Genetic dissection of leg and back feather follicle density in yellow-feathered broiler: integrative GWAS and transcriptome analysis reveal the regulatory role of SERPINF1.

In recent years, chilled chicken has emerged as a new market trend. Skin feather follicle density, an important carcass appearance trait characterized by "fine and dense" features, is increasingly preferred by consumers. This study analyzed hair follicle density in the leg and back regions of 1,382 yellow-feathered broiler. The results showed that back feather follicle density was significantly higher than that of the leg (P < 0.01), with a significant positive correlation between the two regions. Meanwhile, feather follicle density in both the leg and back showed negative correlations with abdominal fat weight, body weight, dressed weight, full-eviscerated weight, semi-eviscerated weight. mRNA-seq analysis of leg and back skin tissues from four individuals identified differentially expressed genes (DEGs) affecting feather follicle density traits across different anatomical locations, including GTF2A1, RPSA2, COX3, and CNKSR2. Furthermore, Genome-Wide Association Study (GWAS) analysis of 505 chickens identified 223 single-nucleotide polymorphisms (SNPs) significantly associated with leg feather follicle density and 107 SNPs associated with back feather follicle density, including candidate SNPs such as C19014967G, C17514817T, G1847078C, and C34389948G, as well as candidate genes including ELF5, MAP3K1, HIF1AN, and SERPINF1. mRNA-seq analysis of skin tissues from high and low feather follicle density groups in the leg (TG vs. TD) and back (BG vs. BD) identified 541 leg-related DEGs and 1,130 back-related DEGs, respectively. Joint analysis of TG vs. TD and BG vs. BD revealed 174 commonly DEGs, including candidate genes such as NSA2, IGF2, RPL17, and NRP1. Through integrated GWAS and RNA-seq analysis, five genes significantly associated with leg feather follicle density and twelve candidate genes associated with back feather follicle density were identified. Notably, individuals with the AA genotype at the SERPINF1 SNP locus Chr19:5636537 showed extremely significantly higher feather follicle density than those with the GG genotype, and both mRNA and protein expression levels of SERPINF1 were significantly upregulated in high feather follicle density individuals.