Scientia Agricultura Sinica ›› 2026, Vol. 59 ›› Issue (6): 1348-1360.doi: 10.3864/j.issn.0578-1752.2026.06.015

• ANIMAL SCIENCE·VETERINARY SCIENCE • Previous Articles    

Whole-Genome Resequencing Reveals the Genetic Mechanisms Underlying Feather Coloration in Jingyuan Chicken

YANG LiJuan(), CHEN SiYu, ZHAO Wei, ZHU Ling, GUO Lei, MA LiNa, MA RuiMin, ZHANG Juan()   

  1. College of Animal Science and Technology, Ningxia University, Yinchuan 750021
  • Received:2025-09-30 Accepted:2026-01-14 Online:2026-03-16 Published:2026-03-24
  • Contact: ZHANG Juan

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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

Fig. 1

Analysis of the population genetic structure of the Jingyuan chicken A: Chromosome density map following genotyping quality control; B: Principal component analysis (PCA) plot following genotyping quality control; C: Population K-structure diagram; D: Population G-matrix diagram"

Fig. 2

Genome-wide selection signals and association analysis of black feather traits in Jingyuan chicken A: Combined analysis of Fst and θπRatio for black feathers; B: Manhattan plot of XP-CLR for black feathers; C: Manhattan plot and Q-Q plot from genome-wide association study (GWAS) for black feathers; D: Venn diagram of results from Fst, θπRatio, XP-CLR, and GWAS for black feathers."

Fig. 3

Genome-wide selection signals and association analysis of hemp feather traits in Jingyuan chicken A: Combined analysis of Fst and θπRatio for hemp feathers; B: Manhattan plot of XP-CLR for hemp feathers; C: Manhattan plot and Q-Q plot from genome-wide association study (GWAS) for hemp feathers; D: Venn diagram of results from Fst, θπRatio, XP-CLR, and GWAS for hemp feathers"

Fig. 4

Genome-wide selection signals and association analysis of white feather traits in Jingyuan chicken A: Combined analysis of Fst and θπRatio for white feathers; B: Manhattan plot of XP-CLR for white feathers; C: Manhattan plot and Q-Q plot from genome-wide association study (GWAS) for white feathers; D: Venn diagram of results from Fst, θπRatio, XP-CLR, and GWAS for white feathers"

Fig. 5

Inter-population Fst analysis and functional enrichment analysis of the Jingyuan chicken A: Fst analysis of black feathers vs. hemp feathers; B: Fst analysis of black feathers vs. white feathers; C: Fst analysis of hemp feathers vs. white feathers; D: GO pathway enrichment analysis; E: KEGG pathway enrichment analysis"

Table 1

Core candidate genes selected using a multi-method approach"

基因名称 Gene 基因全称 Full name 染色体 Chromosome 位置 Location (bp) 长度Length (bp)
NLRC5 NLR family CARD domain containing 5 11 631 380-666 403 35 023
POT1 protection of telomeres 1 1 21 910 949-21 977 311 66 362
IPP intracisternal A particle-promoted polypeptide 8 21 578 712-21 586 099 7 387
DCUN1D4 defective in cullin neddylation 1 domain containing 4 4 66 182 460-66 219 871 37 411
XRCC4 X-ray repair cross complementing 4 Z 62 968 695-63 173 439 204 744
PALM2AKAP2 PALM2-AKAP2 fusion Z 65 952 061-66 041 197 89 136
UGCG UDP-glucose ceramide glucosyltransferase Z 66 456 960-66 484 254 27 294
GNG10 G protein subunit gamma 10 Z 66 590 949-66 596 903 5 954
PRIM2 primase (DNA) subunit 2 3 86 320 097-86 404 844 84 747
SSBP2 single stranded DNA binding protein 2 Z 63 726 110-63 893 187 167 077
ZBTB34 zinc finger and BTB domain containing 34 17 10 852 388-10 877 691 25 303
DHFR dihydrofolate reductase Z 64 257 284-64 273 367 16 083
SLC46A2 Solute Carrier Family 46 Member 2 Z 66 053 949-66 060 686 6 737
SLF1 SDE2 C-Terminal Like Family Member 1 Z 58 014 361-58 053 135 38 774
SHOC1 Shortage In Chiasmata 1 Z 66 537 993-66 588 226 50 233
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