Individual and epistatic genetic effects of quantitative trait loci affecting growth, feed intake, body composition and meat quality in pigs
Selection of pigs has focussed on the improvement of lean growth with simultaneous reduction in fat tissue, due to the high economic importance of these traits. As a consequence, a large number of quantitative trait loci (QTL) have been reported for these traits. In contrast, very few QTL have been reported for chemical body composition (protein and lipid). Knowledge about the deposition rates of these components is important to accurately predict the nutritional requirements of pigs and to determine selection objectives for optimal development of body tissues and feed intake capacity. Therefore, the principle aims of this thesis were to investigate the genomic regulation of physical and chemical body composition as well as feed intake, feed efficiency and meat quality in a commercial pig population. Data for all analyses were derived from a three generation full-sib design created by crossing Pietrain sires with a crossbred dam line. In total, 386 animals were genotyped for 96 molecular markers covering 11 chromosomes. Phenotypic data were available for 315 F2 animals for carcass characteristics measured at slaughter weight, chemical body composition measured at different target weights throughout growth, feed intake measured throughout growth, and meat quality traits collected post-slaughter. Individual QTL analyses of several autosomes and chromosome X uncovered a large number of QTL in different regions of the genome for physical body composition traits as well as novel QTL for chemical body composition and deposition. Associations between QTL for chemical and physical body composition were also detected. The results highlighted that different stages of growth are under different genomic regulation. Further QTL were detected for feed intake and feed efficiency and interesting causative biological reasons for QTL of feed efficiency were derived in associations with QTL for body composition and growth. Epistatic QTL analyses were performed to investigate the contribution of interactions (epistasis) to the genomic regulation of physical and chemical body composition as well as growth and feed intake. Epistasis was found to contribute to the entire growth period, however, different epistatic QTL pairs contributed to different stages of growth. Epistatic QTL pairs mostly accounted for higher proportions of the phenotypic variance than QTL detected from individual QTL analyses. A large number of QTL were identified, which could not be detected from individual QTL analyses, mainly because these QTL did not express individually significant additive or dominance effects and only expressed their effects through interactions with other QTL. Individual and epistatic QTL analyses uncovered numerous QTL as well as epistatic interactions influencing meat quality traits, including pH, meat colour and conductivity, traits which influence the quality of pork. The work of this thesis gives substantial insight into the genomic regulation of economically important traits of pigs. The research highlights that the genomic regulation of growth and body composition, feed intake and meat quality is complex, involving numerous QTL located in different regions of the genome, controlled partly by imprinting effects, as well as a complex network of interactions between QTL. The results obtained in this study can be used in pig breeding to optimise breeding programmes and for marker assisted selection.