A Survey of Epistasis within Angus Steers

It is hypothesized that quantitative traits, where many genes contribute to phenotype, have underlying multi-locus interactions since no single variant explains a vast proportion of phenotypic variation. There is particular interest within cattle to understand how these interactions, defined as epistasis, play a role in carcass development and quality. To study this, data from 3,958 Angus steers genotyped with the BovineSNP50 BeadChip were used to conduct a survey of epistasis via the epiSNP software package. Twelve phenotypes of interest related to growth and carcass composition were analyzed. The results of this survey indicated that some pairwise interactions (p-values < 1.0e-7) are present within four traits: hot carcass weight (HCW), ultrasound-measured intramuscular fat (USIMF), weight at ultrasound (USWT), and weaning weight (WW). A number of small epistatic networks resulted from the pairwise analysis within the top 100 most significant interactions of each trait. These networks vary in size, containing a few to dozens of loci. In order to understand these networks and compare the genes associated with these loci, the Ingenuity Pathway Analysis package was employed. Analysis is on-going for the four traits with evidence of epistasis, though early results indicate that genes associated with significant loci within HCW, USIMF, and USWT are associated with amino acid metabolism, and connective tissue development and disorder networks. However, single locus effects seem to have more impact on the trait rather than any epistatic interactions. This is consistent with previous research indicating less phenotypic variation explained by loci interaction and more from additive variation.