Table 2. Exhaustive two-dimensional GWAS-scan for epistasis identifies six significant interactions, representing four unique pairs, associated with the root length mean.
| Pair | SNP1 1 | SNP2 1 | Interaction (mm) | p-value 2 (GWA) | p-value 3 (SS) | R2 *(95% CI) |
|---|---|---|---|---|---|---|
| 1 | rs346846662 (3_66596) | rs347034954/rs347048583 (3_9273674/3_9272294) | 0.55 | 1.5×10−10 | 0.003 | 0.1486 (0.1384–0.1588) |
| 2 | rs347005428 (1_17257526) | rs346595296/rs346511785 (5_15862026/5_15862525) | 0.63 | 1.7×10−10 | 0.28 | 0.1332 (0.1203–0.1441) |
| 3 | rs346846662 (3_66596) | rs347177728 (5_18241640) | 0.63 | 3.0×10−10 | 0.37 | 0.1287 (0.1143–0.1430) |
| 4 | rs347374065 (3_10891195) | rs347377866 (5_1027939) | 0.63 | 2.3×10−10 | 0.95 | 0.1289 (0.1142–0.1436) |
1Name of associated SNP(s) at the epistatic locus as on the Affymetrix single nucleotide polymorphism (SNP) chip (our abbreviation as Chromosome_PositionInBp);
2p-value for the interaction effect of the two loci in the epistatic GWA analysis [40];
3Probability that the pair is a false-positive when accounting for the small sample-size (SS) [42].
*R2, phenotypic variance explained per pair.