Mapping Epistatic Interactions for Trait Analysis

Pairwise epistatic interactions were mapped by Bloom et al.^{3 (link)}. Networks of epistatic loci were inferred by connecting loci that displayed pairwise interactions. The R-package igraph³⁵ was used to visualize individual networks and to identify network hubs. The GWA analysis for growth on indoleacetic acid containing medium among the segregants with the BY-allele at the hub-locus was performed using the qtscore function in the R-package GenABEL^{36 (link)}. Genome-wide significance was determined using a Bonferroni-corrected significance threshold for the number of tested markers
$\left(p<\frac{0.05}{28,220}=1.8\times {10}^{-6}\right)$ . The additive genetic variance explained by a certain set of QTL was calculated as the R² from a fixed effect model without interactions.