Evaluation of approaches to detect quantitative trait loci for growth, carcass, and meat quality on swine chromosomes 2, 6, 13, and 18. I. Univariate outbred F2 and sib-pair analyses.

Results from univariate outbred F2 interval mapping and sib-pair analyses of 12 growth and 28 carcass traits to identify QTL on SSC 2, 6, 13, and 18 were compared. Phenotypic and genetic data were recorded on a three-generation resource population including 832 F2 pigs from a cross between three Berkshire sires and 18 Duroc dams. Thirty markers with an average spacing of approximately 16 cM were genotyped across the four chromosomes. The outbred F2 mixed model included the effects of sex, birth month, and year, one-QTL additive, dominance and imprinting coefficients calculated every 1 cM using interval mapping, and a random family effect. The general sib-pair model used to describe the phenotypic differences between sib-pairs included the same systematic and random effects and a one-QTL additive coefficient calculated every 1 cM. The outbred F2 analysis found significant evidence of QTL on SSC 2 associated with 105-d weight, backfat thicknesses, LM area, fat percent, shear force, juiciness, marbling, and tenderness. In addition, QTL were identified on SSC 6 relating to 42-d weight and LM area, and on SSC 18 for fat and moisture percents. In most instances, the outbred F2 approach offered greater power to detect QTL; however, the sib-pair analysis offered greater power in several instances. The trait-specific superiority could be due to the relative advantage of each model within a trait data set. The two approaches provided complementary evidence for QTL segregating between the Berkshire and Duroc breeds used in the study that may be used to aid marker-assisted introgression and selection and candidate gene studies to improve swine growth and meat quality characteristics.