Table 3. Single-nucleotide polymorphic (SNP) markers with the largest effect on various traits.
| Trait | Heritability (%) |
SNP location |
Minor allele frequency |
Significance |
||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Linkage group | Scaffold | Position (basepair) | Asian | European | Hybrid | P-value | FDR | R2 (%) | ||
| FF | 67 | 16 | S71.0 | 485233 | 0 | 0.1 | 0.03 | 4×10−7 | 0.006 | 8 |
| TA | 17 | 2 | S895.0 | 79244 | 0.13 | 0 | 0.11 | 1×10−5 | 0.165 | 8 |
| Shape | 58 | 13 | S83.0 | 565142 | 0.09 | 0.41 | 0.13 | 1×10−5 | 0.197 | 6 |
| RUS | 54 | 8 | S398.0 | 140201 | 0.22 | 0 | 0.03 | 1×10−6 | 0.021 | 10 |
| SCU | 61 | 15 | S149.0 | 728797 | 0.17 | 0 | 0.02 | 8×10−6 | 0.098 | 9 |
| OCOL | 86 | 9 | S155.0 | 757109 | 0 | 0.07 | 0.02 | 2×10−5 | 0.172 | 6 |
Abbreviations: FDR, false discovery rate; FF, fruit firmness; MAF, minor allele frequency; OCOL, skin over-colour; RUS, skin russet cover; SCU, scuffing; TA, titratable acidity.
Genomic location, MAF in different genetic groups, probability of significance (P-value), FDR and percent variance explained (R2) are shown for each SNP.