A genome-wide association analysis for carcass and meat quality traits in Duroc pigs

• Published in: Journal of animal science Vol. 94; pp. 119 - 120
• Main Authors: Gonzalez, R, Eusebi, P G, Quintanilla, R, Figueiredo, T, Manunza, A, Noguera, J L, Clop, A, Amills, M
• Format: Journal Article
• Language: English
• Published: Champaign Oxford University Press 01.09.2016
• Subjects: Animal populations; Association analysis; Chromosomes; Electrical resistivity; Genomes; Genomics; Genotype & phenotype; Heritability; Hogs; Meat; Meat quality; Muscles; Quantitative trait loci; Single-nucleotide polymorphism; Swine
• ISSN: 0021-8812; 1525-3163

In the current work, we have analyzed the genomic architecture of carcass and meat quality traits in a Duroc commercial population of 350 individuals distributed in five half-sib families. The following carcass phenotypes were recorded: backfat thickness between third and fourth ribs (mm, BFT34R), backfat thickness at last rib (mm, BFTLR), lean meat percentage (LE%), carcass weight (kg, CW), and ham weight (kg, HW). With regard to meat quality traits, we measured in the gluteus medius (GM) and longissimus dorsi (LD) muscles the following parameters: electric conductivity (CE) and pH at 24 h (pH24) as well as lightness (L·), redness (a·) and yellowness (b·). Pigs were typed with the 60K Illumina Porcine BeadChip by using standard protocols. Single-SNP association analysis were performed under an additive genetic model with the Genome-wide Efficient Mixed-Model Association (GEMMA) software. The proportion of phenotypic variance explained by the SNPs ranged between negligible (L· at GM and LD) to moderate (HW, BFT34R, a· at GM and LD, and b· at LD), evidencing a considerable amount of missing heritability for some of these traits. We found genome-wide significant associations for LD CE on pig chromosomes (SSC) 4 (104 Mb), 5 (15 Mb) and 13 (137 Mb). We also identified chromosome-wide significant associations for CW (SSC11), HW (SSC11), BFTLR (SSC12), BFT34R (SSC12), LE% (SSC13 and SSC16), GM CE (SSC5), LD pH24 (SSC16), GM pH24 (SSC17), LD a· (SSC10), GM a· (SSC3), GM L· (SSC16). In keeping with previous QTL results obtained in the same population, we observed different trait-associated regions for the GM and LD muscles indicating that meat quality traits are regulated, at least in part, by muscle-specific factors. Moreover, we compared our data with similar datasets obtained in other purebred pig populations and we observed a limited positional concordance among trait-associated regions, suggesting the existence of a high level of genetic heterogeneity for these phenotypes among porcine breeds.