Identification of molecular markers associated with comb traits through genome-wide association study on a specialized strain of yellow feathered broilers

It is of great significance to identify candidate genes and molecular markers related to the comb development, in order to accelerate comb breeding progress of yellow feathered broiler. Herein, 400 terminal male chickens of the fast-type yellow feathered broiler (60 day old on the market) were selected as the research subjects, and their genomic genetic variation information was obtained using resequencing and genome-wide association study (GWAS). We identified 4 SNPs and 80 SNPs that were significantly correlated and potentially significantly correlated with comb height. Meanwhile, 4 SNPs and 5 SNPs were potentially significantly correlated with comb thickness and comb length, respectively. Several candidate genes related to comb traits were identified, including AR, HSF3, PIP4K2A, ATF6β, NTM, LRP1, etc. Except for SNP6 (rs317557994) locus with low genetic diversity, the other 12 SNP loci have moderate genetic diversity. Linkage disequilibrium (LD) analysis showed that 13 SNP loci were not in a strong linkage state. The association analysis between single marker and comb traits showed that AA and GA at SNP1 (rs312669246) locus, CC and CT at SNP2 (rs313331126) locus, AA and GA at SNP3 (rs313205409) locus, and AA and GA at SNP4 (rs314830898) locus were the dominant genotypes for comb height. The TT and CT genotypes at SNP5 (rs312557738), AA at SNP6 (rs317557994), GG at SNP7 (rs738748642), and AA and GA at SNP8 (rs312962270) were the dominant genotypes for comb thickness. TT at SNP9 (rs313797960), AA at SNP10 (rs312371971), AA at SNP11 (rs313637016), CC and CA at SNP12 (rs738049404), and GG at SNP13 (rs3388194039) were all the dominant genotypes for comb length. In chicken breeding, it is expected to assist in improving the selection of comb traits and accelerating the generation progress of comb development by selecting dominant genotypes at SNP1-SNP13 loci and eliminating other disadvantaged genotypes. These findings provide important references for further studying the regulatory mechanisms of comb development and cultivating new high-quality broiler breeds (crossed lines) with larger comb.