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 classified into subtypes based on the difference in length between primary and primary-covert feathers of 1-day-old chicks. In this study, a chick with its primary feathers shorter than its primary-covert feathers is identified as Subtype 1 (T1), and a chick with its primary feathers as long as its primary-covert feathers is identified as 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 using a 600 K SNP chip, and two genomic regions on Chromosome 3 and 10 were identified as being associated with late-feathering subtypes by Genome-wide association study (GWAS). Twelve hair follicle samples of flight feathers from 12 1-day-old Shouguang chicks, including 6 of each subtype, were collected. RNA sequencing analysis was performed, and no overlapping genes were found between differentially expressed genes (DEGs) identified by differential expression analysis and candidate genes by GWAS. In order to find the relationship between the two sets of 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 21 DEGs were enriched in the largest subnetwork associated with muscle function. Considering the spatiotemporal characteristics of gene differential expression and the fact that the two most significant SNP loci in GWAS were located on EFL1 and CDC40, we propose that the two genes are more suitable as candidate genes for late-feathering subtypes.