Identification and evaluation of quantitative trait loci influencing growth, carcass composition, and meat quality traits in pigs

A three-generation resource population for identifying quantitative trait loci (QTL) for growth, carcass and meat quality traits was previously constructed at Michigan State University by crossing pigs from the Duroc and Pietrain breeds. The initial genome scan of this population included 510 F2 animals genotyped with 124 microsatellite markers and analyzed using a line-cross model. For the second scan, 20 additional markers on 9 chromosomes (SSC3 - 7, 12, 15, 16 and 18) were genotyped for 954 F2 animals, and 20 markers used in the first scan were genotyped for 444 additional F2 animals. Three least-squares Mendelian models for QTL analysis were fit to each trait: a line-cross (LC) model, a half-sib (HS) model, and a combined line-cross and half-sib (CB) model.;A total of 41 QTL for growth traits were identified on SSC4, 6 - 9, 11, 15, 16, and 18. The LC analysis revealed 26 QTL, including 7 new QTL (SSC7, 15 and 18) which were not detected in the first scan. The HS analysis revealed 12 QTL, and 3 additional QTL were detected using the CB model. A total of 91 QTL for carcass and meat quality traits were identified. The LC analysis revealed 50 QTL including 14 new QTL (SSC3, 6, 7, 12, 16, and 18). The HS analysis revealed 38 QTL including 13 QTL detected on SSC15. In addition, 3 QTL were detected using the CB model. Increasing the number of markers and animals facilitated detection of new QTL, as well as confirmation of previously identified QTL. Also, three different least-squares models made it possible to detect new QTL segregating either between or within breeds.;Based on results of the initial genome scan, five putative QTL regions (SSC3, 6, 12, 15, and 18) for carcass and meat quality traits were selected for further evaluation in an US purebred Duroc population. A total of 81 gene-specific single-nucleotide polymorphisms (SNP) were genotyped of which 33 were segregating and were analyzed for associations with pH, color, marbling, days to 113 kg, backfat thickness, and LMA. The MDH1 SNP on SSC3 was associated with pH traits. A combined genotype of PRKAG3 T30N and I199V on SSC15 was associated with ultimate pH. The HSPG2 SNP on SSC6 was associated with marbling score and days to 113 kg. Markers for NUP88 and FKBP10 on SSC12 were associated with 45-min pH and L*, respectively. Significant associations were observed for the SSC15 marker SF3B1 with L* and LMA, and for the SSC18 marker ARF5 with ultimate pH and color score. Thus, results observed for SNP markers in the US Duroc population were consistent with our previous genome scan.;Based on QTL detected on SSC18 and its biological function, corticotropin-releasing hormone receptor 2 (CRHR2) was evaluated as a potential candidate gene affecting stress response and influencing carcass and meat quality traits. Association analyses were performed for carcass and meat quality traits recorded for the MSU resource population and for a population exposed to a halothane challenge test, as well as for stress response phenotypes recorded for the halothane challenge population. CRHR2 genotype was significantly associated with pH and temperature, drip loss, cook yield, moisture and protein percent, b*, ham weight, and dressing percent in the resource population, and CRHR2 genotype exhibited a suggestive association with blotching, L* and color score in the halothane challenge population.;Identification and subsequent validation of QTL influencing growth, carcass and meat quality traits in resource and commercial populations will facilitate successful implementation of marker assisted selection programs in order to achieve genetic improvement.