Epistat : a computer program for identifying and testing interactions between pairs of quantitative trait loci

Abstract

We describe a computer program, Epistat, which combines statistical methods and color-graphic displays to facilitate the analysis of interactions between pairs of quantitative trait loci (QTLs). Epistat organizes genetic-mapping data and quantitative-trait values into graphic displays which illustrate the individual effects of single loci as well as the interactions between any two loci. Keyboard commands allow the user to search the data set for individual QTLs and to test for interactions between QTLs. For a given trait, the program displays the effects of the alleles at each of two loci on the quantitative-trait value, as well as the effects of the interactions between these alleles. Loglikelihood ratios are used to compare the likelihood of explaining the effects by null, additive, or epistatic models. Examples of interactions in soybean are presented for near-infrared transmittance (NIT), seed number, and reproductive period. Epistat has been used to find numerous interactions between QTLs in soybean in which trait variation at one locus is conditional upon a specific allele at another.