Table 2.
List of causative genes obtained from GWAS.
| Trait | SNPs Position |
p_Wald | Locus | Gene Name | Description | |
|---|---|---|---|---|---|---|
| 1 | SI_SFW | 1999390 | 7.86 × 10−9 | LOC_Os01g04490 | Ser/Thr protein kinase | protein modification process, kinase activity |
| 2 | S_SFW | 20146031 | 7.08 × 10−8 | LOC_Os01g36330 | expressed protein | - |
| 3 | SI_SFW | 22455127 | 7.86 × 10−9 | LOC_Os02g37140 | expressed protein | - |
| 4 | SI_SFW | 23113356 | 7.86 × 10−9 | LOC_Os02g38210 | elongation factor Tu | translation factor activity and hydrolase activity |
| 5 | S_RFW | 12601958 | 2.52 × 10−7 | LOC_Os05g22260 | crooked neck, putative | nucleic acid metabolic process, binding |
| 6 | SI_SFW | 1048462 | 1.46 × 10−8 | LOC_Os06g02850 | expressed protein | - |
| 1048463 | 1.46 × 10−8 | |||||
| 7 | SI_SFW | 1361687 | 1.46 × 10−8 | LOC_Os06g03520 | DUF581 domain-containing protein | - |
| 8 | S_CMS | 24510573 | 7.54 × 10−8 | LOC_Os06g41040 | pentatricopeptide | - |
| SI_CMS | 24510573 | 2.3 × 10−7 | ||||
| 9 | S_CMS | 24516977 | 6.75 × 10−8 | LOC_Os06g41050 | expressed protein | response to abiotic stimulus, DNA metabolic process, cell cycle, reproduction |
| S_CMS | 24517076 | 2.51 × 10−7 | ||||
| SI_CMS | 24516977 | 2.4 × 10−7 | ||||
| 10 | S_CMS | 24577287 | 2.51 × 10−7 | LOC_Os06g41110 | tubulin binding cofactor C | involve in the folding and assembly of α- and β-tubulin monomers |
| 11 | S_CMS | 24628013 | 2.51 × 10−7 | LOC_Os06g41160 | expressed protein | carbohydrate metabolic process, metabolic process |
| 24628494 | 2.51 × 10−7 | |||||
| 12 | S_RFW | 21151187 | 2.52 × 10−7 | LOC_Os07g35350 | glucan endo-1,3-beta-glucosidase precursor | carbohydrate metabolic process, hydrolase activity |
| 13 | S_RFW | 21365153 | 2.52 × 10−7 | LOC_Os07g35660 | DUF26 kinases | kinase activity, protein modification process |
| 14 | SI_RDW | 6056897 | 8.8 × 10−8 | LOC_Os08g10340 | OsFBX278–F-box domain-containing protein | - |
| 6056962 | 8.8 × 10−8 | |||||
| 15 | RDW | 22317650 | 9.82 × 10−9 | LOC_Os09g38850 | OsWAK91–OsWAK receptor-like protein kinase | kinase activity, protein binding |
| 16 | SI_SFW | 17049126 | 7.86 × 10−9 | LOC_Os11g29380 | MCM2–Putative minichromosome maintenance MCM complex subunit 2 | multicellular organismal development and embryo development |
| 17 | SI_SFW | 17065481 | 7.86 × 10−9 | LOC_Os11g29400 | 6-phosphogluconate dehydrogenase | catalytic activity |
| 18 | SI_SFW | 17130888 | 7.86 × 10−9 | LOC_Os11g29520 | NBS-LRR disease resistance protein | protein binding, response to stress |
| 19 | SI_RDW | 17953322 | 8.8 × 10−8 | LOC_Os11g30830 | expressed protein | transferase activity, response to endogenous stimulus |
| 20 | SI_RDW | 19167004 | 9.7 × 10−9 | LOC_Os11g32470 | NEF1 | response to water deprivation |
| 21 | SI_SFW | 22502331 | 7.86 × 10−9 | LOC_Os11g37950 | WIP3–Wound-induced protein precursor | protein and carbohydrate binding, response to abiotic and biotic stress |
| 22 | SFW | 27245040 | 7.08 × 10−9 | LOC_Os11g44990 | NB-ARC domain-containing protein | protein binding, response to stress |
| 27245051 | 7.08 × 10−8 | |||||
| 23 | SI_RDW | 18009787 | 9.7 × 10−9 | LOC_Os12g30070 | disease resistance protein RPM1 | trigger plants defense systems against biotic stress |
| 24 | SFW | 22127633 | 7.08 × 10−8 | LOC_Os12g36100 | kinesin-4 | nucleotide binding, motor activity |
| 25 | RFW | 23267837 | 2.52 × 10−7 | LOC_Os12g37860 | expressed protein | regulation of gene expression, epigenetic |