For the 28 selected markers, two criteria were used to select: (1) causal variants within known flowering time genes (Ef-cd, Hd1, Ghd7 and Ghd8) and (2) lead variants in loci significantly associated with ATI.
| VarID | Chrom | Position | REF | ALT | Source |
|---|---|---|---|---|---|
| vg0140363925 | 1 | 40363925 | GAGGA | G | causal variants within OsMADS51 |
| vg0205101625 | 2 | 5101625 | C | CA | ATI GWAS lead variants |
| vg0223990288 | 2 | 23990288 | C | A | causal variants within OsCOL4 |
| vg0223991055 | 2 | 23991055 | GTGCA | G | causal variants within OsCOL4 |
| vg0230096330 | 2 | 30096330 | A | G | causal variants within DTH2 |
| vg0300718648 | 3 | 718648 | A | T | causal variants within Ehd4 |
| vg0301208026 | 3 | 1208026 | C | CT | ATI GWAS lead variants |
| vg0301666408 | 3 | 1666408 | A | AGTACACGATCACGCATGGCCTCTGTGTTGTGTACTCGT | causal variants within MIR528 |
| vg0313227329 | 3 | 13227329 | C | T | ATI GWAS lead variants |
| vg0416552855 | 4 | 16552855 | C | T | ATI GWAS lead variants |
| vg0423388047 | 4 | 23388047 | C | T | ATI GWAS lead variants |
| vg0602235191 | 6 | 2235191 | A | G | causal variants within Hd17 |
| vg0602928178 | 6 | 2928178 | G | A | causal variants within RFT1 |
| vg0602940130 | 6 | 2940130 | A | T | causal variants within Hd3a |
| vg0602942292 | 6 | 2942292 | C | A | causal variants within Hd3a |
| vg0609338004 | 6 | 9338004 | CTT | C | causal variants within Hd1 |
| vg0609338220 | 6 | 9338220 | CAAGA | C | causal variants within Hd1 |
| vg0627917507 | 6 | 27917507 | GA | G | ATI GWAS lead variants |
| vg0700383094 | 7 | 383094 | T | C | ATI GWAS lead variants |
| vg0709154489 | 7 | 9154489 | G | C | causal variants within Ghd7 |
| vg0729627357 | 7 | 29627357 | AGAACGTTG | A | causal variants within Ghd7.1 |
| vg0803961806 | 8 | 3961806 | G | A | ATI GWAS lead variants |
| vg0804334281 | 8 | 4334281 | GGCCTTCTC | G | causal variants within Ghd8 |
| vg0804334416 | 8 | 4334416 | CT | C | causal variants within Ghd8 |
| vg0913872114 | 9 | 13872114 | C | A | ATI GWAS lead variants |
| vg0916354642 | 9 | 16354642 | C | A | ATI GWAS lead variants |
| vg1017076177 | 10 | 17076177 | T | C | causal variants within Ehd1 |
| vg1102454121 | 11 | 2454121 | C | T | causal variants within RCN1 |