Genome-wide Association Studies For Pig Meat Traits And Exploration Of Major Genes

Skeletal muscle is mainly constituted by muscle fibers, fat, connective tissue, and blood vessels and nervus, in which the muscle fiber traits and the intramuscular fat content are the principal elements affected the meat quality. In this study, pigs of F2 generation from a Large white×Minzhu intercross were used to estimate the genetic parameters of muscle fiber traits and some meat quality traits, and the genome-wide association study (GWAS) analysis on muscle fiber traits and intramuscular fat content were carried out by high-density SNP chips. The significant locus related to muscle fiber area and intramuscular fat content, major candidate genes were also screened. The results showed as fellows.The genetic parameters of muscle fiber traits and some meat quality traits were estimated by Multiple Trait Derivative Free REML (MTDFREML). The heritability of muscle fiber diameter, muscle fiber density, muscle fiber area, intermediate muscle fiber ratio, red muscle fiber ratio, and white muscle fiber ratio were 0.39,0.46,0.36,0.58,0.69,0.65 respectively, and the heritability of pH24, water content, water loss rate, IMF, L value, marbling were 0.50,0.51,0.71,0.52,0.35 and 0.57. The heritability of these traits were surpassed 0.3, belonged to high heritability traits (h2>0.3). There were moderate to high positive correlation between IMF and muscle fiber density, pH24, L value, marbling (rA=0.38-0.91), and moderate to high negative genetic correlation between IMF and muscle fiber diameter, muscle fiber area, white muscle fiber ratio, intermediate muscle fiber ratio, water content (rA=-0.46～-0.74).The GWAS analysis on muscle fiber traits were developed in full-sib and half-sib population by Mixed Linear Models. The significant SNPs significantly correlated to muscle fiber diameter, muscle fiber area, muscle fiber density were located on SSC3, SSC4, SSC5, SSC6, SSC7, SSC14. The expression of annotated genes(Sirt2、NFKBIB、KATNB1、ACP1) near the significant SNPs related to muscle fiber area were detected by real-time PCR in Large White and Minzhu population with different ages, the results revealed that Sirt2 and ACPI had significant difference, so Sirt2 and ACP1 might be the major candidate genes of muscle fiber area.The GWAS analysis on intramuscular fat content were carried out,30 of the 35 SNPs significantly correlated to IMF were located on SSC12. The candidate gene MAP2K4 near the significant SNP locus H3GA0022758 and ALGA0119023 was well studied. The whole cDNA of MAP2K4 (3324 bp) was cloned, which included ORF (846 bp),5’-UTR (120bp),3’-UTR (2358). The MAP2K4 protein consisted of 281 amino acids. The expression of MAP2K4 were detected by real-time PCR in different tissues of Large White and in Minzhu and Large White at different days of ages, the results revealed that it was widely expressed in multiple tissues, higher in muscle. and Minzhu higher than Large White at 120 days of age. The A>G polymorphism in MAP2K4 promoter(Chr12:59330365) was significantly associated with IMF in Beijing black swine. Genotyping of F2 generation using by the highest significant SNP locus(MARC0017000) were performed, and the expression of 10 annotated genes(USP43、DHRS7C GSG1L2、GLP2R、RCVRN、GAS7、MYH1、ADPRM, TMEM220 and MYH2) in the highest and second-highest significant region related to IMF content were determined in different genotype individual, only MYH2 had significant difference. From the above results, MAP2K4和MYH2 might be the candidate gene for future research.