Genome-Wide Associaiton Study Of Loci Affecting Body Weight And Carcass Traits In Beijing-You Chicken

Body weight and carcass traits are important economic traits. The development of high-throughputgenotyping platforms and relevant statistical methods has enabled genome-wide association studies(GWAS) in chicken. In order to identify molecular markers and possible candidate genes associatedwith body weight and carcass traits, we conducted a GWAS using the Illumina60K SNP Beadchip togenotype Beijing-You chickens.The experimental birds (728males) came from the Experimental Station of Institute of AnimalScience, CAAS. They were slaughtered at d100.A total of15traits were measured for this study: bodyweight at d1, d28, d56, d80, d100(BW1,BW28,BW56,BW80,BW100), carcass weight(CW), dressingpercentage(DP), eviscerated weight(EW), eviscerated weight percentage(EWP), breast muscleweight(BMW), breast muscle percentage(BMP), thigh muscle weight(TMW), thigh musclepercentage(TMP), abdominal fat weight(AFW), abdominal fat percentage(AFP). All chickens weregenotyped using Illumina60K SNP Beadchip. We performed GWAS mainly by a compressed mixedlinear model (MLM) but a general linear model (GLM) was also used in TASSEL3.0.Threesignificance levels were set as follows:highly significant (P<5.19E-8),significant (P<2.59E-6) andsuggestive significance (P<5.19E-5).The results of the MLM revealed that four SNPs reached the suggestive significance level forBW56, two of which were also significant by GLM. The MLM detected three SNPs suggestivelyassociated with BW80. A total of eight SNPs were identified as being suggestively associated withBW100and3of them were significant by GLM. Some genes concerned with body weight were found,such as LCORL, LDB2and DACH1.The results of the MLM showed that three SNPs reached the significance level, seven SNPsreached the suggestive significance level for CW, and three were significant by GLM. The genesLCORL and LDB2were found in proximity to these loci. The analyses showed one SNP to besignificantly associated with EW significantly and eight were suggestively associated, five of the eightwere significant by GLM analysis. No SNPs were identified to be associated with EWP. The results ofthe MLM revealed that three SNPs were suggestively associated with DP, one of which was significantby GLM; LCORL and CHRNA9were found near these SNPs. The results of the MLM revealed12SNPssignificantly associated with BMW, and7of them reached the highly significant level for BMW. Mostof these SNPs located on59.8~68.5Mb of Chr3. Some important candidate genes were identified, suchas FABP7and GJA1. The results for BMP and BMW were similar. One SNP was significantlyassociated with TMW and three were suggestively associated; some genes, including NUTF2werenearby. Analysis by MLM revealed two SNPs suggestively associated with TMW,1of which wassignificant by GLM analysis and FOXN4was nearby. Two SNPs reached the suggestive significancelevel for AFW, and both were significant by GLM analysis with PUM1being nearby. Analysis by MLM found two SNPs to be suggestively associated with AFP, one of which was significant by GLM, andASB6was found in the vicinity of these loci.