Egg production traits are economically critical in poultry farming. However, the genetic mechanisms underlying these traits in indigenous chicken breeds remain largely unknown. In this study, we conducted a genome-wide association study (GWAS) using whole-genome sequencing data from 315 Wuhua yellow chickens, an indigenous breed characterized by low egg production but considerable genetic diversity. Phenotypic assessments included age at first egg (AFE), egg number (EN), and clutch size traits across three laying stages. The SNP-based heritability estimates ranged from 0.10 to 0.38, with AFE showing negative genetic correlations with EN and clutch-related traits. We identified 871 significant SNPs (51 genome-wide and 820 suggestive) associated with egg production traits and annotated 379 candidate genes. This study revealed that SCUBE1 and KRAS are important regulators of AFE through follicular development and metabolic pathways. Notably, IGF1 and PTK2 are associated with clutch size and EN, primarily through the mTOR and insulin signaling pathways. Additionally, 13 quantitative trait loci (QTLs) overlapped with known reproductive loci, including SOX5 and PPFIBP1. Functional enrichment analyses underscored the significant involvement of the identified genes in cell adhesion, hormone signaling, and oocyte maturation pathways. These findings improve our understanding of the genetic architecture of egg production traits in indigenous chickens and highlight potential molecular targets for marker-assisted selection to enhance egg yield while preserving genetic diversity.

Chickens have extensive phenotypic variation. The Wuhua yellow chicken (WHYC) is an important traditional yellow-feathered chicken in China, characterized by white tail feathers, white flight feathers, and strong disease resistance. However, the genomic basis of traits associated with WHYC is still poorly understood. In this study, whole genome resequencing was performed with an average coverage of 20.77-fold to investigate heritable variation and identify selection signals in WHYC. Reads were mapped onto the chicken reference genome (Galgal5) with a coverage of 85.95%. After quality control, 11,953,471 SNPs and 1,069,574 InDels were obtained. In addition, 41,408 structural variants and 33,278 copy number variants were found. A comparative genomic analysis of WHYC and other yellow-feathered chicken showed that selected regions were enriched in genes involved in transport and catabolism, immune system, infectious diseases, signal transduction, and signaling molecules and interaction. Several genes associated with disease resistance were identified, including IFNA, IFNB, CD86, IL18, IL11RA, VEGFC, and ATG10. Furthermore, PMEL and TYRP1 may contribute to the coloring of white feathers in WHYC. These findings improve our understanding of the genetic characteristics of WHYC and may contribute to future breed improvement.

A rare variant of the Wuhua yellow chicken rooster exhibits a distinct plumage phenotype characterized by a white belt across the dorsal region and wing shoulder. This variant provides a valuable model for studying regional pigmentation genetics. Using pool sequencing, we identified candidate genes via high-depth sequencing (average 52 × coverage) of DNA pools from 35 brown-belted and 35 white-belted roosters. Integrated analysis of allele frequency differences, Fisher's exact test, and population differentiation revealed 49 shared candidate genes, with 23 concentrated in a 3.83 Mb region on chromosome 12 (13.12-16.95 Mb). Notably, MITF and two adjacent genes exhibited strong selection signals across all methods. Functional enrichment analyses highlighted significant terms related to melanocyte differentiation and the melanogenesis pathway, with MITF serving as a core regulator. Comparative genomic evidence further supported the conserved role of MITF in pigment deposition across vertebrates. We propose MITF as the primary genetic regulator of the white-belted phenotype, potentially modified by other genes such as PRICKLE2. This study provides insights into the genetic architecture of regional depigmentation and underscores the role of MITF in avian plumage patterning.

Region-specific feather pigmentation is widespread in birds, yet the genetic mechanisms enabling independent control of body and tail plumage remain poorly understood. The white-tailed (WT) phenotype in Wuhua yellow chickens, which exhibit yellow body plumage but pure white tail feathers, provides an ideal model for dissecting such modular genetic regulation. Genetic analysis of F₁ and F₂ populations (n = 137) derived from a cross with Huaixiang (black-tailed, BT) chickens revealed an autosomal dominant inheritance pattern for the WT trait, with a 3:1 segregation ratio (105 WT: 32 BT; χ² = 0.20, P = 0.66) in the F₂ generation-independent of the yellow body plumage locus. Integrating genome-wide association study of 47 F₂ roosters with population resequencing (n = 50), we identified a highly significant locus on chromosome 33 (P = 1.35E-8) harboring PMEL as the sole credible candidate. Tail follicle transcriptome profiling (4 WT vs. 4 BT) uncovered 1,712 differentially expressed genes, with coordinated downregulation of the entire melanogenesis pathway (normalized enrichment score = -1.914, FDR = 0.003). PMEL ranked among the most strongly suppressed genes (log₂FC = -2.18, FDR = 5.58E-06). Furthermore, genome-wide alternative splicing analysis identified 2,764 significant events among 30,473 detected, indicating widespread post-transcriptional regulation. Consistent with this global pattern, the PMEL locus exhibited markedly reduced splicing complexity in WT chickens, characterized by a systematic shift toward simpler isoforms. Thus, four orthogonal lines of evidence-genomic association, transcriptional repression, pathway-level melanogenesis shutdown, and splicing simplification-converge on PMEL as the causal gene underlying this autosomal dominant, tail-specific depigmentation. Our findings establish PMEL as the primary regulator underlying this autosomal dominant trait, paving the way for understanding modular avian coloration and enabling its application in precision breeding programs.

This study investigated the effects of boiling, roasting, and frying on the quality and flavor characteristics of Shiqi pigeon (Columba livia domestica) meat. Changes in color, texture, microstructure, and volatile profiles were systematically evaluated using colorimetry, texture profile analysis, scanning electron microscopy, electronic nose analysis, and Fourier transform infrared spectroscopy (FTIR). Thermal processing significantly influenced physicochemical properties and flavor profiles. Fried samples exhibited the highest hardness (27.79 N), chewiness (33.13 mJ), and maximum shear force (30.23 N), while boiled samples showed the lowest hardness (22.12 N) and puncture hardness (12.20 N), indicating improved tenderness. Electronic nose PCA explained 85.4% of total variance (PC1: 59.5%; PC2: 25.9%), clearly discriminating the three treatments. Color measurements showed that frying induced the greatest total color difference (ΔE > 1, p < 0.05), followed by roasting and boiling. FTIR analysis revealed pronounced shifts in amide I bands in fried samples, indicating stronger protein secondary structure alterations. Overall, different thermal processing methods produced distinct quality and flavor characteristics in pigeon meat, providing scientific guidance for process optimization and product development.