Search Results (2,077)

Porcine rotavirus (PoRV) has emerged as a primary pathogen causing viral diarrhea in pigs, resulting in significant economic losses. This study was conducted to systematically characterize the epidemiology and genotypic characteristics of PoRV in Guangxi, China. A total of 870 diarrheic pig samples were collected from Guangxi during 2020–2025. The qRT-PCR results indicated an overall PoRV-positive rate of 41.38% (360/870), and the annual positivity rate showed an overall upward trend. The genetic evolutionary analysis of the VP4, VP6, and VP7 genes indicated that PoRV predominantly belonged to the A group and the predominant P genotype observed was P[13] (76.83%), while the G genotypes were G5 (36.56%) and G9 (33.33%). The most prevalent genotype combinations were G9P[13]I5 and G5P[13]I5. CH-GXGL-PoRV-3151-2021, a PoRV strain isolated from positive samples, was identified via RT-PCR, qRT-PCR, whole-genome sequencing, and IFA. This strain was assigned the 11-segment genotype constellation G9-P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1 based on whole-genome sequencing. NSP1 and NSP2 showed high similarity to human rotavirus strains, whereas VP1–VP4, VP6, VP7, and NSP3–NSP5 showed high similarity to porcine rotavirus strains. This study indicates the widespread circulation of PoRV in Guangxi, with multiple G genotypes, including G9, G5, G4, G3, G2, and G26, being detected. The isolated G9P[23]I5 strain exhibits the same genotype as the strains that have become increasingly prevalent in recent years. This strain may represent a possible reassortant between porcine and human rotaviruses. This study offers significant insights into the epidemiology of PoRV and the prevalent genotypes in Guangxi, thereby supporting the development of targeted prevention strategies and novel vaccines. Full article

Enterovirus G (EV-G) is an important enteric pathogen widely circulating in swine populations and is characterized by considerable genetic diversity and recombination potential. In recent years, recombinant EV-G strains carrying exogenous papain-like cysteine protease (PLCP) gene insertions have been increasingly reported; however, their genotype distribution and molecular characteristics in major pig-producing regions remain poorly understood. In this study, 356 clinical samples collected from Guangxi, southern China, between 2020 and 2025 were screened for EV-G, and 13 representative strains were subjected to whole-genome sequencing and sequence analysis. The overall EV-G positivity rate in Guangxi was 20.51% (73/356). Phylogenetic analysis showed that the 13 Guangxi EV-G strains were mainly classified into three genotypes, G1, G2, and G8, with G1 being the predominant genotype. Notably, PLCP gene insertions of 573–642 nt were identified at the 2C/3A junction in seven strains belonging to three distinct genotypes, G1, G2, and G8, demonstrating the cross-genotype distribution of PLCP insertions within a single geographic region. Phylogenetic analysis of the PLCP sequences demonstrated that all Guangxi-derived PLCP sequences clustered within the EV-G-PLCP clade and were clearly separated from the torovirus PLCP clade. Recombination analysis retained three potential recombination events with clearer combined support from RDP4 and SimPlot analyses, involving Guangxi strains GX3008, GX3022, and GX4292. Selection pressure analysis showed that the VP1 gene was overall under negative selection. Collectively, these findings demonstrate the co-circulation of multiple EV-G genotypes, the cross-genotype distribution of PLCP insertions, and the presence of potential recombination events in Guangxi. This study provides new evidence for understanding the genetic diversity, genomic plasticity, and regional molecular characteristics of EV-G, and also provides an important basis for future PLCP-related functional studies and continued EV-G surveillance. Full article

Background/Objectives: Porcine circovirus type 2 (PCV2) remains a major viral agent in pig production worldwide due to its association with economically relevant diseases and productivity losses. Nine genotypes (PCV2a–PCV2i) have been reported, with successive genotype shifts characterized by the historical predominance of PCV2a, the expansion of PCV2b, and the emergence of PCV2d as the predominant genotype in several swine-producing countries. The aim of this study was to characterize the ORF2 gene of PCV2 circulating in Jalisco, Mexico, to provide updated information for regional surveillance and control strategies. Methods: Samples were collected from 80 pig farms located in four regions of Jalisco with different pig density levels and production systems. PCV2-positive samples were subjected to ORF2 amplification and sequencing. Genotype assignment, phylogenetic analysis, and in silico recombination screening using multiple detection methods were performed. All sequences were deposited in GenBank. Results: A total of 70 ORF2-PCV2 sequences were obtained and assigned to two genotypes: PCV2d (51/70, 72.9%) and PCV2a (19/70, 27.1%). The sequences were submitted to GenBank under accession numbers PV235521–PV235590. Recombination analysis identified seven recombinant sequences, and unusual ORF2 extensions were detected in some sequences, evidencing the presence of genetic variants circulating in the region. Conclusions: These findings confirm the predominance of PCV2d in Jalisco while highlighting the continued circulation of PCV2a. The coexistence of both genotypes, together with recombinant sequences and ORF2 extensions, indicates ongoing PCV2 genetic diversification in the region. Continuous molecular surveillance remains essential to monitor viral evolution, support genotype-informed control strategies, and strengthen swine health programs. Full article

Pubertal initiation critically determines reproductive performance in female pigs. Histone H3 lysine 27 trimethylation (H3K27me3) has been implicated in ovarian development. However, its genome-wide regulatory landscape during the pubertal transition remains unexplored. Here, we obtained transcriptomes of GCs treated with the pharmacological H3K27me3 agonist GSK-J4 or H3K27me3 inhibitor EPZ005687. We found that H3K27me3 substantially remodels the transcriptomic landscape of porcine GCs, with differentially expressed genes significantly enriched in pathways governing cell proliferation and apoptosis. Mechanistically, H3K27me3 suppressed GC proliferation by downregulating the expression of PCNA and promoting apoptosis through upregulation of CASP3, thereby delaying pubertal initiation. Furthermore, genome-wide ChIP-seq analysis on porcine ovaries from pre-pubertal and in-pubertal gilts revealed higher H3K27me3 enrichment around transcription start sites in the In-puberty stage than in the Pre-puberty stage. Genes with promoters exhibiting reduced H3K27me3 occupancy during the pubertal transition were enriched in pathways related to sex differentiation and serine-type endopeptidase inhibitor activity. Notably, secretory leukocyte peptidase inhibitor (SLPI) was identified by ChIP-qPCR as a direct target repressed by H3K27me3. Functional validation demonstrated that SLPI promoted GC proliferation and inhibited GC apoptosis in vitro. Intraperitoneal injection of LV-Slpi or sh-Slpi into C57BL/6J mice showed that Slpi accelerated pubertal initiation of mice in vivo. Collectively, our findings confirmed that developmental stage-specific loss of H3K27me3 at the SLPI promoter derepressed SLPI transcription, which in turn promoted porcine GC proliferation, suppressed apoptosis, and facilitated pubertal initiation in mice. These results provided valuable insights into the epigenetic regulation of pubertal initiation in mammals. Full article

Single-cell RNA sequencing (scRNA-seq) has emerged as a transformative technology for resolving cellular heterogeneity and deciphering gene regulatory networks in complex tissues. Despite challenges such as incomplete genome annotation, technical variability across platforms, and limitations in robust cell-type annotation, scRNA-seq has substantially advanced our understanding of the developmental processes, physiological regulation, and disease responses in pigs, an economically and biomedically important species, thereby providing insights into traits of agricultural and translational relevance. By profiling transcriptomes at the single-cell resolution, scRNA-seq enables the identification of rare cell populations, dynamic cellular states, and lineage trajectories that are critical for reproduction, growth, immunity, and metabolic homeostasis. Recent porcine scRNA-seq studies have generated high-resolution cellular atlases spanning embryos, reproductive organs, immune tissues, skeletal muscle, and the gastrointestinal tract, revealing cell-type-specific regulatory mechanisms associated with reproductive performance, muscle accretion, adipogenesis, immune competence, and intestinal functionality. This review summarizes the fundamental principles and analytical strategies of scRNA-seq, highlights its major applications in porcine biology and production, and discusses current challenges as well as future perspectives for integrating single-cell technologies into livestock science. Full article

A study was conducted to determine the effects of the level and source of copper (Cu) on Cu concentrations and the mRNA expression of Cu regulatory proteins in the small intestine of pigs. Thirty weanling castrated male pigs, approximately 21 days of age, were stratified by weight and assigned to dietary treatments consisting of control (6.7 mg Cu/kg from feed ingredients; no supplemental Cu) or 225 mg supplemental Cu from either Cu sulfate (CuSO₄) or tribasic Cu chloride (TBCC). Pigs were harvested on days 35 or 36. The soluble Cu and mucosal Cu concentrations in the duodenum, proximal jejunum, and ileum were higher (p < 0.001) in Cu-supplemented pigs versus controls. Duodenal soluble and mucosal Cu concentrations were higher in (p < 0.05) CuSO₄ versus TBCC-supplemented pigs. However, proximal jejunum and ileum mucosal Cu were higher (p < 0.05) in TBCC versus CuSO₄ pigs. The intestinal copper transporter 1 (CTR1) expression was lower (p < 0.05) in Cu-supplemented pigs compared to control pigs but was not affected by the intestinal section or treatment x section. The duodenal mRNA expression of metallothionein1a (MT1a) was greater (p < 0.05) in Cu-supplemented pigs and was greater in CuSO₄ than TBCC-fed pigs. These data demonstrate that both the Cu level and source affect the Cu uptake and mRNA expression of Cu regulatory proteins throughout the small intestine of weanling pigs. Full article

The CRISPR/Cas9 system has been widely used for gene editing in various species; however, mosaicism remains a significant challenge. This study aimed to improve gene editing efficiency and reduce mosaicism in porcine embryos by exploring double electroporation pre- and post-in vitro fertilization combined with zona pellucida (ZP) removal. We evaluated the effects of these treatments on the development and mutation rates of oocytes/zygotes edited with guide RNAs (gRNAs) targeting GGTA1, CMAH, or B4GALNT2 genes. Double electroporation significantly increased the total and biallelic mutation rates in ZP-intact zygotes but not in ZP-free zygotes edited using GGTA1-targeted gRNAs. All blastocysts from ZP-free zygotes exhibited biallelic mutations following double electroporation. For the CMAH gene, all blastocysts exhibited mutations (biallelic mutations ≥ 80%); however, double electroporation and ZP removal did not affect their mutation rates or efficiency. For the B4GALNT2 gene, double electroporation significantly increased total mutation rates in ZP-intact zygotes, whereas all blastocysts from ZP-free zygotes showed biallelic mutation. These findings suggest that double electroporation, particularly with ZP removal, may enhance gene-editing efficiency, reduce mosaicism and improve the success of genetic modifications. Full article

Cystic echinococcosis (CE), caused by Echinococcus granulosus sensu lato (s.l.), is a significant zoonotic disease affecting livestock and public health worldwide, particularly in endemic regions such as La Araucanía, Chile. This study evaluated the role of cattle in the transmission dynamics of E. granulosus sensu stricto (s.s.) by morphologically and molecular characterizing hydatid cysts (HC) collected from cattle, sheep, pigs, and goats. A total of 123 cysts were obtained from a local slaughterhouse, with cattle contributing the majority of samples (n = 94). Fertility was highest in sheep (76.2%) and low in cattle (3.2%), while cysts from pigs and goats were infertile. PCR amplification and sequencing of the cox1 gene confirmed the predominance of genotype G1 (98.1%), with two additional haplotypes (Eg^B and Eg^C) identified in cattle and sheep. Two cattle samples harbored genotype G3. Phylogenetic analyses grouped all sequences within the E. granulosus s.s. complex. The results corroborate the role of cattle as important sentinels for environmental surveillance of CE due to their exposure and traceability but highlight their lower competence in parasite transmission to definitive hosts compared with sheep. The genetic diversity observed aligns with previous findings in Chile, underscoring the epidemiological significance of E. granulosus s.s. and genotype G1 in the region. Full article

Primary hepatocytes are limited by poor proliferative capacity and a finite replicative lifespan, restricting their utility in long-term in vitro studies. Here, we report the generation of expandable hepatocyte-like progenitor cells from GGTA1 knockout pigs, a large-animal model with reduced immunogenicity. Porcine fibroblasts were directly reprogrammed using a non-integrative episomal system encoding hepatic transcription factors, enabling stable lineage conversion without genomic integration. A simplified two-vector configuration combined with codon optimization enabled evaluation of vector-dependent effects while maintaining genomic safety without viral integration. The resulting cells exhibited hepatocyte-like morphology and gene expression, and transcriptomic analysis revealed a progressive shift toward liver-associated profiles during extended culture. Chromosomal analysis revealed vector-dependent differences in genomic stability, with codon-optimized cells showing increased aneuploidy, indicating a trade-off between proliferative capacity and genomic integrity. The cells also demonstrated sustained proliferative capacity, supported by maintenance of telomere length, increased expression of TERT and MYC, and reduced CDKN1A levels. Importantly, sustained proliferation was supported by complementary evidence from chromosomal and telomeric analyses. Although chromosomal alterations were observed during long-term culture, their biological significance remains to be fully determined. These cells partially recapitulate hepatocyte functions and provide a renewable in vitro system for studies of hepatic biology, proliferation, drug metabolism, toxicity, and repeated in vitro applications. Full article

In addition to its role in energy storage, adipose tissue contributes substantially to energy metabolism, endocrine regulation, and inflammatory processes. Sujiang pigs, a hybrid breed approved by the National Livestock and Poultry Genetic Resources Committee of China as a new national breed in 2013, possess a genetic predisposition for substantial fat deposition, making them an ideal model for investigating the mechanisms underlying adipose tissue accumulation. In this study, back fat (BF; subcutaneous adipose tissue), greater omentum (GOM; visceral adipose tissue), and mesenteric adipose tissue (MAD; visceral adipose tissue) were collected from three 6-month-old male Sujiang pigs for RNA-seq analysis. Comparative analyses identified 3005 differentially expressed genes (DEGs) between BF and GOM, 975 DEGs between BF and MAD, and 892 DEGs between GOM and MAD. To validate the reliability of the sequencing data, five DEGs were randomly selected for RT-qPCR verification. The DEGs were further subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. By integrating protein–protein interaction (PPI) networks with bioinformatics analyses, we identified candidate genes potentially associated with lipid metabolism (e.g., WNT9A, WNT5A, and PDGFRA) and inflammatory responses in adipose tissue (e.g., CSF1R, C1QB, and CD4). These findings indicate potential molecular differences between porcine visceral and subcutaneous adipose tissues and may serve as a reference for further studies on the molecular regulation of adipose tissue metabolism. Full article

Identifying causal genetic variants and candidate genes underlying complex traits remains a central challenge in animal breeding and genetics. Genome-wide association studies (GWAS) are widely used for this purpose. However, their reliance on marginal variant effects and sensitivity to linkage disequilibrium (LD) can lead to redundant and less accurate identification of variants or genes of biological relevance. Here, we propose SNP prioritization (GWAS-based and fine-mapping-based) strategies within a unified framework, designed to improve the selection of more informative variants and candidate genes by explicitly modeling LD structure and genetic architectures of three pig teat-related traits (total teat number, teat symmetry, and teat adequacy). While GWAS prioritization favored variants with strong marginal effects, fine-mapping substantially improved joint explanatory performance and prediction accuracy. For total teat number, the best-performing fine-mapping-derived SNP subset achieved a mean PCC of 0.6599 across 10-fold cross-validation, compared with 0.3755 for GWAS-based prioritization. Similarly, for teat adequacy, the highest mean AUC increased from 0.7012 (GWAS) to 0.8547 (fine-mapping). Moreover, fine-mapping-derived SNP sets identified more coherent and trait-specific biological pathways and functionally relevant candidate genes. Taken together, our findings demonstrate that fine-mapping provides a more accurate and biologically meaningful framework for SNP and candidate gene prioritization, supporting its integration into genetic analysis and breeding applications. Full article

The mechanisms by which ferulic acid (FA) improves meat quality and promotes muscle development in pigs remain unclear. This study evaluated the effects of dietary FA on meat quality and muscle development in Shaziling pigs. A total of 108 pigs (30 kg ± 0.71 kg) were selected and randomly assigned to three groups, with six replicates per group and six pigs per replicate. Pigs were fed a corn–soybean meal basal diet supplemented with 0 mg/kg, 250 mg/kg, or 500 mg/kg of FA for 120 days. Results showed that FA reduced fat percentage, increased lean meat percentage and loin-eye area, enhanced redness and pH, and elevated muscle crude protein content. It also increased muscle fiber diameter and improved antioxidant enzyme activities (p < 0.05). The FA increased the levels of capric acid and methionine in the muscle, while reducing the content of stearic acid (p < 0.05). Furthermore, analysis of muscle development-related genes showed that FA upregulated the expression of PI3K, AKT1, mTOR and downregulated the expression of FOXO1 and MSTN in the muscle (p < 0.05). Analysis of muscle fiber type and glucose metabolism-related genes revealed that FA upregulated the expression of PGC-1α, MYH IIa, MYH I, HK2, and PFK and downregulated the expression of PKM and MYH IIX in the muscle (p < 0.05). In conclusion, FA improves muscle development and meat quality in Shaziling pigs, possibly through modulation of genes associated with PI3K/AKT/mTOR signaling, enhancement of antioxidant capacity, and regulation of muscle fiber type and glucose metabolism. Full article

We conducted whole-genome sequencing to investigate serotypes, virulence-associated genes, antimicrobial resistance determinants, and genetic relationships among Glaesserella parasuis isolates from diseased pigs in Japan, focusing on underrecognized aspects of disease epidemiology and control. Although Glässer’s disease is well recognized in swine production, its epidemiology remains incompletely understood, particularly regarding the relationship between serotype, genotype, and pathogenicity. Serotypes 5 or 12 (5/12) (28.9%) were predominant, followed by serotype 7 (10.8%). Phylogenetic analysis based on core-genome single nucleotide polymorphisms and cluster analysis classified the isolates into three genetic groups, with no clear association between serotype and genetic grouping. One genetic group tended to exhibit a lower proportion of severe clinical cases compared with the others, with a statistically significant difference observed in one comparison but not in the other. These findings provide evidence suggesting genotype-associated differences in disease severity, indicating that pathogenic potential may be more closely linked to genetic background than to serotype. These findings suggest a potential limitation of serotype-based vaccine strategies. Although 86.7% of isolates lacked antimicrobial resistance genes, resistance determinants were identified on contigs predicted to be of plasmid origin. These results indicate that antimicrobial resistance, while not widespread, may be underestimated and could disseminate. Overall, our findings highlight underexplored aspects of Glässer’s disease relevant to improving control and prevention. Full article

Background and Objectives: Among CNS malignancies arising in infancy, ATRT stands out as the most frequently diagnosed in children younger than six months. Disruption of the SMARCB1 gene underlies the overwhelming majority of cases. Progress toward effective treatment has been hampered by two persistent challenges. Current mouse models, while informative, fall short of reproducing the full clinical and biological picture of human ATRT, and their ability to predict therapeutic outcomes in patients remains uncertain. Compounding this, the rarity of the disease makes it difficult to assemble patient cohorts of sufficient size for meaningful clinical trials. At the molecular level, germline loss of SMARCB1 exons 4 and 5 has emerged as a particularly penetrant predisposing event, with affected individuals presenting at an earlier age than those harboring other mutation types. The porcine SMARCB1 gene offers a compelling basis for translational modeling as its protein product is identical to the human ortholog at every amino acid position across isoforms, a degree of conservation that exceeds what is seen in the mouse. Methods: Thus, we hypothesized that germline deletion of exons 4 and 5 would predispose heterozygote swine to ATRT development. In this manuscript, we describe the creation of an ATRT porcine model through a CRISPR/Cas9 mediated gene-editing approach. Results: 15 piglets were produced, two of which had confirmed SMARCB1 targeted excisions. However, none developed tumors. To induce further tumorigenicity, one pig with confirmed exons 4 and 5 excision was crossed with a pig with TP53 exon 2 truncation. In total, 11 piglets were born, of which one contained the original excision without a TP53 mutation. This piglet developed a spinal mass at the T1 level. Conclusion: To our knowledge, this is the first ATRT porcine model ever developed and provides proof-of-concept feasibility for large animal modeling of SMARCB1-deficient rhabdoid tumors. These findings support the continued development of porcine RTPS-1 models toward preclinical application. Full article

Newborn piglets in intensive pig farms are often prone to pulmonary diseases due to underdeveloped fetal lung neural systems, and ATRA is often regarded as an important morphogen that displays pleiotropic functions during embryonic development. However, information about the effect of maternal administration with ATRA on the peripheral neural system of fetal lungs is still scare. Fifteen pregnant sows were assigned to the ATRA0 (0 mg/kg diet), ATRA4, ATRA8, ATRA16 and ATRA32 treatment groups and offered their own feed from d12 to d95 after artificial insemination; then two neonatal pigs with birth weights similar to the average birth weight were taken out from each litter for the collection of lung samples, and samples were subjected to immunofluorescence staining, RNA-seq and RT-qPCR assays. Results indicated that compared to newborn piglets from the ATRA0 treatment group, newborn piglets from the ATRA4 treatment group had higher percentages of GFAP-positive astrocyte cells (p < 0.05) and GFAP-TUBB3 colocalization (p < 0.05) in the lungs. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis showed that differential expressed genes are mainly enriched in the pathways of neuroactive ligand–receptor interaction, GABAergic synapses and cell adhesion molecules. Addition of ATRA at 4 mg/kg to the diet of pregnant sows can enhance the healthy development of the pulmonary nervous systems of fetal pigs. Full article