Genome-wide Association Study Of Meat Quality Traits In Simmental Cattle Based On High-density SNP Chip

Based on the bovine genome sequence program and high-density SNP genotyping technology, wecould find the causative genomic variances that affect bovine beef quality and economic traits amongthe whole genome. In this study, a total of620Simmental bulls which were fed in the Inner Mongoliaulgai region were analyzed by genome-wide association study. The Illumina BovineSNP50andBovineHD chip were used to investigate genotype data. Both General Linear Model (GLM) and MixedLinear Model (MLM) were performed to analyze the economic traits including intramuscular fat,marbling score, share force and backfat thickness. The aim of this study is to identify causative SNPswhich could be associated with meat quality traits by GWAS approach. The results of our study are asfollows.1. For different genotyping density, the genotype from low-density (54K) was imputed tohigh-density (770K) using Mach software. The imputation accuracy was95.08%.2. Genome-wide associations were separately performed in the genotyped (770K) populationwhich were consisted of485individulas and the imputed population which were consisted of620individulas.139SNPs were significantly associated with meat quality traits. Of these SNPs,100SNPswere detected with the485gennotyped samples,69SNPs were detected with the620imputed samples,and30SNPs were commonly detected with both of the two groups.70SNPs of the significant SNPswere located in or close to the reported candidate genes.3. We analyzed the function of the genes which the significant SNPs were inside or nearby.13genes including HTR2A, PDK4, SHB, LIPI, LYPD1, MAN2B1, SPON1, EXOC4, ST8SIA6, GBE1,BACE2, RNLS and VIM play important role in carbohydrate and fat metabolism.4.7SNPs were found on chromosome7located at or close CAST gene, which were associatedwith share force. The SNP BovineHD0700028690was associated with both the share force andintramuscular fat.5.6SNPs on chromosome2which were close to the CXCR4gene were associated withintramuscular fat. The CXCR4gene was associated with vascularisation of organs.6.9SNPs on chromosome8were associated with marbling score in both genotyped and imputedpopulation. These SNPs maybe in an unknown gene associated with marbling score.