Table 2. Candidate genes identified near significant GWAS peaks.
| Candidate gene(ref.) | Trait | Chr. | Gene | Biological pathway | Position* |
|---|---|---|---|---|---|
| SD142 | Plant height | 1 | LOC_Os01g66100† | Gibberellin enzyme | 38,418,739 |
| EP3/LP43 | PL | 2 | LOC_Os02g15950† | F-box transcription factor; cytokinin homeostasis | 9,109,565 |
| OsMADS4744 | Panicle branch number | 3 | LOC_Os03g08754 | MADS-Box transcription factor | 4,468,547 |
| OsKS145 | Panicle NL traits | 4 | LOC_Os04g52230† | Gibberellin enzyme | 31,029,056 |
| CYP90D346 | Panicle branch length, panicle NL traits | 5 | LOC_Os05g11130 | Brassinosteroid enzyme | 6,264,833 |
| GID147 | Booting | 5 | LOC_Os05g33730† | Soluble gibberellin receptor | 19,891,242 |
| OsGA2 oxidase-544 | Shoot biomass | 7 | LOC_Os07g01340‡ | Gibberellin enzyme | 216,325 |
| OsBZR148 | Panicle NL traits | 7 | LOC_Os07g39220 | Transcription factor; brassinosteroid homeostasis | 23,477,027 |
| FZP49 | Secondary panicle branching | 7 | LOC_Os07g47330 | AP2 domain transcription factor | 28,297,303 |
| WRKY250 | Panicle branch length traits | 10 | LOC_Os10g42850† | WRKY transcription factor | 23,095,323 |
Chr., chromosome; GWAS, genome-wide association study; NL, internode length; PL, panicle length; QTL, quantitative trait loci; RIL, recombinant inbred line; SNP, single-nucleotide polymorphism.
*Closest significant SNP. Position in bp based on MSUv7 assembly. Manhattan plots for trait associations are located within Supplementary Figs 6–64.
†Overlap with QTL identified using the IR64 × Azucena RIL population.
‡Identified without heading covariate.