Filtration Of Candidate Gene Related To Meat Prodution And Quality Traits Based On Genome-wide Association Study Technique In Chickens

Meat production and quality are important economic traits in chickens, which were synergisticly influenced by feed nutrition and genetic factor. With the development of molecular nutrition research, it is important to understand the key regulatory gene and molecule mechanism underlying the target traits. The developments of high-throughput genotyping platforms and relevant statistical methods have enabled genome-wide association study (GWAS) for meat production and quality traits in chickens.To identify loci and genes associated with meat production and quality traits, we conducted the GWAS of F2populations derived from a local Chinese breed (Beijing-You chickens) and a commercial fast-growing broiler line (Cobb-Vantress). In this study,400chickens including14parents,19F1chickens, and367F2chickens (184male and183female)from five batches at two-week intervals were genotyped and used. At the day of93, a total of11meat production and16quality traits of chickens from the F2generation were measured.Genotyping was performed with50ng/μL gDNA using the Illumina60K Chicken SNP Beadchip. After quality control steps,42,585SNPs and328chickens were used for the GWAS. The GWAS analysis for meat prodution and quality traits used the compressed MLM and the results from GLM model are also indicated. Both models were performed with the first MDS component as covariates, with batch and sex as fixed effects. In the compressed MLM, relative kinship matrix was a random effect. For AbFW, the eviscerated weight (EW) was a covariate in both models. The mRNA expression patterns of candidate genes from GWAS results were measured using real-time quantity PCR (Q-PCR) from the extremes tratis groups.The results showed that:(1) In this study,64SNP effects involving44SNPs were detected for11meat production traits with genome-wide significance or suggestive (P<5.96×10-5) from compressed mixed linear model (MLM). Twenty-two of44these SNPs were genome-wide significance associated with the traits from general linear moldel (GLM)(P<2.98×10-6). The6.83Mb (78.11-84.94Mb) region on GGA4involving seven SNPs and four genes (SLIT2, QDPR, AFAP1, LRPAP1) were influenced most of these triats. The candidate gene RUVBL1for WW and WNT4for ThW were in WNT signaling pathway. In other chromosomes, some candidate genes, e.g. SYT1, WAPAL, MAPK and EFNA5, influenced most of meat production triats.(2) In the present study,33association signals were detected from the compressed mixed linear model (MLM) for ten meat quality traits:DMBr, DMTh, IMFBr, meat colour L*and b*values, skin colour L*, a*and b*values, AbFW and AbFP. The mRNA expressions of candidate genes identified near significant signals were compared between High and Low phenotype groups. A total of14genes associated with IMFBr, meat colour L*, AbFW, and AbFP, exhibited differential expression levels between the High and Low phenotype groups. These genes were important candidate genes for meat quality traits, such as the protein tyrosine kinase TYRO3and microsomal glutathione S-transferase1(MGST1) for IMFBr, collagen, type I, alpha2(COL1A2) for meat colour L*, the RET proto-oncogene (RET), natriuretic peptide B (NPPB) and sterol regulatory element binding transcription factor1(SREBF1) for abdominal fat (AbF) traits.(3) A total of21candidate genes were selected to validate the accuracy of GWAS method.18including four genes for BrW and14for meat quality traits were significant differentially expressed in the High and Low groups (P<0.05or0.01). The Q-PCR showed that the efficiency of the GWAS was about85%.The results provided new clues for deciphering the molecular mechanisms underlying meat prodution and quality traits in chicken. The exploring of causal variants in these regions and functional characterization of these genes will be required.