Epistatic quantitative trait loci affecting chemical body composition and deposition as well as feed intake and feed efficiency throughout the entire growth period of pigs

Numerous quantitative trait loci (QTL) have been identified for growth and feed intake in pigs, however, there are currently no reports of interactions between QTL (epistasis) for these traits at different stages of growth. A genomic scan for epistatic QTL was conducted on animals from a three generation full-sib population, created by crossing Pietrain sires with a crossbred dam line. All types of two-locus interactions were fitted in the model using Cockerham's decomposition, by regressing on a linear combination of the individual QTL origin probabilities. This study is the first to report epistatic QTL for growth, feed intake and chemical body composition in pigs. Eighteen significant epistatic QTL pairs were identified, seven affecting growth, six affecting feed intake or food conversion ratio, and five affecting chemical body composition. Most interacting QTL resided on different chromosomes; only two were located on the same chromosome. The identified QTL pairs explained substantial proportions of the phenotypic variance, from 5% to 10.3%. All types of digenic epistatic effects were identified with the additive-by-additive effect being the most prevalent. These findings suggest that epistasis is important in the genomic regulation of growth, feed intake and chemical body composition. Furthermore, interactions occur between different pairs of epistatic QTL for the same trait depending on the growth stage, increasing the complexity of genomic networks. This agrees with studies on gene expression levels which showed that those are time and tissue dependent.