Genome-wide association study on carcass traits in an indigenous yellow-feathered meat-type chicken population

Carcass traits are among the most critical production characteristics in broiler chickens. Therefore, the precise identification of genetic variants and candidate genes affecting these traits is highly valuable for enhancing breeding efficiency and overall productivity in poultry. In this study, a genome-wide association study (GWAS) was conducted to analyse seven carcass traits in 1 498 cocks from a Chinese indigenous yellow-feathered meat chicken population, which had been subjected to three generations of selective breeding for improved BW and feed conversion ratio. The assessing traits included breast muscle weight (BMW), BWs at 42 and 56 days (BW42, BW56), carcass weight (CW), eviscerated weight (EW), eviscerated weight with giblets (EWG), and leg weight (LW). Six significant single-nucleotide polymorphism (SNP) sites were identified by using the "Jingxin No. 1″ 55 K SNP microarray and bioinformatic analysis. These SNPs were annotated to six candidate genes on chromosomes 1, 2, 3, 4, 9, and Z, including SPHKAP, ALCAM, CMTM7, ADAT2, LIMCH1 and AP3B1, with the variant in the SPHKAP gene harboured a frameshift deletion in the coding region. Our study identified novel variants related to chicken carcass traits, which provide a new insight into the genetic mechanism of chicken carcass traits. These trait-associated genetic variants could facilitate the selection of more efficient broilers.