Intestinal copper homeostasis governs gut health through its dual roles as an enzymatic cofactor and signaling mediator. This review discusses the molecular basis of copper absorption/transport, genetic regulation, and its functional impacts. Copper-dependent enzymes maintain intestinal barrier function and metabolism, while copper availability shapes the composition of gut microbiota and mucosal immunity. The dysregulation of copper homeostasis, specifically pathological accumulation, contributes to the development of CRC by inducing dysbiosis of gut microbiota, chronic inflammation, and metastasis. This review systematically evaluates copper-targeted therapies and the associated unresolved challenges. Future efforts should prioritize defining cell-specific copper handling, metal interaction networks, and the copper-gut microbiota-immune axis in non-cancer pathologies. Moreover, future studies should also focus on developing stratified biomarker panels and spatially precise interventions to harness copper biology for diagnostic and therapeutic innovation.

Human milk oligosaccharides (HMOs) are a prominent class of bioactive glycans recognized for their pivotal roles as prebiotics, anti-adhesive antimicrobials, and immunomodulators in neonatal development. While traditionally studied in the context of infant nutrition, scalable biotechnological production now allows for their evaluation in swine production to address the relatively lower structural complexity of the porcine milk glycome compared to humans. This review critically evaluates the structural diversity and biosynthesis of HMOs, detailing how specific fucosylated and sialylated structures modulate the porcine gut microbiome and reinforce intestinal barrier integrity. We synthesize current evidence regarding the metabolic fate of these glycans in the piglet and address the translational relevance of using swine as high-fidelity models for human gastrointestinal physiology. Furthermore, the review identifies critical knowledge gaps, specifically the lack of large-scale longitudinal studies and comprehensive cost-benefit analyses required to validate the economic feasibility of HMOs in commercial agriculture. By consolidating these mechanistic insights within the context of global efforts to reduce reliance on antibiotic growth promoters, this work underscores the potential of HMOs as precision nutritional tools to enhance resilience and productivity in sustainable animal production systems.

Sexual dimorphism is a defining vertebrate feature, yet its sex-specific molecular architecture remains poorly understood. Here we established a sex-balanced, uniformly reared chicken cohort to map this landscape, integrating individual whole-genome sequencing with 7,969 bulk and 779,380 single nucleus transcriptomes across 32 tissues from 280 birds. We identified 495,098 independent expression quantitative trait loci for 20,194 genes, including 10,937 loci modulated by cell-type composition. Notably, 340 genes were regulated by 449 loci in a sex-dependent manner, significantly enrichment in endocrine tissues like adipose and the adrenal gland. Furthermore, we fine-mapped 1,219 structural variants, demonstrating their unique roles to tissue- and sex-specific expression beyond SNPs. Ultimately, we showed the utility of these regulatory effects in elucidating the molecular basis of metabolism and complex traits in both chickens and humans. This comprehensive atlas of regulatory effects provides profound insights into the genomic and molecular basis of sexual dimorphism in vertebrates.

Metabolic dysfunction-associated fatty liver disease (MAFLD) has become the most prevalent chronic liver disease worldwide and represents a major hepatic manifestation of systemic metabolic dysfunction. The disease is closely linked to obesity and insulin resistance and progresses from simple hepatic steatosis to metabolic dysfunction-associated steatohepatitis, fibrosis, cirrhosis, and hepatocellular carcinoma. Increasing evidence indicates that MAFLD pathogenesis involves complex interactions among dysregulated lipid metabolism, mitochondrial dysfunction, oxidative stress, inflammatory signaling, bile acid imbalance, and gut microbiota-derived metabolites, reflecting the systemic and multifactorial nature of the disease. However, despite substantial progress in understanding these mechanisms, the integrated regulatory networks driving MAFLD progression and their translational therapeutic implications remain incompletely characterized. In this review, we comprehensively summarize recent advances in the molecular mechanisms underlying MAFLD, focusing on metabolic dysregulation, cellular stress responses, inflammatory pathways, and regulated cell death processes. We further highlight the critical role of interorgan communication particularly the adipose-liver and gut-liver axes and discuss emerging evidence on extracellular vesicles (EVs) as mediators of metabolic and inflammatory signaling. Finally, we evaluate current and potential therapeutic strategies, emphasizing the diagnostic and therapeutic promise of EV-based approaches in MAFLD management, and identifying emerging molecular targets for improved intervention and future clinical translation opportunities.

Geese is one of the few poultry species with complete external genitalia, and the external genitalia abnormal development has become an important factor limiting the reproductive efficiency of the goose industry. Recent studies have shown that the gut microbiota plays an important role in regulating male reproductive processes, but its regulatory mechanisms in male geese's external genitalia development remain unclear. In this study, male geese with normal development (ND) and abnormal development (AD) external genitalia were selected as the research object, and multi-omics were used to investigate the regulatory of the microbe-mediated gut-testis axis on external genitalia development. At the transcriptomic level, we identified key DEGs (KNG1, P2RY4, SSTR5, and HRH3) in the testis and external genitalia between ND and AD groups, which were significantly enriched in the neuroactive ligand-receptor interaction pathway. Metabolomics analysis revealed that DMs in the ND and AD groups were significantly enriched in pathways related to aromatic amino acid metabolism and neural signal transduction. Furthermore, metagenomic results showed that the ND group was identified key bacterial genera g_Blautia and g_Faecousia affecting external genitalia development, which were associated with SCFAs synthesis and neuroendocrine signaling regulation. Integrated with multi-omics data, it was revealed that gut-derived neuroactive metabolic signals may participate in the molecular regulation of external genitalia development in male goose by modulating GPCRs signaling. Our findings not only provide new insights into the gut-testis axis regulates the development of external genitalia in male geese, but also contribute to improving the reproductive performance of male geese.

The present study aimed to investigate the protective effects of 2'-fucosyllactose (2'-FL) on diquat-induced intestinal oxidative injury and the underlying involvement of the gut microbiota and microbial tryptophan metabolism in this process. Thirty-six mice were assigned to CON, diquat, and 2'-FL + diquat groups. The results indicated that the diquat injection significantly impaired the intestinal barrier, suppressed the antioxidant capacities in serum and the jejunum, downregulated the mRNA expression of genes related to redox balance, and elevated proinflammatory cytokines. All these adverse effects were alleviated by 2'-FL administration. Moreover, 2'-FL increased the abundance of Lactobacillus and the contents of indole-3-acetic acid, indole-3-acetonitrile, 3-indoleglyoxylic acid, and melatonin and activated the aryl hydrocarbon receptor (AHR) and its downstream genes, while inhibiting the expression of NF-κB and MLCK. Collectively, 2'-FL mitigated oxidative stress-induced intestinal barrier injury by promoting microbial tryptophan metabolism to activate the AHR pathway, underscoring its potential as a functional prebiotic for improving intestinal health.

Intestinal inflammation compromises nutrient absorption, health, and productivity in laying hens. Here, we isolated a gut-resident Lactobacillus rhamnosus GG (LGG) strain from indigenous chickens and evaluated its prophylactic effects against dextran sulfate sodium (DSS)-induced intestinal inflammation. Oral LGG administration improved growth performance and antioxidant capacity, restored the villus structure, and reinforced epithelial barrier integrity by upregulating tight junction genes. LGG markedly reduced pro-inflammatory cytokines (IL-1β, IFN-γ) and increased TGF-β. 16S rRNA sequencing showed that LGG normalized microbial diversity, corrected the Firmicutes/Bacteroidetes ratio, enriched beneficial taxa (Lactobacillus, Lachnoclostridium), and reduced inflammation-associated genera (Escherichia, Bacteroides). Untargeted metabolomics revealed a significant modulation of tryptophan metabolism, including elevated levels of kynurenic acid, xanthurenic acid, and indoleglyoxylic acid. The microbiota-metabolite correlations indicate a coordinated regulatory axis underlying LGG-mediated protection. These findings demonstrate that native LGG mitigates intestinal inflammation through microbiota remodeling and metabolic reprogramming, supporting its potential as an antibiotic-free strategy for improving gut health in poultry.

Reproductive efficiency forms the cornerstone of poultry production, yet ovarian oxidative stress and brooding that emerge with advancing age accelerate follicular atresia, leading to ovarian atrophy. This subsequently disrupts ovulation and shortens the laying cycle. Despite its economic implications, the molecular mechanisms linking these processes to granulosa cell (GC) fate remain poorly understood. This study aimed to construct ceRNA regulatory networks and unravel how microRNA-30b-5p (miR-30b-5p) and its target gene nuclear receptor subfamily 5 group A member 2 (NR5A2) regulate GC proliferation and apoptosis in chicken atrophic ovaries. In this study, we found that the ovarian tissue undergoes degeneration, with reduced levels of the hormones follicle-stimulating hormone (FSH) and luteinizing hormone (LH), and a significant decrease in ovarian antioxidant activity of broody chickens. Whole-transcriptome sequencing on atrophic ovaries (AO) from 700-day-old Hy-line Gray broody hens and normal ovaries (NO) from actively laying hens identified 260 differentially expressed (DE) lncRNAs, 492 DE circRNAs, 53 DE miRNAs, and 4,493 DE mRNAs. Further, integrative analysis revealed miR-30b-5p as a candidate regulator of GC proliferation and apoptosis. Additionally, functional assays including RT-qPCR, western blotting, flow cytometry, cell counting kit 8 (CCK-8) and 5-ethynyl-20-deoxyuridine (EdU) assay incorporation demonstrated that miR-30b-5p overexpression suppressed GC proliferation (reduced CDK2, Cyclin D1, PCNA, and Bcl-2) and promoted apoptosis (increased Caspase-3 and Caspase-9). Thereafter, target prediction and dual-luciferase reporter assays further confirmed that NR5A2 as a direct target of miR-30b-5p, and that NR5A2 knockdown phenocopied the anti-proliferative and pro-apoptotic effects of miR-30b-5p. Taken together, the findings obtained from this study demonstrate that miR-30b-5p promotes GC apoptosis and inhibits proliferation by targeting NR5A2, thereby contributing to follicular atresia during broodiness in the late laying phase. Targeted modulating of miR-30b-5p may offer a promising strategy to alleviate ovarian atrophy, extend the laying cycle and enhance economic efficiency in poultry production.

Improving eggshell quality in poultry is a key breeding goal, and identifying genetic markers that regulate eggshell calcification is essential for accelerating genetic advancements. This study focused on identifying the keys genes and molecular mechanisms that regulate eggshell calcification in the chicken uterus. The results showed that rapid eggshell mineralization began approximately 4 h after the egg enters the uterus, corresponding with observed morphological and histological changes in the uterine tissue. This is associated with increased energy demands and the production of ion transport proteins. Transcriptome analysis identified calbindin-1 (CALB1), ATPase plasma membrane Ca2+ transporting 2 (ATP2B2), and gga-miR-34b-3p as differentially expressed during eggshell formation. CALB1 and ATP2B2 were predicted targets of gga-miR-34b-3p, with roles in maintaining cellular calcium ion balance. A dual-luciferase reporter assay confirmed that gga-miR-34b-3p directly targeted inhibited CALB1 expression, although no significant changes in the luciferase activity were observed with the co-transfection of ATP2B2 wild-type and gga-miR-34b-3p mimic. Validation experiments showed significant increases in CALB1 and ATP2B2 mRNA and protein levels of CALB1 and ATP2B2 in the chicken uterus during eggshell calcification, with CALB1 predominantly expressed in the cytoplasm of uterine tubular gland cells. Furthermore, primary uterine tubular gland cells, identified using immunofluorescence for Cytokertin 18, demonstrated that silencing CALB1 and ATP2B2 increased intracellular Ca2+ concentration in these cells. Taken together, these findings suggest that the gga-miR-34b-3p/CALB1 regulatory axis maintains calcium ion homeostasis in the uterine tubular gland cells, to facilitate continuous and efficient eggshell calcification and thereby enhancing eggshell quality in chickens.

The development of pre-recruitment follicles plays a critical role in determining egg-laying performance in poultry. This study combines proteomic and metabolomic analyses to explore changes in proteins and metabolites, to elucidate key regulatory mechanism involved in chicken pre-recruitment follicular development. Histological examination revealed a significant increase in yolk deposition in small yellow follicles (SYF) compared to small white follicles (SWF). Metabolomics analysis identified significantly enriched differential metabolites (DMs) between SWF and SYF in pathways such as Lysosome, Ferroptosis, Biosynthesis of unsaturated fatty acids, and Tryptophan metabolism. Particularly, Adenosine-5′-Diphosphate (ADP) was downregulated during follicular recruitment and was significantly enriched in the lysosome pathway. Proteomic analyses revealed that differentially expressed proteins (DEPs) in SWF and SYF were enriched in pathways including Lysosome, Glutathione metabolism, Cholesterol metabolism, Arginine and proline metabolism, and amino acid biosynthesis. Among these DEPs, NAD-dependent protein deacetylase sirtuin 5 (SIRT5) was significantly upregulated, while lysosomal-associated membrane protein 1 (LAMP1) was down-regulated during the development of pre-recruitment follicles. SIRT5 was linked to the negative regulation of reactive oxygen species metabolism, whereas LAMP1 was associated with lysosome and autophagy pathways. Further validation experiments demonstrated high expression of SIRT5 in SYF, particularly in granulosa cells (GCs). Silencing SIRT5 in GCs resulted in increased ROS production and upregulated expression of autophagy-related proteins LC3Ⅱ and Beclin1, as well as lysosome markers LAMP1. Conversely, lipid droplet deposition and p62 expression were suppressed. inhibited. Taken together, these findings suggest that SIRT5 upregulation promotes the development of pre-recruitment follicles by inhibiting the autophagy-lysosome pathway in chicken GCs.

Chengkou mountain chicken, a Chinese indigenous breed, exhibits unique flavor characteristics. However, the genetic basis of its flavor precursor substances remains unexplored. We performed a genome-wide association study (GWAS) using low-coverage whole-genome sequencing (lcWGS) and genotype imputation to explore genetic markers linked to flavor precursors (nucleotides, amino acids, etc.) in Chengkou mountain chicken breast muscle. We identified 44 SNPs potentially or significantly associated with flavor precursor traits and localized 18 genes. Functional analysis revealed eight important candidate genes, including ZBTB20, RFX4, MAMLD1, SYN3, ABTB3, PRPF39, LRFN5, and DGCR14, which may play key roles in influencing flavor precursor substances. Moreover, two SNPs residing in the haplotype block (53,448,483 bp to 53,450,834 bp) on chromosome 1 were significantly associated with a di-unsaturated acyl chain (C20:2) residue and mapped to the ABTB3 gene. This study analyzes the composition of flavor precursor substances in the pectoralis major muscle of Chengkou mountain chicken. Moreover, the SNPs, haplotypes, and candidate genes identified in this study can be used to improve the accuracy of the marker-assisted selection of traits related to flavor precursor substances in the breast muscle of chicken. In addition, the candidate genes that are significantly associated with these traits will potentially lay the foundation for future genetic selection aimed at improving the flavor traits of chicken meat.

As potential substitutes of traditional floor rearing system (FRS) and cage-rearing system (CRS) are currently predominant dryland rearing systems for chickens. However, the influence of these two rearing systems on chicken meat quality are poorly understood. In the present study, a comprehensive comparison of lipidomic, metabolomic, and transcriptome profiles was conducted on the breast muscles of Chengkou mountain chicken (CMC) between CRS (n = 18) and FRS (n = 18) at 120 d of age, which exhibit significant variations in meat quality. Phenotypically, the breast muscle weight and thickness were significantly higher in chicken under FRS (p < 0.05). Metabolomic analysis of breast muscle revealed differential regulation of glycerophospholipid metabolism and linoleic acid metabolism between CRS and FRS. Lipidomic analysis indicated a higher abundance of saturated fatty acids (SFA) and polyunsaturated fatty acids (PUFA) in FRS. Transcriptomic analysis showed that differentially expressed genes (DEGs) were significantly enriched in the oxidative phosphorylation pathway and glycerophospholipid pathway. Integrative lipidomics, metabolomics, and transcriptomics analysis revealed that the improved meat quality of the breast muscle in the FRS chicken is mainly associated with oxidative phosphorylation and glycerophospholipid metabolism. This comprehensive analysis provides valuable insights into the distinct meat quality of rearing system.

Poultry broodiness can cause ovarian atresia, which has a detrimental impact on egg production. Non-coding RNAs (ncRNAs) have become one of the most talked-about topics in life sciences because of the increasing evidence of their novel biological roles in regulatory systems. However, the molecular mechanisms of ncRNAs functions and processes in chicken ovarian development remain largely unknown. Whole-transcriptome RNA sequencing of the ovaries of broodiness and laying chickens was thus performed to identify the ncRNA regulatory mechanisms associated with ovarian atresia in chickens. Subsequent analysis revealed that the ovaries of laying chickens and those with broodiness had 40 differentially expressed MicroRNA (miRNAs) (15 up-regulated and 25 down-regulated), 379 differentially expressed Long Noncoding RNA (lncRNAs) (213 up-regulated and 166 down-regulated), and 129 differentially expressed circular RNA (circRNAs) (63 up-regulated and 66 down-regulated). The competing endogenous RNAs (ceRNA) network analysis further revealed the involvement of ECM-receptor interaction, AGE-RAGE signaling pathway, focal adhesion, cytokine-cytokine receptor interaction, inflammatory mediator regulation of TRP channels, renin secretion, gap junction, insulin secretion, serotonergic synapse, and IL-17 signaling pathways in broodiness. Upon further analysis, it became evident that THBS1 and MYLK are significant candidate genes implicated in the regulation of broodiness. The expression of these genes is linked to miR-155-x, miR-211-z, miR-1682-z, gga-miR-155, and gga-miR-1682, as well as to the competitive binding of novel_circ_014674 and MSTRG.3306.4. The findings of this study reveal the existence of a regulatory link between non-coding RNAs and their competing mRNAs, which provide a better comprehension of the ncRNA function and processes in chicken ovarian development.

BACKGROUND:Several core breeding and supporting lines of the Qingyuan partridge chicken, a representative local chicken breed in China, have been developed over 20 years. Consequently, its economic traits related to growth and reproduction have been significantly improved by breeding selection and commercial utilization, but some characteristic traits, such as partridge feathers, high meat quality and sufficient flavor, have always been retained. However, effective methods for genetic assessment and functional gene exploration of similar trait groups are lacking. The presence of identical haplotype fragments transmitted from parent to offspring results in runs of homozygosity (ROH), which offer an efficient solution. In this study, genomes of 134 Qingyuan partridge chickens representing two breeding populations and one preserved population were re-sequenced to evaluate the genetic diversity and explore functional genes by analyzing the diversity, distribution, and frequency of ROH.RESULTS:The results showed a low level of genomic linkage and degree of inbreeding within both the bred and preserved populations, suggesting abundant genetic diversity and an adequate genetic potential of the Qingyuan partridge chicken. Throughout the long-term selection process, 21 genes, including GLI3, ANO5, BLVRA, EFNB2, SLC5A12, and SVIP, associated with breed-specific characteristics were accumulated within three ROH islands, whereas another 21 genes associated with growth traits including IRX1, IRX2, EGFR, TPK1, NOVA1, BDNF and so on were accumulated within five ROH islands.CONCLUSIONS:These findings provide new insights into the genetic assessment and identification of genes with breed-specific and selective characteristics, offering a solid genetic basis for breeding and protection of Qingyuan partridge chickens.

The Chengkou mountain chicken, a native Chinese poultry breed, holds significant importance in the country’s poultry sector due to its delectable meat and robust stress tolerance. Muscle growth and development are pivotal characteristics in poultry breeding, with muscle fiber development during the embryonic period crucial for determining inherent muscle growth potential. Extensive evidence indicates that non-coding RNAs (ncRNAs) play a regulatory role in muscle growth and development. Among ncRNAs, circular RNAs (circRNAs), characterized by a closed-loop structure, have been shown to modulate biological processes through the regulation of microRNAs (miRNAs). This study seeks to identify and characterize the spatiotemporal-specific expression of circRNAs during embryonic muscle development in Chengkou mountain chicken, and to construct the potential regulatory network of circRNAs-miRNA-mRNAs. The muscle fibers of HE-stained sections became more distinct, and their boundaries were more defined over time. Subsequent RNA sequencing of 12 samples from four periods generated 9,904 novel circRNAs, including 917 differentially expressed circRNAs. The weighted gene co-expression network analysis (WGCNA)-identified circRNA source genes significantly enriched pathways related to cell fraction, cell growth, and muscle fiber growth regulation. Furthermore, a competitive endogenous RNA (ceRNA) network constructed using combined data of present and previous differentially expressed circRNAs, miRNA, and mRNA revealed that several circRNA transcripts regulate MYH1D, MYH1B, CAPZA1, and PERM1 proteins. These findings provide insight into the potential pathways and mechanisms through which circRNAs regulate embryonic muscle development in poultry, a theoretical support for trait improvement in domestic chickens.

Iron is a vital trace element that plays an important role in humans and other organisms. It plays an active role in the growth, development, and reproduction of bacteria, such as Bifidobacteria. Iron deficiency or excess can negatively affect bacterial hosts. Studies have reported a major role of iron in the human intestine, which is necessary for maintaining body homeostasis and intestinal barrier function. Organisms can maintain their normal activities and regulate some cancer cells in the body by regulating iron excretion and iron-dependent ferroptosis. In addition, iron can modify the interaction between hosts and microorganisms by altering their growth and virulence or by affecting the immune system of the host. Lactic acid bacteria such as Lactobacillus acidophilus (L. acidophilus), Lactobacillus rhamnosus (L. rhamnosus), and Lactobacillus casei (L. casei) were reported to increase trace elements, protect the host intestinal barrier, mitigate intestinal inflammation, and regulate immune function. This review article focuses on the two aspects of the iron and gut and generally summarizes the mechanistic role of iron ions in intestinal immunity and the remodeling of gut microbiota.

Prolonged exposure to high temperatures and humidity can trigger heat stress in animals, leading to subsequent immune suppression. Lipopolysaccharides (LPSs) act as upstream regulators closely linked to heat stress, contributing to their immunosuppressive effects. After an initial examination of transcriptome sequencing data from individual samples, 48 genes displaying interactions were found to potentially be associated with heat stress. Subsequently, to delve deeper into this association, we gathered chicken bone marrow dendritic cells (BMDCs). We combined heat stress with lipopolysaccharides and utilized a 48 × 48 Fluidigm IFC quantitative microarray to analyze the patterns of gene changes under various treatment conditions. The results of the study revealed that the combination of heat stress and LPSs in a coinfection led to reduced expressions of CRHR1, MEOX1, and MOV10L1. These differentially expressed genes triggered a pro-inflammatory response within cells via the MAPK and IL-17 signaling pathways. This response, in turn, affected the intensity and duration of inflammation when experiencing synergistic stimulation. Therefore, LPSs exacerbate the immunosuppressive effects of heat stress and prolong cellular adaptation to stress. The combination of heat stress and LPS stimulation induced a cellular inflammatory response through pathways involving cAMP, IL-17, MAPK, and others, consequently leading to decreased expression levels of CRHR1, MEOX1, and MOV10L1.

Different rearing systems have varying effect on animal welfare and meat quality of poultry. Currently, there are no established standards for the rearing systems of Chinese indigenous chickens. Our study aimed to investigate the effects of different rearing systems on the meat quality, gene profiles, and metabolites of Chinese indigenous chickens (Nanchuan chicken). 10-wk-old Nanchuan chickens (n=360) were randomly divided into 3 groups (cage, net, and free-range groups), with 6 replicates per group (20 chickens per replicate). The experiment lasted for 12 wk. At 154-days-old, 36 healthy chickens (6 males and 6 females per group) were randomly selected, euthanized, and their breast muscles were collected to assess the meat quality parameters and histomorphological characteristics. Additionally, breast muscles from 18 random hens (3 males and 3 females per group) were used for metabolomics and RNA-seq analysis. The results showed that rearing systems significantly affected the meat quality and myofiber characteristics. The meat quality of breast muscles from free-range chickens was superior to that of caged chickens, characterized by more tender meat and smaller myofiber cross-sectional areas. Integrative metabolomics and transcriptomics analysis revealed that the differentially expressed genes of chicken breast muscles were primarily involved in the myofiber differentiation. Mechanically, the improved meat quality of breast muscle in free-range chickens were mainly associated with enhanced skeletal muscle differentiation facilitated by fibromodulin, increased levels of up-regulated Acetyl-L-carnitine and Propionylcarnitine level, and decreased levels of Nonanoic acid and Elaidic acid abundance (Graphical abstract). This provides a comprehensive understanding of the most effective and sustainable breeding, production, and rearing systems for Chinese indigenous chickens. It also contributes to the current knowledge of the molecular mechanisms underlying the effects of rearing systems on growth performance and meat quality of chickens.

Egg production, regulated by multiple tissues, is among the most important economic traits in poultry. However, current research only focuses on the hypothalamic-pituitary-ovarian axis, ignoring the most important organ for substance metabolism in the body, the liver. Eggs are rich in lipids, proteins, and other nutrients, which are biosynthesized in the liver. Therefore, here the liver was included in the study of the hypothalamic-pituitary axis. This study used hypothalamus (HH_vs_LH), pituitary (HP_vs_LP), liver (HL_vs_LL), and ovary (HO_vs_LO) tissue samples from high- and low-laying Chengkou mountain chickens (CMC) for epihistological, transcriptome and metabolomic analyses aimed at improving the reproductive performance of CMC. The results showed that the liver of the high-laying group was yellowish, the cell boundary was clear, and the lipid droplets were evenly distributed. The ovaries of the high-laying group had a complete sequence of hierarchical follicles, which were rich in yolk. In contrast, the ovaries of the low-laying group were atrophic, except for a few small yellow follicles, and numerous primordial follicles that remained. The transcriptome sequences yielded 167.11 Gb of clean data, containing 28,715 genes. Furthermore, 285, 822, 787, and 1,183 differentially expressed genes (DEG) were identified in HH_vs_LH, HP_vs_LP, HL_vs_LL and HO_vs_LO and the DEGs significantly enriched 77, 163, 170, 171 pathways, respectively. Metabolome sequencing yielded 21,808 peaks containing 4,006 metabolites. The differential metabolite analysis yielded 343 and 682 significantly different metabolites (SDM) that significantly enriched 136 and 87 pathways in the liver and ovaries, respectively. A combined analysis of the transcriptome and metabolome of the liver and ovaries identified "CYP51A1-4α-carboxy-stigmasta7, 24(24(1))-dien-3β-ol" and "ACSS1B-estrone 3-sulfate" and other multiple gene-metabolite pairs. The DEGs in the hypothalamus and pituitary mainly enriched signaling transduction. In contrast, the DEGs and SDMs in the liver and ovaries mainly enriched the substance metabolism pathways: "gap junction", "extracellular matrix (ECM)-receptor interaction", "Steroid biosynthesis", and "Steroid hormone biosynthesis". These results suggest that the hypothalamic-pituitary axis may affect egg production mainly by regulating lipid metabolism in the liver and ovaries.

Growth traits constitute critical factors in the breeding program of broiler chickens. The Chengkou mountain chicken A-lineage (CMC-A) represents a breed specifically bred for meat production. To further explore the growth performance of the CMC-A population, this study conducted whole-genome sequencing on 464 CMC-A roosters to systematically evaluate their genetic diversity. Additionally, runs of homozygosity (ROH) islands and genome-wide association studies (GWASs) were employed to identify the loci and functional genes influencing the growth traits in Chengkou mountain chickens. The results revealed a high level of genetic diversity and low levels of inbreeding in Chengkou mountain chickens. Several genes associated with stress resistance, muscle growth, and fat deposition were pinpointed through ROH island identification. Moreover, 52 SNP loci were detected, along with 71 candidate genes. These findings enhance our understanding of the genetic architecture underlying the growth traits in Chengkou mountain chickens and provide a theoretical foundation for subsequent breeding endeavors.