Most ReadThe differences in egg production performance among hens are closely linked to the efficiency of follicle selection, which is characterized by granulosa cell differentiation and progesterone production. In this study, by integrating ATAC-seq and mRNA-seq analyses on granulosa cells from pre-hierarchical (Pre-GCs) and hierarchical (Post-GCs) follicles, we set out to identify key regulatory factors involved in chicken follicle selection.
ATAC-seq analysis revealed 21,616 upregulated and 6,344 downregulated differentially accessible peaks in Post-GCs compared to Pre-GCs. Enrichment analysis of the top 400 upregulated and downregulated peaks (ranked by |log2FC|) identified 106 upregulated and 81 downregulated genes encoding transcription factors (TFs). mRNA-seq analysis showed 1,337 upregulated and 2,282 downregulated differentially expressed genes in Post-GCs compared to Pre-GCs. Among these, 146 genes were uniquely expressed in Pre-GCs, and 40 genes were uniquely expressed in Post-GCs. Integrated ATAC-seq and mRNA-seq analyses revealed that chromatin accessibility and gene expression were not always positively correlated. Additionally, four significantly upregulated core TFs (CREM, ESRRB, NR5A1, GATA6) and one significantly downregulated TF (ETS1) genes were identified. The upregulated TFs were associated with 651 significantly upregulated target genes across both mRNA and ATAC-seq data, while the downregulated TFs were associated with 236 significantly downregulated target genes. KEGG enrichment of these target genes identified core genes enriched in pathways closely related to follicle selection, such as Wnt signaling pathway. In the protein-protein interaction (PPI) network of core upregulated target genes, genes such as SMAD2 and PPARA occupied central positions, while genes such as LEF1 and RAC2 were central in the PPI network of core downregulated target genes. Among these core TFs, GATA6 is confirmed to promote the expression of key cholesterol and progesterone synthesis genes to enhance both cholesterol and progesterone production, with follicle-stimulating hormone further amplifying its effect on progesterone synthesis.
Our integrated ATAC-seq and mRNA-seq analyses define key epigenetic and transcriptional changes during chicken follicle selection. We highlight core transcription factors, including CREM, ESRRB, NR5A1, GATA6 and ETS1, and their stage-specific target networks. Functional assays show that GATA6 promotes cholesterol and progesterone synthesis, providing mechanistic insight and candidate targets for improving hen reproductive performance.
Scutellaria baicalensis, a traditional Chinese medicine (TCM), has demonstrated significant therapeutic efficacy in treating respiratory diseases caused by Mycoplasma gallisepticum (MG). However, the effective components of Scutellaria baicalensis are complex, and the material basis for its efficacy anti-MG infection remains unclear. This study aims to elucidate the molecular mechanism by which Scutellaria baicalensis exosome-like nanoparticles (SBELNs) and the key effector molecule, miR159a, regulate inflammation-induced injury caused by MG infection.
SBELNs were isolated from Scutellaria baicalensis root by ultracentrifugation. The in vivo and in vitro transport of SBELNs was investigated through live imaging and laser confocal microscopy after staining with DIR fluorescent dye. Key miRNAs were screened via RNA sequencing, and target genes were predicted using online databases. The interaction between miR159a and its target gene, cyclic nucleotide-gated channel alpha 1 (CNGA1), was validated using a dual-luciferase reporter assay. Furthermore, the regulatory network of the miR159a/CNGA1 axis was systematically analyzed.
SBELNs can specifically target lung tissue. Subsequently, SBELNs release bioactive components that alleviate the lung inflammatory damage caused by MG infection. This beneficial effect stems from two aspects. Firstly, the flavonoid metabolites encapsulated in SBELNs directly suppress the inflammatory damage caused by MG infection. Secondly, the microRNA in SBELNs regulates calcium ion homeostasis via the miR159a/CNGA1 axis. This relieves the intracellular calcium overload induced by MG and participates in the regulation of the immune system by modulating calcium ions. The microRNA in SBELNs regulates calcium ion homeostasis through the miR159a/CNGA1 axis, thereby alleviating MG-induced intracellular calcium overload, mitochondrial damage, excessive ROS, and overactivation of the NF-κB inflammatory pathway.
This article expounds that SBELNs alleviate lung injury caused by MG infection by regulating calcium homeostasis. This discovery demonstrates the anti-infective capability SBELNs, but also supports the development of natural drug delivery systems.
Subclinical mastitis (SCM) is a major constraint in dairy production and is driven by complex host-pathogen interactions. Although transcriptional responses associated with SCM have been widely investigated, the epigenetic mechanisms that stably regulate these programs remain less well characterized, particularly in crossbred cattle populations. This study aimed to characterize DNA methylation-based regulatory networks by integrating whole-genome methylation and transcriptome data from milk somatic cells of Vrindavani (Bos taurus × Bos indicus) cattle. Whole-genome methylation (n = 6) and corresponding transcriptome profiling (n = 6) were performed on milk somatic cells from SCM-affected and healthy control cows.
Differential methylation analysis (q-value < 0.05) identified 62,940 differentially methylated cytosines (DMCs), 7,706 differentially methylated regions (DMRs), and 6,203 differentially methylated genes (DMGs), with a predominant bias toward hypomethylation in SCM. Integrative analysis using stringent thresholds for both methylation (≥ 10%) and expression change (|log2 fold change| ≥ 1; P of GMM < 0.001) identified 1,407 differentially methylated and expressed genes (DMEGs). Functional enrichment analysis revealed 47 KEGG pathways and 30 Gene Ontology biological process terms (FDR < 0.05), primarily associated with immune signaling and inflammatory responses. In contrast, a subset of DMEGs showed methylation-associated repression of lactation- and metabolism-related genes. Selected genes were experimentally validated by qPCR, including upregulation of the inflammatory mediator S100A8 and downregulation of CSN3 (κ-casein), a key milk protein gene.
These findings provide an integrated view of the DNA methylation and transcriptional landscape of SCM in milk somatic cells and demonstrate that epigenetic remodeling is associated with coordinated activation of immune pathways alongside repression of lactation-associated functions. The results contribute to understanding the molecular basis of subclinical mastitis and may inform future efforts toward biomarker development and epigenetically informed strategies for improving disease resilience in dairy cattle.
Selective breeding has substantially improved productive and reproductive traits in pigs. Yet, these traits are biologically interconnected, and selection for one often affects others in unintended ways. While genomewide association studies (GWAS) have uncovered many loci linked to these traits, they provide limited insight into causal mechanisms. Mendelian randomization (MR) provides a robust framework for inferring causality and identifying shared genetic determinants. Here, we integrated MR, colocalization, and functional genomics to investigate the biological links between growth, carcass composition, and reproduction in pigs.
Using average daily gain (ADG) as the exposure, MR revealed potentially significant causal effects (P < 0.05) of ADG on carcass composition traits, including backfat thickness (BFT: ) and loin muscle depth (LMDEP:
), suggesting a potential causal contribution of increased ADG to both fat deposition and muscle development. Additionally, ADG showed a negative causal association with age at first farrowing (AFF:
), indicating that faster growth promotes earlier sexual maturity and reproductive onset. In addition to the statistical evidence, gene annotation of instrumental variants (IVs) identified overlapping candidate genes, which may help explain the causal associations observed across the four exposure-outcome analyses. Among these, MC4R and CDH20 were supported by colocalization analysis, indicating shared genetic signals potentially linking growth, carcass composition, and reproductive traits. Integrative analysis supported the tissue-specific roles of these genes in regulating growth, carcass composition, and reproduction.
Our findings suggest a shared genetic architecture and provide potential evidence of a causal influence of ADG on carcass composition and reproductive traits in pigs. This integrative framework supports the development of multi-trait breeding strategies that enhance productivity while managing inherent trade-offs in regulating complex traits.
Improving milk yield and feed efficiency is pivotal for climate-smart dairy systems, as rumen mediated fermentation governs energy and nitrogen utilization and thereby greenhouse-gas emission intensity. Soybean isoflavones (SIF) may modulate rumen fermentation, yet their effects on rumen function, microbiome features, host endocrine/metabolic responses, and lactation performance-particularly across cows with divergent milk-yield phenotypes-remain unclear.
Fifty-six lactating Holstein cows (28 high-yield cows, HY; 28 low-yield cows, LY) were divided into two categories by milk yield. Within each yield category, cows were randomly assigned to one of two dietary treatments: a basal diet (Control) or the basal diet supplemented with SIF at 0.01% of dry matter. This yielded a 2 × 2 factorial design with four experimental groups (n = 14 per group): high-yield control (HCON), high-yield SIF (HSIF), low-yield control (LCON), and low-yield SIF (LSIF). SIF increased milk yield by 8.75% and improved fat-corrected milk (+ 7.20%), dry matter intake (+ 3.20%), and feed efficiency (+ 3.26%), with larger gains in HY cows (milk yield + 8.89%; feed efficiency + 4.55%). Rumen fermentation shifted toward a more energetically favorable profile, with lower acetate (- 2.70%), higher propionate (+ 4.55%), and a reduced acetate-to-propionate ratio (- 7.02%), accompanied by increased microbial crude protein (+ 21.53%) without changes in pH or NH3-N. SIF altered endocrine status irrespective of phenotype, increasing estradiol and progesterone while decreasing prolactin and growth hormone, and reduced blood ALP, lactate, and triglycerides. Metagenomics indicated phenotype-dependent microbial and functional responses to SIF: HY cows showed enrichment of taxa (e.g., Caudoviricetes sp., Eubacterium sp., and Butyrivibrio sp.) associated with amino-acid, cofactor metabolism and propionate pathways, whereas LY cows exhibited enrichment of Prevotella sp. and Bacteroides sp. with functions favoring carbohydrate degradation. The HCON group exhibited greater abundances of Prevotella sp. and Hallella spp. with enhanced carbohydrate degradation functions, whereas the LCON group was enriched in Ruminococcus sp. and Methanobrevibacter sp., associated with methane metabolism.
In conclusion, this study highlights the potential of SIF supplementation to improve lactation efficiency, modulate rumen microecology and endocrine function in dairy cows. These findings establish a theoretical framework for achieving efficient and precise feeding management on large-scale dairy farms.
Early embryo loss is an important factor affecting the reproductive capacity of cattle. Recent studies have revealed that during the process of embryonic genome activation (EGA), epigenetic modification, such as histone lactylation remodeling, is crucial for early embryonic development. However, the effects of histone lactylation on early embryonic development in bovines and the related mechanisms remain unknown. In this study, in vitro fertilized embryos were utilized to investigate the effects of histone lactylation on EGA and early embryo development in cattle.
Histone lactylation, including pan-lysine lactylation, histone H3 lysine 9 lactylation, and histone H3 lysine 18 lactylation, occurred mainly in the nucleus and significantly decreased from the 8-cell stage to the morula stage and increased from the morula stage to the blastocyst stage. Decreased or increased levels of histone lactylation induced by GSKA or sodium lactate supplementation inhibited early bovine embryo development and blastocyst lineage differentiation. Furthermore, single-cell RNA sequencing data and 5-ethynyluridine staining revealed that a reduction in histone lactylation levels altered the expression of genes associated with DNA transcription and RNA polymerase activity, thereby impairing EGA. Importantly, β-nicotinamide mononucleotide rescued the inhibitory effects of GSKA supplementation on bovine EGA and early embryonic development.
Histone lactylation maintains early bovine embryo development by regulating EGA. Our findings provide a theoretical reference for addressing early embryo loss and thereby increasing the reproductive capacity of cattle.
As global demand for milk and meat increases, young ruminants need rapid gut development and sufficient mucosal immunity immediately after birth. However, their growing intestines face oxidative and microbial challenges that can harm long-term performance. This review systematically summarizes recent advances in how host genetics, early nutrition, and emerging microbiota interact to influence intestinal development and mucosal immunity under standard rearing conditions. We explore how the host regulates the gut microbiota, the microbiota's role in maintaining gut integrity, barrier function, development, intestinal cell health, mucosal immunity, and how diet modulates gut microbiota composition in young ruminants. Microbial signals promote increased villus length and better epithelial functions. Conversely, dysbiosis delays gut closure, weakens barrier integrity, and skews immunity toward proinflammatory responses. Feeding strategies such as colostrum timing, milk replacers, and the addition of starter fiber and probiotics can alter microbial communities within days. Nonetheless, challenges remain in standardizing neonatal feeding practices, identifying microbe metabolite indicators of gut health, and integrating precision feeding technologies. By mapping the three-way interaction among host, microbiota, and diet, this review offers a blueprint for neonatal ruminant feeding that enhances both animal welfare and the productivity of future ruminant systems. This review also provides a novel mechanistic integration of host genetics, gut microbiota succession, and dietary interventions in young ruminants, filling the gap of fragmented multi-omics analyses in existing literature and offering targeted insights for optimizing gastrointestinal development and production efficiency.
Transitioning to a high-grain (HG) diet significantly alters rumen fermentation by increasing the production of short-chain fatty acids (SCFAs) and lowering rumen pH, which may contribute to subacute ruminal acidosis (SARA) and damage to the ruminal epithelium. Rapid adaptation of rumen epithelium to these metabolic shifts is essential to maintain homeostasis, but the transcriptional mechanisms underlying this adaptation remain poorly understood.
We analyzed the temporal progression of gene expression and metabolomic profile in rumen papillae collected during low-grain feeding (LG) and one week after transitioning to a HG diet (HG1), or four weeks after (HG4) in cows classified as susceptible or resistant to SARA. RNA sequencing identified 955 differentially expressed genes (DEGs) across time points, revealing a biphasic adaptation pattern. Early responses (HG1) showed moderate transcriptional changes, while HG4 was characterized by substantial transcriptional remodeling. Pathway analysis indicated three major functional categories affected during adaptation: cellular stress response, metabolic adaptation, and protein processing. Notably, sterol biosynthesis genes showed transient upregulation at HG1 followed by downregulation at HG4, coinciding with morphological changes in rumen wall thickness and n-butyrate concentration in rumen fluid. Correlation analyses comparing gene expression patterns and metabolite level changes triggered by the dietary transition revealed potential links between metabolic and transcriptional adaptation. Of particular interest, valerate levels at HG1 correlated with genes involved in tissue remodeling at HG4, implying that valerate may contribute to delayed epithelial responses. Next, transcriptional differences between SARA-susceptible and SARA-resistant animals included genes related to inflammation, cell structure, and metabolism that persisted across all time points, suggesting underlying intrinsic differences in SARA susceptibility that are present before and persist during dietary challenge. Key genes consistently differentially under-expressed in SARA-susceptible animals, CCDC196 and MYO7B, represent potential biomarkers for SARA predisposition. Finally, the SARA-resistant group showed a greater number of transcriptome-metabolome correlations, suggesting more coordinated epithelial responses to diet change compared to the SARA-susceptible group.
Our findings provide insights into the molecular mechanisms underlying rumen adaptation to HG diets and individual variation in SARA susceptibility, providing a basis for developing strategies to optimize dietary transitions in ruminant production systems.
Growth performance and carcass traits are economically vital in poultry breeding. In Wenchang chickens, reducing excessive abdominal fat represents a critical breeding objective. However, as a typical carcass trait, abdominal fat thickness has traditionally been measurable only post-slaughter, resulting in inefficient and costly selection processes that hinder genetic progress for these traits. To overcome this limitation, we developed an integrated approach combining non-invasive ultrasound phenotyping and multi-model genomic selection to evaluate growth and fat-related traits in Wenchang chickens.
We genotyped 3,737 chickens using the "Jingxin No.1" 55K SNP array and performed longitudinal measurement of abdominal fat thickness (AFT) via ultrasound imaging. A comprehensive evaluation of genomic prediction models revealed that WGBLUP (informed by wssGWAS), and GBLUP models based on LD-pruned whole-genome sequencing (WGS) data significantly outperformed standard GBLUP, with accuracy gains of 5.25% and 6.58%-15.30%, respectively. Among the machine learning algorithms tested, kernel ridge regression (KRR) and support vector regression (SVR) achieved the highest predictive improvement (3.00%-4.15%) while maintaining superior computational efficiency, whereas ensemble methods provide no consistent advantage.
Our work established ultrasound imaging as a scalable, non-invasive phenotyping platform for poultry breeding. Results demonstrated that integrating wssGWAS-derived biological priors with WGS data substantially improves genomic prediction accuracy for complex traits. This integration, enhanced by computationally efficient machine learning algorithms, provides a powerful and practical strategy to accelerate genetic gain.
The fact that feeding pigs with probiotic-fermented agricultural by-products improves pork quality has been repeatedly demonstrated and widely applied, but the underlying mechanisms remain unclear. This study explored the effects of fermented extruded brewers' spent grain (FEBSG) on meat quality in growing-finishing pigs, as well as its regulatory mechanisms.
Sixty Duroc × Landrace × Yorkshire pigs (52.25 ± 2.10 kg) were randomly assigned to five dietary treatments, in which FEBSG replaced 0, 5%, 10%, 15%, and 20% of soybean meal (SBM). The experiment spanned 10 weeks.
Compared with the control, 20% FEBSG significantly increased final body weight, average daily feed intake, and average daily gain, while decreasing feed to gain ratio (P < 0.05). Both 15% and 20% FEBSG improved carcass characteristics and meat quality, including higher carcass weight, loin eye area, and intramuscular fat content, along with lower drip loss and shear force (P < 0.05). These treatments also enhanced flavor-related amino acids and unsaturated fatty acids (P < 0.05), and improved umami and sweet taste profiles. Moreover, 20% FEBSG increased muscle fiber density and reduced fiber diameter, upregulated MyHC Ⅰ, MyHCⅡa, PGC-1α, AMPKα1, TFAM, and SDH activity, and downregulated MyHC Ⅱb and LDH activity (P < 0.05). Proteomic analysis identified 69 differentially expressed proteins, with enrichment in AMPK and PPAR signaling pathways. Metagenomic analysis revealed increased abundance of short-chain fatty acid-producing bacteria, including Clostridium, Lactobacillus, Prevotella, and Bartonella. Correlation analysis demonstrated associations between gut microbiota diversity and meat quality traits, as well as between dominant microbial genera and differentially expressed proteins, volatile fatty acids, muscle fiber characteristics, and the AMPK/PGC-1α/TFAM signaling pathway.
Partial replacement of SBM with FEBSG positively influenced growth performance and pork quality in pigs, with the underlying mechanisms may involve the activation of the AMPK/PGC-1α/TFAM signaling pathway via the gut-muscle axis, thereby enhancing mitochondrial biogenesis, muscle development, and metabolism.
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