The gut microbiota of chickens not only modulates host immune function and production performance through nutrient metabolism but also serves as a reservoir for antibiotic resistance genes (ARGs), whose accumulation exacerbates bacterial resistance. This study integrated 108 cecal microbiome samples from six Yunnan native chicken breeds under free-range and caged farming systems, constructing a comprehensive catalog comprising 12,715 microbial genomes. We systematically revealed the dual mechanisms by which the gut microbiota regulates host phenotypes and ARG dissemination. Metagenomic analysis demonstrated that Alistipes, Prevotella, and Spirochaeta synergistically regulate body weight and immune indices through metabolic networks, which are linked to the significant enrichment of carbohydrate-active enzymes. GH23 and GT2 presented the greatest abundance, highlighting their pivotal role in dietary fiber metabolism. A total of 1327 ARGs were identified, spanning seven resistance mechanisms dominated by antibiotic efflux and target alteration. Alistipes_sp._CAG:831 presented the highest ARG abundance and diversity, with ARG levels strongly correlated with host bacterial abundance. Metagenomic-phenotype association networks further revealed that environmental stress drives disparities in ARG enrichment by altering the microbial community structure. This study elucidates the gut microbiota-host interaction network in Yunnan native chickens and provides critical insights into ARG transmission dynamics, offering a theoretical foundation for antibiotic resistance risk assessment and sustainable poultry farming strategies.

Poultry is a source of meat that is in great demand in the world. The quality of meat is an imperative point for shoppers. To explore the genes controlling meat quality characteristics, the growth and meat quality traits and muscle transcriptome of two indigenous Yunnan chicken breeds, Wuding chickens (WDs) and Daweishan mini chickens (MCs), were compared with Cobb broilers (CBs). The growth and meat quality characteristics of these two indigenous breeds were found to differ from CB. In particular, the crude fat (CF), inosine monophosphate content, amino acid (AA), and total fatty acid (TFA) content of WDs were significantly higher than those of CBs and MCs. In addition, it was found that MC pectoralis had 420 differentially expressed genes (DEGs) relative to CBs, and WDs had 217 DEGs relative to CBs. Among them, 105 DEGs were shared. The results of 10 selected genes were also confirmed by qPCR. The differentially expressed genes were six enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathways including lysosomes, phagosomes, PPAR signaling pathways, cell adhesion molecules, cytokine–cytokine receptor interaction, and phagosome sphingolipid metabolism. Interestingly, four genes (LPL, GK, SCD, and FABP7) in the PPAR signal pathway related to fatty acid (FA) metabolism were elevated in WD muscles, which may account for higher CF, inosine monophosphate content, and AA and FA contents, key factors affecting meat quality. This work laid the foundation for improving the meat quality of Yunnan indigenous chickens, especially WD. In future molecular breeding, the genes in this study can be used as molecular screening markers and applied to the molecular breeding of chicken quality characteristics.

Skeletal disorder is of concern to the poultry industry as it affects animal welfare and production performance. Traditional Chinese medicine could improve bone quality and reduce the incidence of bone disease, but the molecular regulation of Chinese medicine formula (CMF) on improving bone quality in broilers is still unclear. This study was performed to research the effects of CMF on skeletal performance of Cobb broilers and reveal the molecular regulation. A total of 120 one-day-old Cobb broilers were randomly allocated into 4 equal groups of 30 chickens, with 5 replicates and 6 chickens in each replicate. The control (CON) group was fed a diet without CMF, while the CMF1, CMF2, and CMF3 groups were supplemented with different CMF at 6,000 mg/kg diet, respectively. The broilers were raised to 60 d of age, then bone tissues were collected for biomechanical properties, micro-CT detection and transcriptomic sequencing analysis. The results showed that CMF3 improved the biomechanical properties of broiler tibia, via increasing the elastic modulus (P < 0.05), yield strength (P > 0.05), maximum stress (P < 0.05) and fracture stress (P < 0.05) of the tibia. Micro-CT analysis indicated that CMF3 increased the bone mineral density (BMD), bone volume/total volume (BV/TV), bone surface density (BS/TV), trabecular number (Tb.N), trabecular thickness (Tb.Th), and decreased the trabecular separation (Tb.Sp) of femur cancellous bone (P < 0.05). RNA-seq analysis revealed 2,177 differentially expressed genes (DEGs) (|log₂FoldChange| ≥ 1, FDR < 0.05) between the CMF3 group and CON group. Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) analysis showed 13 pathways mostly associated with bone growth and development and bone metabolism, and we identified 39 bone-related DEGs. This study suggests that CMF3 could improve bone strength and bone microstructure of broilers, and showed a positive effect on bone performance. Our research could provide a theoretical reference for the development of pollution-free feed additives to improve the skeletal performance of broilers, which could help promote healthy farming of chickens.

Congenital caudal body truncation in chickens—the rumpless phenotype—provides a powerful model for studying vertebrate axis elongation. This trait has been linked to misexpression of IRX1 and IRX2 in the embryonic tail bud, and breed-specific candidate mutations, including a deletion upstream of IRX1 proposed for the Piao breed, have been reported, yet whether the various breeds share a common causal basis has remained unresolved. By combining whole-genome resequencing, long-read sequencing, and population genomic analyses of four geographically isolated rumpless breeds (Chinese Piao, Japanese Uzurao, Belgian Barbu de Grubbe, and Chilean Araucana), we identify distinct tandem duplications of the IRX1/IRX2 intergenic region that converge on a single ∼700 bp conserved noncoding element, which we designate EnhRp. Haplotype and breakpoint analyses reveal that these duplications arose through at least two mutational events rather than a single shared origin. Functional assays in chicken embryos demonstrate that duplicating EnhRp acts as a hypermorphic gain-of-function mutation, elevating enhancer activity in the tail bud in a dose-dependent manner, consistent with the ectopic IRX1/IRX2 expression. Our findings support a model of parallel evolution in which distinct structural variants recurrently target a specific cis-regulatory element across at least two independent lineages, highlighting the critical role of noncoding variation in shaping morphological diversity.

Chickens are a vital dietary protein source globally, yet their immune function is increasingly compromised by interconnected challenges including breed specific genetic heterogeneity, viral infections, intestinal microbial dysbiosis, and environmental stressors—all of which hinder sustainable poultry production. The chicken immune system, anchored by central immune organs (bursa of Fabricius, thymus) and peripheral immune organs (spleen, lymph nodes), relies on the coordinated interplay of innate and adaptive immunity to fend off exogenous pathogens. However, the holistic regulatory networks linking genetic background, pathogenic pressure, microbial communities, and environmental cues in shaping chicken immunity remain incompletely resolved. Immune related gene polymorphisms (e.g., MHC-B, TLR4) underpin interbreed differences in immune response magnitude and specificity, while viral pathogens such as Newcastle Disease Virus (NDV) and infectious bursal disease virus (IBDV) disrupt T/B lymphocyte dynamics, alter the expression of immune regulatory microRNAs (miR-155, miR-21) and pro−/anti-inflammatory cytokines (IL-1β, IFN- γ ), and thereby perturb immune homeostasis. The intestinal microbiota, a key mediator of immune function, interacts with intestinal epithelial cells via metabolites (e.g., short-chain fatty acids, bile acids) or modulates the gut immune microenvironment through microbial transplantation, yet the specific targets of core functional taxa and their metabolites in chicken intestinal immunity along with comparative divergences from mammalian systems remain poorly defined. Environmental stressors, particularly heat stress, perturb amino acid metabolism, induce reactive oxygen species accumulation, and disrupt immune cell homeostasis, with synergistic immunosuppressive effects when combined with high density farming and nutritional deficiency. This review synthesizes chicken immune regulation by integrating genetic variation, viral pathogens, intestinal microbiota, and environmental stressors, and defines key regulatory pathways from a host-microbe-environment perspective.

The flavor of chicken meat is formed by a series of complex chemical reactions, and the flavor precursors are affected by regulatory genes. In order to study the differences of muscle flavor precursors between Tengchong Snow chickens and AA broilers, integrated metabolomics and transcriptomics analyses were used to investigate muscle metabolite profiles and the key genes involved in the metabolism of muscle flavor compounds. The results showed that 42 significantly differentially metabolites were detected, and (5-L-Glutamyl)-L-glutamate, gamma-Glutamylalanine, S-Adenosylhomocysteine, Homo-L-arginine and GMP were important flavor metabolites. The key candidate genes with high correlation with flavor precursor metabolites were identified through correlation analysis as NME2 , AMPD1 , GADL1 , ASNS , CARNS1 , and CTH . In addition, the gene-metabolite interaction network for flavor formation in chicken breast muscle was constructed. This study could provide some basic data for the formation mechanism of local chicken excellent meat quality, and provide reference for the development and utilization of local chicken breeds and the selection and breeding of high-quality broilers.