关键词: 静原鸡, 羽毛颜色, 基因组, 全基因组关联分析, 选择清除分析

Abstract:

【Background】Feather color is an important morphological and economic trait in poultry breeds, and understanding its genetic mechanisms is of great significance for the conservation and genetic improvement of local chicken genetic resources. The Jingyuan chicken, a distinctive local breed in China, exhibits rich diversity in feather color, providing an ideal model for studying the genetic basis of plumage coloration. Systematically exploring this genetic foundation is crucial for enhancing breeding competitiveness. 【Objective】This study aimed to utilize whole-genome resequencing to identify genetic markers and candidate genes associated with black, hemp, and white feather traits in Jingyuan chickens, thereby providing a theoretical basis for elucidating the molecular mechanisms underlying feather color formation and for molecular breeding. 【Method】A total of 150 healthy 126-day-old Jingyuan hens with different feather colors (black, hemp, and white) were selected from the Jingyuan Chicken National Conservation Farm. Blood samples were collected via wing vein puncture for high-quality genomic DNA extraction, followed by whole-genome resequencing. A multi-strategy cross-validation approach was employed: four independent methods, including genetic differentiation coefficient (Fst) calculation based on sliding windows, nucleotide diversity ratio (θπ ratio) analysis, cross-population composite likelihood ratio (XP-CLR) test, and genome-wide association study (GWAS), were used to systematically screen candidate genes associated with black, hemp, and white feather colors, respectively. Venn diagrams were used to identify key significant candidate genes specific to each feather color by taking the intersection of genes identified by these methods. Furthermore, cross-population comparative analysis was conducted using Fst analysis between different feather color populations to identify significant selection signal regions associated with feather color. Gene annotation and Venn diagram intersections were used to identify core candidate genes shared across feather colors. Finally, GO functional annotation and KEGG pathway enrichment analysis were performed to systematically analyze the biological functions and regulatory networks of the identified candidate genes. 【Result】The study systematically identified several key genes associated with feather color formation in Jingyuan chickens. Black feather traits were significantly associated with the LMO3, RERGL, and RTTN, and hemp feather traits were linked to the CDH19 and SLC25A1, while white feather traits were primarily governed by the IKZF1. Cross-feather color comparative analysis further identified 15 core candidate genes: NLRC5, POT1, IPP, DCUN1D4, XRCC4, PALM2AKAP2, UGCG, GNG10, PRIM2, SSBP2, ZBTB34, DHFR, SLC46A2, SLF1, and SHOC1. This indicated that feather color variation in Jingyuan chickens was regulated by multiple genes. Functional enrichment analysis revealed that these genes were significantly involved in important biological processes, such as the G protein-coupled receptor signaling pathway and transmembrane receptor signal transduction, forming a complex regulatory network for feather color. 【Conclusion】Through integrated multi-omics analysis, this study identified important candidate genes associated with feather color formation in Jingyuan chickens and preliminarily revealed their potential regulatory pathways. The findings not only provided novel molecular clues and technical support for the genetic dissection of feather color traits in Jingyuan chickens, filling some gaps in the research on feather color regulation mechanisms in local chicken breeds, but also offer scientific basis and practical guidance for the precise conservation, targeted breeding, and innovative utilization of genetic resources from local high-quality chicken breeds. Furthermore, this study accumulated key data for research in frontier areas, such as the molecular pathways and genetic regulatory networks of feather pigmentation in poultry, thereby enriching the theoretical system of genetic research on functional traits in livestock and poultry.

Key words: Jingyuan chicken, feather color, genome, GWAS, selective sweep analysis