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.
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.
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.
Citrulline (Cit), an effective precursor of arginine (Arg), escapes hepatic catabolism to be almost completely absorbed into the systemic circulation, thereby being efficiently converted to Arg in the kidneys to enhance its systemic bioavailability. This study investigated the effects of dietary Cit supplementation on lactation performance in sows, as well as the underlying mechanisms related to intestinal health in their suckling piglets, using multi-omics analyses.
Dietary Arg and Cit supplementation significantly increased average daily feed intake of lactating sows. Milk fat content and plasma nitric oxide (NO) concentration increased significantly in the Arg group and the 40%Cit group (P < 0.05), while milk threonine content increased slightly (P = 0.084). Consequently, the average daily gain of suckling piglets over the 21-day lactation period was also significantly improved. Furthermore, maternal 40%Cit supplementation improved the intestinal health of offspring by enhancing jejunal morphology and upregulating the expression of the tight junction protein occludin (P < 0.05), indicating a strengthened intestinal barrier. Mechanistically, this was achieved by activating the mTOR/S6 pathway in the piglets' jejunum. Maternal 40%Cit supplementation upregulated the expression of proteins related to mitochondrial fusion and fission (MFN2 and MFF, P < 0.05), and the protein expression of OPA1 showed an increasing trend (P = 0.097), indicating the structural and functional status of mitochondria was improved. Maternal 40%Cit supplementation also modulated the gut microbiota of piglets, increasing the abundance of beneficial bacteria (Lachnoclostridium). Metabolomic analysis of sow milk identified 58 differential metabolites. Among these metabolites, palmitic acid levels were significantly increased and positively correlated with the abundance of Lachnoclostridium in the intestine (P < 0.05).
Dietary Cit supplementation enhanced sow lactation performance and improved intestinal barrier function in their offspring via activation of the jejunal mTOR/S6 pathway and improved mitochondrial structure and function in the piglet jejunum. These benefits were further supported by modulation of the gut microbiota and alterations in the milk fat and metabolome, ultimately promoting piglet growth.
Starch serves as the primary energy source for high-producing dairy ruminants, which include both dairy cows and dairy goats. Optimizing starch digestion is crucial for ensuring high milk production and maintaining animal health. This narrative review summarizes and discusses recent findings concerning the degradability of starch in these species. Dietary starch is classified into three distinct types based on the basis of its degradation characteristics: rumen degradable starch (RDS), which ferments in the rumen; rumen escape starch (RES), which is subsequently digested in the small intestine; and resistant starch (RS), which resists complete digestion and enters the large intestine. This review systematically links feed processing methods, which directly influence starch structure, to their subsequent effects on the gut microbiota composition and host metabolic regulation. Three key insights emerge from this synthesis of literature. First, processing techniques such as steam-flaking critically alter the ratio among the three starch types, thereby shifting the effective site of digestion. Second, the optimal application of RDS differs significantly between dairy cows and dairy goats, primarily because these species exhibit distinct digestive physiologies. Nutritionists must carefully account for these species-specific differences to effectively prevent metabolic disorders. Third, the primary site of starch digestion significantly reshaped the gut microbiota profile. While a proper balance supports beneficial bacteria, excessive RS reduces energy efficiency, whereas an overload of RDS can readily lead to severe rumen acidosis. Therefore, balancing the proportions of RDS, RES, and RS is vital for helping animals effectively manage the elevated energy demands experienced during peak lactation. Future research must focus on developing precise starch management strategies tailored to the specific needs of various ruminant species.
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.
Waterfowl, primarily ducks, constitute a major commercial poultry species globally, their production efficiency is heavily influenced by dietary protein and amino acid intake. Although the National Research Council (NRC, Nutrient requirements of poultry, 1994) established fundamental recommendations for protein and amino acid requirements in ducks, tremendous improvements and changes (growth speed, rearing system, and dietary strategy) have been made in duck industry over the past decades. Consequently, these standards no longer adequately reflect the nutritional needs of modern duck production systems. This review presents updated estimates of dietary crude protein and key amino acid requirements, including methionine, lysine, threonine, tryptophan, and arginine, etc., which are essential for formulating precision diets to maximize growth performance, carcass yield in meat ducks, as well as reproductive performance in laying ducks and breeders. Furthermore, the functional roles of these amino acids as critical regulators of physiological processes are systematically examined, including lipid metabolism (methionine and threonine), intestinal barrier integrity (threonine), regulation of feed intake via nitric oxide (arginine), and the modulation of behavior and stress responses (tryptophan). The implementation of low-protein dietary strategies (crude protein levels as low as 15% for growing meat ducks, and 14.5% for laying ducks) is also discussed for maintaining performance while improving nitrogen utilization efficiency. The recent publication of updated Chinese national feeding standards for meat-type (GB/T 45103-2024) and laying ducks (GB/T 41189-2021) incorporates these modern research advances, representing a significant milestone and providing a modern framework to guide the global duck industries. In summary, this review highlights the urgent need to move beyond outdated nutritional standards and adopt modern, evidence-based amino acid requirements tailored to modern duck production. The integration of low-protein diet strategies along with a refined understanding of amino acid functions is crucial for optimizing duck production, enhancing nutrient efficiency, and reducing environmental impacts. Future research should focus on establishing the precise requirements for other essential amino acids and certain non-essential amino acids, and further elucidating how amino acids molecularly modulate gene expression, signaling pathways, and gut microbiota to develop innovative and sustainable nutritional strategies for ducks.
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.
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.
Baicalin is a bioactive flavonoid from Scutellaria baicalensis Georgi with antioxidant, anti-inflammatory and antibacterial properties. However, its bitter taste and susceptibility to ruminal degradation limit its practical use in mammals. Enteric coating technology might overcome these limitations by enabling targeted intestinal release. This study investigated effects of dietary supplementation with baicalin and coated baicalin on rumen fermentation, gastrointestinal microbiota, immune function and growth performance in Hu sheep.
Thirty-six lambs with similar body weight (33.01 ± 2.68 kg) were randomly assigned to three groups (4 replicates per group, 3 sheep per replicate). The control group was fed basal diet (CON) while treatment I (BAI) and treatment II (C-BAI) groups were fed a basal diet supplemented with 0.1% baicalin and coated baicalin, respectively. After a 60-d feeding trial, baicalin and coated baicalin supplementation improved total weight gain and average daily gain compared with CON group (P < 0.05). In addition, BAI and C-BAI groups exhibited higher total antioxidant capacity (P < 0.05) and catalase activity (P < 0.05) with associated lower malondialdehyde levels (P < 0.05). Immunoglobulin G and anti-inflammatory cytokines interleukin-4 (IL-4) were also increased (P < 0.001). Notably, IgM, IL-10 and IL-4 in the C-BAI group exceeded those of the BAI group (P < 0.001). Microbiome analysis revealed that baicalin supplementation enriched abundance of beneficial bacterial taxa including Firmicutes and Lachnoclostridium (P < 0.05) and reduced potential pathogen abundance, e.g., Treponema and Ralstonia (P < 0.05). The C-BAI group also showed increased abundance of the beneficial Bradyrhizobium compared with CON (P < 0.05). Metabolomic analysis revealed that baicalin altered propionate and tyrosine metabolic pathways (P < 0.05), while coated baicalin modulated penicillin metabolism and glyceride metabolism in jejunum (P < 0.05) increasing ATP production. Overall, these results indicated enhanced nutrient metabolism and gut health in the presence of dietary baicalin.
Dietary supplementation with baicalin and coated baicalin improved growth performance, antioxidant status, immunity and beneficially modulated the microbiome-metabolome crosstalk in Hu sheep. Notably, uncoated baicalin exerted more pronounced effects on growth performance and supported a role for baicalin as a potential and functional feed additive.
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