Ubiquitin-specific peptidase 18 (USP18) possesses both deubiquitinating and deISGylating activities and plays a crucial role in regulating innate immune responses and antiviral defense. However, the function of USP18 in Japanese encephalitis virus (JEV) replication remains unclear. In this study, the expression pattern of the porcine USP18 gene following JEV infection was examined by quantitative real-time PCR (qRT-PCR) and Western blot analysis. The effects of USP18 overexpression and siRNA-mediated knockdown on JEV replication and the expression of type I interferon (IFN-I) signaling pathway genes were examined. Protein-protein interactions between USP18 and IFN-I pathway components were predicted by AlphaFold3 and validated by co-immunoprecipitation (Co-IP) and confocal immunofluorescence colocalization assays. The results showed that JEV infection significantly upregulated USP18 expression. Overexpression of USP18 significantly inhibited JEV replication, whereas USP18 knockdown enhanced viral replication and suppressed IFN-I signaling-related gene expression. Moreover, USP18 was found to interact with the key IFN-I signaling proteins IRF3 and MAVS, and USP18 promoted IRF3 phosphorylation, suggesting that USP18 suppresses JEV replication by positively regulating IFN-I-mediated antiviral responses. These findings provide new insights into the antiviral mechanism of porcine USP18 and offer potential molecular targets for disease-resistant breeding and antiviral therapy in pigs.

BackgroundPseudorabies virus (PRV) is a major swine pathogen that causes substantial economic losses. The dynamic remodeling of host cell chromatin plays a pivotal role during viral infections. However, the epigenetic mechanisms underlying PRV-host interactions remain unclear.MethodsThis study integrates ATAC-seq and RNA-seq to investigate the dynamic changes in host chromatin accessibility and gene transcription during PRV infection. The accessible chromatin regions were analyzed for enrichment in genomic features and transcription factor binding motifs. RNA-seq data were used to identify differentially expressed genes and dysregulated pathways. The two datasets were integrated to examine correlations between chromatin accessibility and gene expression.ResultsPRV infection induces a genome-wide elevation in host chromatin accessibility, which progressively intensifies throughout the course of infection. These accessible chromatin regions are predominantly enriched in promoters and binding motifs for bZIP family transcription factors, such as BATF, ATF3, and AP-1, suggesting these transcription factors may play an important role in PRV infection. RNA-seq analysis reveals that PRV infection significantly dysregulates genes involved in metabolic and immune response pathways, with extensive transcriptional suppression observed in the late stages. Integration of ATAC-seq and RNA-seq data demonstrates that chromatin accessibility is positively correlated with gene expression for the majority of differentially expressed genes. However, certain genes exhibit discordant regulation, implying the existence of more complex regulatory mechanisms.ConclusionThis study provides valuable epigenetic insights into the PRV-host interaction and establishes a theoretical framework for developing novel antiviral strategies.

Jiangshan black-bone chicken is well known for its nutritional and health-promoting benefits, and the high melanin content in its muscles gives it a distinctive black appearance. Melanin possesses strong free radical scavenging ability, which may influence the antioxidant capacity and flavor characteristics of muscle tissue. Therefore, we conducted RNA sequencing and non-targeted liquid chromatography-mass spectrometry (LC-MS)-based metabolomics sequencing on the pectoralis major muscles of Jiangshan black-bone chickens and ordinary chickens (Baier buff chickens), to investigate differences in muscle metabolic regulation between two types of chickens. We detected 88 differentially expressed genes (DEGs) and 124 differential metabolites (DMs), identified enrichment in the "Oxidative phosphorylation", "Glutathione metabolism", and "Melanogenesis" pathways. As a result, genes CHAC1, GSTA2, DCT, EDNRB, TYRP1, ATP5F1EP2 and metabolites "Adenosine diphosphate (ADP)", "Phosphate (Pi)", "Pyrophosphate (PPi)", "Oxidized glutathione (GSSG)", "Spermine", contributed to differences in antioxidant capacity between the pectoralis major muscles of Jiangshan black-bone chickens and Baier buff chickens. Our results indicated that the Jiangshan black-bone chickens could generate more adenosine diphosphate (ADP), thereby enhancing glutathione metabolism and melanin synthesis, which may facilitate the removal of reactive oxygen species (ROS) in muscle tissue.

Melanin deposition in the breast muscle is a defining economic and nutritional trait of Jiangshan black-bone chickens, yet the biological architecture governing this phenotype is intricate. While the phenotypic characteristics are well-documented, the dynamic interplay between transcriptomic regulation and metabolic shifts driving melanin accumulation during critical embryonic stages remains underexplored. This study aimed to elucidate the temporal molecular mechanisms of melanin deposition in breast muscle during embryonic development (Embryonic day 13 - Embryonic day 21, E13-E21) by integrating transcriptome and metabolome analyses. We quantified melanin content and performed RNA-sequencing and LC-MS/MS metabolomics on breast muscle tissue collected across five developmental stages (E13, E15, E17, E19, and E21). Results showed a significant increase in melanin content from E13 to E19, stabilizing by E21. The multi-omics integration identified 8,651 differentially expressed genes (DEGs) and 712 differential metabolites (DMs). Pathway analysis revealed significant enrichment in broader amino acid metabolism, MAPK signaling, and neuroactive ligand-receptor interactions. Furthermore, targeted candidate analysis on the classical melanogenesis network successfully highlighted key regulatory genes such as DCT, TYRP1, and MC1R. Metabolome analyses shows that amino acid metabolism plays an important role in melanin synthesis. Correlation analysis unveiled a tight linkage between metabolites (phenylpyruvate, glycerol, 1-myristoyl-2-palmitoyl-sn‑glycero-3-phosphocholine (PC), 1,2-dipalmitoyl-sn‑glycero-3-phosphoethanolamine (PEA)) and functional genes related to immunity (IL4I1, MLKL) and lipid remodeling (PNPLA2, CCNB1). Furthermore, specific alterations in sulfur metabolism genes (CBS, CTH, GPX1) suggested a regulatory mechanism balancing eumelanin and pheomelanin synthesis. Crucially, the reliability of these transcriptomic and conjoint analyses was robustly confirmed via targeted qRT-PCR validation of key genes regulating melanogenesis, membrane dynamics, and sulfur amino acid metabolism. These findings highlight the intricate interplay between the transcriptome and metabolome underlying muscle hyperpigmentation and provide novel insights into the molecular breeding targets for optimizing meat quality in poultry.

Dendrobium officinale Kimura et Migo (D. officinale) is a traditional Chinese medicinal herb with recognized anti-inflammatory, antioxidant, and immunomodulatory properties. This study evaluated whether dietary supplementation with D. officinale leaf powder could influence bone mass, mechanical strength, and molecular markers of bone metabolism in caged laying hens. A total of 192 healthy 19-week-old Jinghong No. 1 hens were randomly assigned to three dietary groups: a control group fed a basal diet and two treatment groups supplemented with 1200 or 3600 mg/kg of D. officinale leaf powder for 16 weeks. Tibial and femoral bone strength and mineral density did not differ significantly among treatments (p > 0.05). However, tibial breaking strength displayed upward trends in both supplemented groups (p = 0.08), and similar tendencies were observed for femoral bone mineral content and bone density (p = 0.08). At the molecular level, dietary supplementation produced selective changes in gene expression. The low-dose diet significantly increased VEGFA expression (p < 0.05), whereas the high-dose diet resulted in significantly higher TGF-β1 expression (p < 0.05). Several other genes related to bone formation, bone resorption, or cytokine signaling exhibited numerical increases but did not reach statistical significance. These findings indicate that D. officinale leaf powder may modulate bone metabolic processes at the transcriptional level, although these molecular alterations were not accompanied by significant improvements in bone mass.

Goose blood has anticancer properties and was recorded in ancient China, but the specific molecular mechanisms underlying this effect still require further exploration. In this study, SW1990 cells were treated with goose serum or plasma, and transcriptome analysis was performed to explore the function of goose blood on cancer cells. Metabolomic profiling was also performed on goose serum, goose plasma, chicken serum, and chicken plasma to identify the bioactive substances responsible for the anticancer effect. The study examined the effects of goose plasma and serum on SW1990 cells and compared the metabolites between goose and chicken blood. Wound scratch, CCK-8, and Annexin V-PI assays showed that goose plasma and serum inhibited SW1990 cell proliferation at 24 and 48 h. Both treatments reduced cell viability, with serum inducing early and late apoptosis and plasma inducing late apoptosis. RNA sequencing (RNA-seq) identified 2259 (1418 upregulated, 841 downregulated) and 2731 (1844 upregulated, 887 downregulated) differentially expressed genes (DEGs) in the plasma and serum groups versus the negative control (NC), respectively, and 689 DEGs between the plasma and serum groups. Gene Ontology (GO) and KEGG pathway analyses revealed that the DEGs were enriched in processes such as lipid metabolism, JAK-STAT, and IL-17 pathways. Untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis identified distinct metabolites in goose and chicken blood, with unique metabolites and differential ones between groups. In SW1990 cells, four metabolite subclusters matched the plasma and serum effects. In summary, goose blood can suppress cancer cells by regulating gene expression to affect the key signaling pathways involved in cancer cell apoptosis and autophagy. Certain metabolites present at high concentrations in goose blood, such as cucurbitacin D and Oleoyl-L-carnitine, may also contribute to the inhibition of cancer cell proliferation and migration. These findings suggest that goose blood holds broad application prospects as a future auxiliary drug for cancer treatment, and this study provides a theoretical basis for the further application of goose products.

Chickens are a primary source of protein in the human diet, with demand increasing annually. However, research on genes that promote chicken meat development remains relatively limited. Therefore, in this study, breast muscle samples (pectoralis major, n = 10 per group) from chickens at five developmental stages (D1, D35, D70, D105, and D140) were selected to investigate genetic-level changes and identify additional genes influencing chicken meat development. Differential expression analysis between adjacent stages (|FC| > 1.5, p < 0.05) revealed 42 differentially expressed genes (DEGs) shared across four comparisons, primarily enriched in muscle development pathways such as focal adhesion, the regulation of the actin cytoskeleton, and Wnt signaling. Weighted gene coexpression network analysis (WGCNA) revealed that four modules were significantly correlated with body weight and breast muscle weight phenotypes. By integrating the hub genes of the four modules and the DEGs, we identified key genes, including MEGF10, MYOM2, TM4SF1, HNMT, NR4A3, and Wnt5a. Furthermore, we conducted a comparative analysis of key gene expression trends across commercial broilers (CBs) and Beijing You (BJY) chickens. MYOM2 and Wnt5a exhibited distinct expression patterns during the early developmental stage of Xianju (XJ) chickens, suggesting that these genes may be critical factors distinguishing XJ chicken breast muscle development from that of other breeds. In all three chicken breeds analyzed, the expression levels of HNMT and MEGF10 gradually decreased with increasing age, indicating that their functions are universal in poultry muscle development. In summary, our findings revealed key regulatory genes that influence breast muscle development, offering candidate targets for marker-assisted selection in poultry breeding programs.

The recombinant signal binding protein for immunoglobulin kappa J region (RBPJ) is the central effector of the Notch signaling pathway, which is a highly conserved pathway that regulates developmental and differentiation processes impacting tissue development, morphology, and function. The duck oviduct undergoes dramatic morphological and functional remodeling as laying egg or not, wherein fibroblasts play critical roles in extracellular matrix (ECM) remodeling and tissue homeostasis. However, the regulatory role of RBPJ in duck oviduct fibroblasts remains poorly understood. This study investigated the effects of RBPJ on the proliferation and molecular networks of duck fibroblasts using a RBPJ-overexpression model combined with RNA-seq and LC-MS/MS-based proteomic analysis. A RBPJ-overexpressing fibroblast model was successfully established. Compared to the control group (C), RBPJ overexpression (OE) significantly increased cell proliferation at 24 h (P < 0.01), as verified by CCK-8 and EdU assays. RNA-seq identified 130 differentially expressed genes (DEGs; |log2(fold change) | ≥ 1, P < 0.05), with significant enrichment of the Cytoskeleton in muscle cells pathway. Proteomic analysis detected 569 differentially expressed proteins (DEPs; |Fold change| ≥1.5, P < 0.05), primarily enriched in ECM-receptor interaction. Integrated transcriptome-proteome analysis revealed 12 key molecules. Among which, EGF is well-documented regulators of cell proliferation; ACTN2 (Actinin alpha 2), MYPN (Myopalladin) and COL21A1 (Collagen type XXI alpha 6 chain) were significantly enriched in pathways including ECM-receptor interaction, Cytoskeleton in muscle cells, and Focal adhesion. Collectively, these results indicate that RBPJ promotes fibroblast proliferation and regulates structural modulating by EGF, ACTN2, MYPN and COL21A1 at both the transcriptional and protein levels. Tissue-level verification demonstrated that the mRNA and protein expression levels of RBPJ in the oviduct of laying ducks were significantly elevated compared to ceased laying ducks (P < 0.05). Furthermore, the expression patterns of the 12 key DEGs in tissues aligned with the findings from cell study. This study provides novel molecular insights into RBPJ-mediated regulation of oviduct fibroblast function, offering a better understanding of duck oviduct remodeling during the laying cycle.

Pseudorabies virus (PRV) is an important α-herpesvirus. However, the chromatin state and transcriptional regulatory mechanisms of its genome upon entry into host cell nuclei remain poorly understood. In this study, we employed the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) to analyze chromatin accessibility and the transcriptome of the PRV genome in PK15 cells at multiple time points post-infection. ATAC-seq analysis revealed that the proportion of viral reads increased progressively over time, from 0.01% at 4 h to approximately 1.09% and 13% at 8 h and 12 h, respectively. A total of 112 ATAC peaks were identified, distributed across the PRV genome without apparent low-accessibility regions. Fragment length analysis demonstrated that the PRV genome does not adopt the regularly phased nucleosome organization typical of the host genome. RNA-seq analysis detected 66 expressed PRV genes, which were classified into four kinetic expression clusters, corresponding to immediate-early/early (IE/E), early (E), early-to-late transitional (E-L), and late (L) gene groups. Virus-host correlation analysis revealed significant associations between PRV gene expression and multiple host inflammation-related genes. Integrated multi-omics analysis further confirmed the concordance between chromatin accessibility dynamics and transcriptional activity changes. Collectively, these findings indicate that the PRV genome maintains a predominantly open and accessible chromatin state throughout lytic infection, providing new insights into the epigenetic regulatory mechanisms of α-herpesviruses.

In the domain of swine production, body weight (BW) and average daily gain (ADG) are recognized as the primary performance indicators. Nevertheless, the genetic architecture of ADG and BW in Dongliao black (DLB) pigs remains to be fully elucidated. In this study, we performed a genome-wide association analysis of BW, ADG, and body mass index (BMI) in 358 DLB pigs of different days of age. The genome-wide association study (GWAS) showed the following: (1) The most significant single nucleotide polymorphism (SNP) detected for BW was on Sus scrofa chromosome (SSC) 11:100,808 (p-value = 1.16 × 10-6) that was also the most significant SNP for ADG. (2) The most significant SNP associated with BMI was SSC17:51,463,521 (p-value = 5.16 × 10-8). (3) SNPs SSC10:6,523,844 and SSC17:23,852,682 were identified in both BW and ADG. A meta-analysis was conducted on BW at different days and demonstrated SSC5:39,028,335 (p-value = 8.37 × 10-6) which was not identified in the results of each single trait. The regions of two SNPs (SSC11:100,808, SSC4:10,703,277) exhibited considerable influence on both BW and ADG and the related regions were selected for linkage disequilibrium (LD) analyses that exhibited a notable linkage. In addition, several genes were identified that are associated with obesity and play roles in lipid metabolism, including MACROD2, PHLPP2, CYP2E1, and STT3B.

Epsilon-polylysine (ε-PL) is a natural antimicrobial peptide that has been broadly applied in the food industry as a preservative. The effects of ε-PL on the intestinal microbiota, animal metabolism, and its potential as a ''new feed additive'' require further exploration. In this study, ninety Hy-Line Brown laying hens were randomly divided into three groups. Egg-laying performance, egg quality, and liver parameters were measured; expression of gut barrier, immunity, and ferroptosis related genes in each intestinal segment were detected; microbiome and metabolomic analyses were performed. The results demonstrated that dietary ε-PL supplementation significantly increased average egg weight and egg quality (P < 0.05). It also markedly, ε-PL supplementation significantly increased the villus height to crypt depth ratio in the duodenum and ileum (P < 0.01), significantly reduced the mRNA levels of interleukin-1 beta (IL-1β) and interleukin-6 (IL-6), and elevated the mRNA levels of interleukin-10 (IL-10) and tumor necrosis factor-alpha (TNF-α) in the intestine (P < 0.05). Moreover, ε-PL inhibited intestinal mucosal ferroptosis (P < 0.05) and mitigated severe fatty liver development, as evidenced by a significantly reduction in hepatic malondialdehyde (MDA) content (P < 0.01). Microbiota analysis revealed that ε-PL supplementation significantly increased the abundance of Lactobacillus and Saccharimonadales; while decreasing the abundance of Anaerotruncus and Slackia in the cecal microbiota. Additionally, ε-PL supplementation enhanced the amino acid metabolism, lipid metabolism, the digestive system, arginine biosynthesis, tryptophan metabolism, bile secretion, and steroid hormone biosynthesis in the intestine, which might contribute to improved egg quality and intestinal absorptive capacity, as well as the inhibition of fatty liver formation. In summary, dietary ε-PL supplementation exerts multiple beneficial effects in laying hens, including enhancing egg quality, alleviate inflammation, boosting antioxidant capacity, improving intestinal morphology, modulating gut microbiota, and protecting liver health.

Endothelin Receptor Type B (EDNRB) is expressed in a variety of cells during embryonic stage, including melanocyte precursors cells. Our previous studies found that 11 bp deletion of EDNRB caused the two-end black (TEB) coat color in Chinese pigs. In this study, we aimed to explore the mutant EDNRB on the formation of TEB coat color in Chinese pigs. We constructed recombinant plasmid for wild and mutant EDNRB and EDN1, respectively, and transfected the recombinant plasmid into mouse B16 melanoma cells in groups. Real-time fluorescent quantitative PCR (RT-qPCR) was performed to detect expression of genes that participate in melanin pathway, including PLCγ, Raf, MITF. Comparing to the wild-type EDNRB cells, expression of the three genes in the cell line expressing mutant EDNRB cells was significantly reduced. We measured the melanin content produced by transfected recombinant granulocytes of wild and mutant EDNRB and found that the amount of melanin in mutant EDNRB cells was significantly lower than that of the wild. Wound-healing assay confirmed that the migration and mobility rate of mutant EDNRB cells were significantly lower than the wild. Co-immunoprecipitation further confirmed that mutant EDNRB could not interact with the EDN1 protein. In conclusion, this study revealed that the 11 bp deletion of EDNRB reduced the melanin production, which may be caused by inhibiting the expression of PLCγ, Raf, and MITF. The mutant EDNRB reduced melanocyte migration and could not interact with the EDN1 protein. We explored the effect of mutant EDNRB in Chinese pigs with TEB coat color, and the results provided a reference for exploring molecular mechanism of mutant EDNRB on the formation of TEB coat color pigs.

The aim of the study was to investigate the mechanisms of the N-acetyl-L-glutamic (NAG) diet in improving rooster semen quality after cryopreservation. A total of 60 individually housed chickens were randomly allocated to three groups: a basal diet group (C), a basal diet supplemented with 2 g/kg NAG group (NL), and a basal diet supplemented with 4 g/kg NAG group (NH). Semen quality was evaluated on days 15 and 30, including fresh sperm motility and cryopreservation efficacy. Serum biochemical parameters, hormone levels, immune indices, semen metabolites, and gut microbiota composition were assessed at 30 d. NAG supplementation significantly improved semen quality. At 15 and 30 d, both NL and NH groups showed a significant increase in the total motile sperm ratio (TM) in fresh semen compared to the control (P ≤ 0.05). At 30 d, group NH exhibited significantly higher percentage of sperm in a straight-line trajectory (LIN) in fresh semen than both the C and NL groups. After cryopreservation, the sperm TM and LIN from chickens with NAG dietary for 30 days were significantly better in the NL group compared to C and NH groups (P ≤ 0.05). Metabolomic analysis identified significant upregulation of metabolites, including melatonin and ferulic acid, in cryopreserved semen from NAG-supplemented groups, while 5-hydroxylysine and inosine-1-phosphate were significantly reduced. Serum antioxidant capacity, as measured by glutathione peroxidase (GSH-Px) was significantly higher, while malondialdehyde (MDA) levels lower in NAG groups compared to C (P ≤ 0.05). No significant differences in immune markers or reproductive hormones were observed across groups. Gut microbiota analysis revealed that NAG supplementation enhanced beneficial bacterial populations. In conclusion, NAG supplementation improved sperm motility and cryopreservation outcomes, potentially by increasing the levels of semen melatonin and ferulic acid and reducing the body oxidative stress. And it can improve the overall health level by regulating the gut microbiota through diet. These findings highlight NAG’s potential as a dietary supplement to improve semen quality and overall reproductive efficiency in poultry.

Antibiotic resistance has become a global health concern, driving the need for sustainable alternatives in animal husbandry. This study explores the potential of natural feed additives as a viable solution to enhance poultry growth and health while reducing reliance on antibiotics. Chinese herbal medicines and probiotics have been widely studied as green, healthy, and safe antibiotic alternatives in livestock and poultry production. A total of 120 chickens were randomly divided into four groups: a control group and three treatment groups supplemented with 1% Pulsatilla chinensis powder, 3% fresh Acer truncatum, or 1% Clostridium butyricum. The results showed that Pulsatilla chinensis powder significantly increased gamma-glutamylcysteine (p < 0.05), UDP-N-acetylglucosamine (p < 0.05), tyramine (p < 0.01), and leucine (p < 0.05). Acer truncatum notably altered cecal metabolites, including L-tyrosine (p < 0.05), α-ketoisovaleric acid (p < 0.01), myristoleic acid (p < 0.01), glutathione (p < 0.05), and PGA1 (p < 0.05). Clostridium butyricum modified cecal metabolites such as L-glutamine (p < 0.05), riboflavin (p < 0.05), L-Carnitine (p < 0.05), ergocalciferol (p < 0.01), and α-tocotrienol (p < 0.05).

Chicken semen cryopreservation is crucial for utilizing high-quality cockerel genetics, but semen is highly sensitive to cryoinjury, leading to poor preservation outcomes. This study aimed to establish a theoretical foundation for selecting cockerels for semen cryopreservation through serum testing and to improve semen quality via DNA methylation editing. Semen and serum samples were collected from 102 Xiaoshan cockerels, with semen cryopreserved and thawed following standardized protocols. Post-thaw semen quality and serum testosterone (T) levels were assessed. Eight cockerels were selected based on motile sperm quality, and whole-genome bisulfite sequencing (WGBS) was used to analyze sperm DNA methylation. The results showed a significant positive correlation between serum T levels and sperm motility. There were notable differences in sperm motility and serum T levels between high-quality and low-quality semen groups but no differences in estradiol (E2), superoxide dismutase (SOD), or glutathione peroxidase (GSH-Px) levels. A total of 217 differentially methylated regions (DMRs) and 116 differentially methylated genes (DMGs) were identified. Key genes such as PRKACB (protein kinase, cAMP-dependent, catalytic, beta) and ACSL1 (long-chain-fatty-acid--CoA ligase 1) were associated with sperm motility. These findings provide important insights for improving semen cryopreservation and contribute to breeding practices and the development of cryoprotectants.

OBJECTIVE:Growth traits are one of the most important economic traits in pigs, including body weight and average daily gain. However, the available genetic markers for these traits are limited, especially concerning Chinese indigenous pigs and their hybrid breeds. METHODS:To identify SNP markers and candidate genes affecting body weight and average daily gain traits, we performed a genome-wide association study (GWAS) for these traits in 358 Dongliao black pigs using three single-locus and three multiple-locus models. All pigs were genotyped using the China Chip-1 porcine SNP50K BeadChip. RESULTS:The GWAS revealed 39 significant quantitative trait loci (QTLs) affecting body weight and average daily gain traits. Among these, 26 QTLs were significantly correlated with body weight traits. Thirteen QTLs showed significant correlations with average daily gain traits. Some candidate genes associated with body weight and average daily gain traits include MACROD2, ASB13, ATP12A, ZDHHC17, WDR37 and TENM4. Of the three single-locus models examined, only the general linear model identified significant SNPs, identifying a total of 27 significant QTLs, which was the largest among the models assessed. The three multiple-locus models, multiple-locus mixed-model, FarmCPU and Bayesian-information and LD iteratively nested keyway, identified 4, 12 and 13 significant QTL loci, respectively. CONCLUSION:We newly identified 18 QTLs that are significantly correlated with body weight and average daily gain traits. Our results provided a foundation for biomarker breeding and enhancement of body weight and average daily gain traits in pigs.

Transmissible gastroenteritis virus (TGEV) is a major enteric pathogen causing severe diarrhea in swine, with substantial implications for the biosecurity of intensive pig production worldwide. The E3 ubiquitin ligase TRIM7 has emerged as a key regulator of host antiviral immunity, yet its role in TGEV infection remains elusive. Here, we report that TRIM7 is abundantly expressed in porcine intestinal tissue and significantly upregulated upon TGEV challenge in IPEC-J2 cells. Functional studies demonstrated that TRIM7 restricts TGEV replication in IPEC-J2 cells through two distinct mechanisms. Firstly, molecular interaction and co-immunoprecipitation assays revealed that TRIM7 mediates ubiquitin-dependent degradation of the TGEV nucleocapsid (N) protein. Secondly, RNA-seq analysis combined with RIG-I signaling modulation experiments established that TRIM7 enhances RIG-I-mediated type I interferon (IFN) signaling to suppress viral propagation. These findings uncover a dual antiviral role for TRIM7 in countering TGEV infection, highlighting its potential as a therapeutic target for TGEV control.

The objective of this study was to identify the AlkB family genes in poultry using bioinformatics, and to explore their molecular characteristics, evolutionary relationships, and expression patterns to clarify their potential functions in poultry. (1) Methods: The study utilized the NCBI database to obtain chicken genome data, and screened and validated AlkB family members (ALKBH1-5, ALKBH8, and FTO) by hmmsearch and TBtools. MEGA 11.0 was used for phylogenetic analysis, PHYRE2 and I-TASSER predicted protein structures, and the String database was used to construct an interoperability network. Finally, the tissue expression profiles were analyzed by using The Human Protein Atlas online database and qRT-PCR. (2) Results: Phylogenetic analysis revealed distinct avian and mammalian clusters, with chicken AlkB proteins exhibiting low sequence homology but conserved 3D structures compared to mammals. Chromosomal synteny and conserved domains highlighted evolutionary divergence, with ALKBH4 lacking typical AlkB structural motifs. Protein interaction networks linked ALKBH1/2/3/5/8/FTO, underscoring functional coordination in poultry adaptation. Tissue-specific expression showed high AlkB levels in brain tissues, while ALKBH5 dominated in muscle. During differentiation, ALKBH3, ALKBH5, and FTO expression significantly increased during myoblast differentiation. (3) Conclusions: This study identified seven AlkB family genes in poultry, revealing their phylogenetic classification into two subfamilies, conserved structural domains, chromosomal synteny, and tissue-specific expression patterns.

Background: The Jinwu pig is a novel breed created by crossbreeding Jinhua and Duroc pigs, displaying superior meat quality, strong adaptability to coarse feed, high production performance, and a rapid growth rate. However, research on its reproductive traits and genomic characteristics has not been systematically reported. Methods: In this study, we investigated the genetic basis of reproductive traits in Jinwu pigs us-ing a genome-wide association study. We analyzed 2831 breeding records from 516 Jinwu sows to evaluate the effects of fixed factors (farrowing season, parity, and mated boar) on six reproductive traits: the total number of births (TNB), number born alive (NBA), number of healthy offspring produced (NHOP), weak litter size (WLS), number of stillbirths (NS), and number of mummies (NM). Results: A total of 771 genome-wide significant single-nucleotide polymorphisms (SNPs) and ten potential candidate genes associated with pig reproductive traits were identified: VOPP1, PGAM2, TNS3, LRFN5, ORC1, CC2D1B, ZFYYE9, TUT4, DCN, and FEZF1. TT-genotype-carrier individuals of the pleiotropic SNP rs326174997 exhibited significantly higher TNB, NBA, and NHOP trait-related phenotypic values. Conclusions: These findings provide a foundation for the reproductive breeding of Jinwu pigs and offer new insights into molecular genetic breeding in pigs.

Introduction:Diarrhea after weaning of piglets is one of the most serious diseases in pig herds, which brings huge economic losses to the pig industry. Diarrhea in piglets after weaning has a significant impact on the composition of gut microbiota, which leads to the disturbance of normal metabolic processes. Method:To investigate the effects of weaning diarrhea on gut microbiota and its metabolites, 84 samples were collected from 42 piglets pre-weaning and post-weaning, including 17 samples from post-weaning diarrheal piglets. The samples were sequenced for 16S rRNA and untargeted metabolites. Results:A total of 3,192 ASVs, 20 phyla, and 286 genera were identified. A total of 32 genera were detected by difference analysis between healthy post-weaning piglets and diarrhea post-weaning piglets. It was observed that post-weaning diarrhea led to a reduction in the relative abundance of Bacteroides, UCG-002, Christensenellaceae_R-7_group, Escherichia-Shigella, Pyramidobacter, Lactobacillus and a substantial increase in the relative abundance of Prevotellaceae_NK3B31_group, Muribaculaceae, Prevotella, Holdemanella, Collinsella, Blautia. A total of 360 differential metabolites were detected between healthy and diarrheal weaned piglets. 5-Hydroxyferulic acid methyl ester, D-Saccharic acid 1,4-lactone, 3-Methylhistidine were significantly enriched in post-weaning diarrheal piglets. These differential metabolites were enriched in the Nucleotide metabolism, ABC transporters, Biosynthesis of amino acids, Nicotinate and nicotinamide metabolism, Valine, leucine and isoleucine biosynthesis, Pyrimidine metabolism, Alanine, aspartate and glutamate metabolism, Purine metabolism, Caffeine metabolism, Butanoate metabolism pathways. Discussion:Taken together, this study systematically reveals the dynamic succession and structure of the gut microbiota and metabolites in diarrhea and healthy piglets pre-weaning and post-weaning. Our findings provide a reference for the microbiological and metabolite etiology associated with post-weaning diarrhea.