Weizhen Luo, Duxue Cheng, Shaokang Chen, Ligang Wang, Yong Li, Xiaojun Ma,Xin Song,et
InternationalJournal of Biological Sciences,2012 8(4):580-595.
Abstract:Pork quality is an economically important trait and one of the main selection criteria for breeding in the swine industry. In this genome-wide association study (GWAS), 455 pigs from a porcine Large White × Minzhu intercross population were genotyped using the Illumina PorcineSNP60K Beadchip, and phenotyped forint ramuscular fat content (IMF), marbling, moisture, color L*, color a*, colorb* and color score in the longissimus muscle (LM). Association tests between each trait and the SNPs were performed via the Genome Wide Rapid Association using the Mixed Model and Regression-Genomic Control (GRAMMAR-GC) approach.From the Ensembl porcine database, SNP annotation was implemented using Susscrofa Build 9. A total of 45 SNPs showed significant association with one or multiple meat quality traits. Of the 45 SNPs, 36 were located on SSC12. These significantly associated SNPs aligned to or were in close approximation topreviously reported quantitative trait loci (QTL) and some were located within introns of previously reported candidate genes. Two haplotype blocksASGA0100525-ASGA0055225-ALGA0067099-MARC0004712-DIAS0000861, andASGA0085522-H3GA0056170 were detected in the significant region. The first block contained the genes MYH1, MYH2 and MYH4. A SNP (ASGA0094812) within an intron of the USP43 gene was significantly associated with five meat quality traits. The present results effectively narrowed down the associated regions compared to previous QTL studies and revealed haplotypes and candidate genes on SSC12 for meat quality traits in pigs.
Keywords:F2design; genome-wide association study; meat quality trait; pig; SNP