Abstract
Meat and carcass quality attributes are of crucial importance influencing consumer preference and profitability in the pork industry. A set of 400 Berkshire pigs were collected from Dasan breeding farm, Namwon, Chonbuk province, Korea that were born between 2012 and 2013. To perform genome wide association studies (GWAS), eleven meat and carcass quality traits were considered, including carcass weight, backfat thickness, pH value after 24 hours (pH24), Commission Internationale de l’Eclairage lightness in meat color (CIE L), redness in meat color (CIE a), yellowness in meat color (CIE b), filtering, drip loss, heat loss, shear force and marbling score. All of the 400 animals were genotyped with the Porcine 62K SNP BeadChips (Illumina Inc., USA). A SAS general linear model procedure (SAS version 9.2) was used to pre-adjust the animal phenotypes before GWAS with sire and sex effects as fixed effects and slaughter age as a covariate. After fitting the fixed and covariate factors in the model, the residuals of the phenotype regressed on additive effects of each single nucleotide polymorphism (SNP) under a linear regression model (PLINK version 1.07). The significant SNPs after permutation testing at a chromosome-wise level were subjected to stepwise regression analysis to determine the best set of SNP markers. A total of 55 significant (p<0.05) SNPs or quantitative trait loci (QTL) were detected on various chromosomes. The QTLs explained from 5.06% to 8.28% of the total phenotypic variation of the traits. Some QTLs with pleiotropic effect were also identified. A pair of significant QTL for pH24 was also found to affect both CIE L and drip loss percentage. The significant QTL after characterization of the functional candidate genes on the QTL or around the QTL region may be effectively and efficiently used in marker assisted selection to achieve enhanced genetic improvement of the trait considered.
Highlights
Consumer demands for pork depend on various meat quality parameters such as odor, flavor, tenderness and Submitted Sept. 8, 2015; Revised Sept. 29, 2015; Accepted Oct. 3, 2015 juiciness
From the summary statistics of the phenotypes of the studied traits, the highest variability of 66.08% was found in drip loss (%), followed by filtering (39.12%), marbling scores (30.69%), shear force (SF) (25.70%), heat loss (24.71%), Commission Internationale de l’Eclairage (CIE) b (21.53%), CIE a (7.12%), CIE L (5.57%) and pH 24 hour postmortem (4.14%)
A total of 55 single nucleotide polymorphism (SNP) were detected on different chromosomes after the stepwise regression procedures for the meat and carcass quality traits
Summary
Consumer demands for pork depend on various meat quality parameters such as odor, flavor, tenderness and. The identification of the genomic regions underlying pork quality traits and their applications via marker-assisted selection would allow pig breeders to select at an early age (Luo et al, 2012). Berkshire (Susscrofa domesticus) pork possesses some merits of meat quality traits such as richness, texture, marbling, juiciness, tenderness and flavor (Goodwin and Burroughs, 1995). Several GWAS in pigs were reported in many pure and crossbreds for various traits including meat and carcass quality traits (Sanchez et al, 2014). The main objectives in this study were to perform GWAS with a high-density Porcine SNP62K BeadChip (Illumina, San Diego, CA, USA) in Berkshire to detect significant SNPs or QTLs associated with meat and carcass quality traits, and to detect candidate genes influencing the traits nearby the detected QTLs
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