Abstract
Small white-feather chickens (SWFC) have become popular as a hybrid strain recently. Shank color is a notable economic trait in this strain. Despite numerous studies on the green shank trait from both physiological and genetic perspectives, research focusing specifically on the green shank trait in hybrid chickens (HC) remains limited. In this study, to investigate the genetic mechanisms and molecular basis of the green shank trait in HC, we created a population by intercrossing white-feathered and yellow-feathered broilers, both with yellow shanks. Physiological analysis confirmed that melanin deposition in the shank dermis is the primary cause of the green shank trait in HC. By combining genome-wide association studies (GWAS) and population genomics analysis, the 83.20-85.68 Mb region on the Z chromosome was identified as a candidate region for the green shank trait in HC. Transcriptome sequencing revealed differentially expressed genes (DEGs) between green shank and yellow shank individuals, with MTAP and CDKN1A identified as candidate genes in the genomic region associated with the green shank trait. Notably, the green shank trait includes a light green phenotype. Our study is the first to identify genes associated with different color depths of the green shank. The candidate genes influence both the biosynthesis and deposition of pigments.