Identifying candidate genes for late-feathering subtypes of the Shouguang Chicken by genome-wide association study and differential expression analysis

Late-feathering phenotype can be divided into different subtypes based on the length difference between primary and primary-covert feathers of one-day old chicks. In this study, a chick with its primary feathers shorter than primary-covert feathers is identified as Subtype 1 (T1), a chick with its primary feathers as long as primary-covert feathers is Subtype 2 (T2). The objective of this study was to obtain candidate genes for late-feathering subtypes in Shouguang chickens. Fifty-three Shouguang chickens were genotyped with a 600 K SNP chip and two genomic regions in Chromosome 3 and 10 were identified to be associated with late-feathering subtypes by GWAS. Twelve hair follicle samples of flight feathers from 12 one-day old Shouguang chicks, including 6 of each subtype, were collected. RNA sequencing analysis was performed and no overlap genes were found between differentially expressed genes (DEGs) by differential expression analysis and candidate genes by GWAS. In order to find the relationship between the two set genes, a protein‐protein interaction (PPI) network was constructed using all protein-coding genes in the two sets and the result showed that four genes ( CDC40, EFL1, AK9, and ZBTB24 ) from GWAS and 28 DEGs were enriched in the top one cluster associated with muscle function. Considering the spatiotemporal characteristics of gene differential expression and the fact that two most significant SNP loci in GWAS were located on EFL1 and CDC40, we suggested that the two genes be more suitable as candidate genes for late-feathering subtypes.