| Chromosome | SNP physical position (bp) | HTR | Candidate gene containing SNP (AGP v2 position in bp) | LES | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| P-value | q-Value | Allelea | Nb | Allele effectc | (R2)d | P-value | Allele effects | R2 | |||
| 5 | 183,737,260e | 3.8 × 10−5 | 0.267 | G | 142 | −0.101 | 7.7 | RING-H2 finger/U-box domain-containing protein: 183,736,532–183,737,776 | 8.6 × 10−3 | +0.626 | 3.1e |
| A | 89 | 0.0 | 0.0 | ||||||||
| 7 | 148,173,418e | 3.5 × 10−5 | 0.267 | G | 198 | +0.162 | 7.8 | NEP-interacting protein 2/RING-H2 finger domain: 148,172,765–148,175,864 | 1.4 × 10−4 | −1.337 | 6.6 |
| A | 31 | 0.0 | 0.0 | ||||||||
| 9 | 121,167,503e | 2.9 × 10−5 | 0.267 | A | 161 | +0.130 | 8.6 | EF1-α protein family: 121,171,302–121,173,779 | 9.4 × 10−4 | −0.916 | 5.4e |
| G | 52 | 0.0 | 0.0 | ||||||||
| 10 | 21,693,685e | 3.3 × 10−7 | 0.014 | A | 83 | +0.128 | 12.0 | DNA polymerase α/ε-subunit B: 21,678,999–21,694,247 | 8.1 × 10−6 | −1.093 | 9.1e |
| G | 147 | 0.0 | 0.0 | ||||||||
| 10 | 21,722,883f | 4.1 × 10−6 | — | C | 65 | +0.109 | 10.1 | HSP70: 21,722,658–21,727,770 | 8.2 × 10−7 | −1.205 | 11.9e |
| T | 156 | 0.0 | 0.0 | ||||||||
| 10 | 21,823,409e | 8.7 × 10−5 | 0.182 | A | 96 | +0.108 | 9.8 | UEV/ELC/Vps23p/TSG101: 21,821,274–21,820,222 | 2.2 × 10−5 | −1.032 | 9.7e |
| C | 119 | 0.0 | 0.0 | ||||||||
↵a Alleles are from homozygote genotypes.
↵b N, total number of lines with the specific SNP genotype.
↵c Positive allelic effects for HTR and LES imply a suppressive and enhancing effect on the HR phenotype, respectively.
↵d R2, proportion of phenotypic variance explained by SNP.
↵e Based on SNPs from Illumina chip.
↵f Based on SNPs obtained by GBS.