Identification of Candidate Genes Associated with Black-Tailed and White-Tailed Plumage Traits in B380 Chickens Based on Multi-Omics Analysis

To investigate the molecular mechanisms underlying black-tailed and white-tailed feather coloration in Babcock B380 and to identify key candidate genes and loci associated with tail feather color. It provides a theoretical basis for poultry breeding and molecular breeding of feather color related traits

A natural population consisting of 80 Babcock B380 hens with either black-tailed or white-tailed phenotypes was used in this study. The morphology and distribution of melanosomes within tail feather follicles were analyzed using histological sections observed under light microscopy and transmission electron microscopy. Transcriptome data were utilized to identify differentially expressed genes (DEGs), and weighted gene co-expression network analysis (WGCNA) was performed to identify co-expression modules associated with tail feather color and to screen hub genes within key modules. The expression levels of selected DEGs were subsequently validated by quantitative real-time PCR (qRT-PCR). Furthermore, based on genotypic data from the natural population, a genome-wide association study (GWAS) was conducted to identify genetic loci associated with black-tailed and white-tailed feather coloration in Babcock B380 chickens. The identified loci were further validated at the population level and subjected to integrative analysis. In addition, codon usage bias of PMEL mRNA was analyzed.

Microscopic observations revealed that melanosomes were predominantly deposited in the feather shaft region of chicken feather follicles, with the melanosome area being significantly greater in black-tailed chickens than in white-tailed chickens. Transcriptome analysis identified 373 DEGs, which were significantly enriched in melanin biosynthesis–related pathways. Key pigmentation-related genes, including PMEL, TYR, TYRP1, and SLC45A2, were highly expressed in black-tailed feather follicles. Weighted gene co-expression network analysis (WGCNA) identified 25 co-expression modules, among which the MEmagenta module was closely associated with melanosome biosynthesis. Integrated analyses of network connectivity and protein–protein interaction networks identified ten potential hub regulatory genes: PMEL, PIAS2, NDEL1, MSRA, HDLBP, GCNT4, FMR1NB, TBLX1, ST3GAL5, and RAB11A. qRT-PCR validation showed that the expression patterns of 4 DEGs were consistent with the RNA-seq results. GWAS identified a total of 968 significant SNPs located on chicken chromosomes 1, 5, and 34, which were annotated to 221 genes. Among these, 7 SNPs within the PMEL gene showed significant associations with tail feather color. Notably, the rs316665588 locus was significantly associated with black-tailed and white-tailed feather phenotypes. Codon bias index (CBI) analysis indicated that the mutation at this locus resulted in a transition from the rare codon UGU to the more frequently used codon UGC.

The melanosome distribution area in feather follicles was significantly larger in B380 black-tailed chickens than in their white-tailed counterparts. Transcriptome analysis identified 4 key DEGs associated with plumage coloration and revealed 10 potential hub regulatory genes. PMEL was identified as a candidate gene underlying the black-tailed and white-tailed phenotypes in B380 chickens, and the synonymous T/C mutation at rs316665588 represents a key candidate locus contributing to the formation of black/white tail plumage.