al., 2014) | phosphate uptake |
MRL,RGA | seq6_29405495 | full, Pop1 | C/T | 6 | 29405495 | 3.30E-08 | OsMPK4 (Agrawal et al., 2003) | salicylic acid and jasmonic |
 |  |  |  |  |  |  |  | acid-signaling pathway |
MRL,RL,RGA | seq7_5182658 | full, Pop2 | A/G | 7 | 5182658 | 1.25E-08 | SQS (Manavalan et al., 2012) | root length |
 |  |  |  |  |  |  |  | drought tolerance |
MRL,RL | seq8_433198 | full, Pop1 | G/T | 8 | 433198 | 1.25E-05 | Â | Â |
RN | seq8_15949787 | Pop2 | G/C | 8 | 15949787 | 6.51E-07 | qtl (Lilley et al., 1996) | dehydration tolerance |
MRL,RN | seq8_18343904 | Pop1,Pop2 | T/G | 8 | 18343904 | 1.05E-08 | Â | Â |
MRL,RN | seq8_18364190 | full, Pop1,Pop2 | C/T | 8 | 18364190 | 1.77E-08 | Â | Â |
MRL | seq8_18365309 | Pop1 | C/T | 8 | 18365309 | 1.00E-07 | Â | Â |
MRL,RL,RGA | seq9_11941704 | Pop1 | T/C | 9 | 11941704 | 6.28E-09 | Â | Â |
MRL,RL | seq9_15520580 | Pop1 | A/C | 9 | 15520580 | 2.45E-07 | OsGL1–1 (Islam et al., 2009) | drought tolerance |
MRL,RL | seq11_368662 | full, Pop2 | A/G | 11 | 368662 | 5.23E-06 | Â | Â |
MRL | seq12_16592156 | Pop1 | T/C | 12 | 16592156 | 2.00E-08 | DEC (Itoh et al. 2012) | cytokinin signaling pathway root length |