Genome-wide association study of growth traits in the Jinghai Yellow chicken

Growth is one of the most economically important traits in the poultry industry. In this study, we identified single-nucleotide polymorphisms (SNPs) and candidate genes associated with growth traits of the Jinghai Yellow chicken. Genome-wide association studies were conducted using the Illumina 60 K SNP Chicken array to genotype 400 Jinghai Yellow chickens. For each bird, the body weights at hatching and at 2, 4, 6, 8, 12, 14, and 16 weeks were recorded. The SNPs that were significantly associated with the growth traits were identified using the general linear regression model. The results revealed a total of 18 SNPs that reached Bonferroni genome-wide significance (P < 1.80E-6). Three proximal genes (BTRC, NLK, and NF1) were found to participate in the Wnt-signaling pathway and mitogen-activated protein kinase signaling pathway. Haplotype analysis identified 19 significant haplotypes and identified a region 152.4-156.3M on GGA1 affecting 3 growth traits (BW4, BW14, and BW16). These results may help identify the exact locations of body weight quantitative trait loci on a genome level and indicate variants that can be used for subsequent investigations for Jinghai Yellow chicken.