Search Results (788)

Bovine leukemia virus (BLV) causes enzootic bovine leukosis (EBL), yet its pathogenic mechanisms remain largely unclear. In particular, the role of BLV genomic integration sites (IS(s)) in BLV-induced leukemogenesis has not been fully elucidated. Here, we identified a total of 235 ISs from 99 BLV-infected cattle with lymphoma, of which 4.3% and 46.8% were located within exon and intron, respectively, while no preferential integration into CpG islands or repetitive regions was observed. All identified ISs were distinct, and no identical sites were detected among the samples. We identified 246 genes related with these ISs and protein–protein interaction analysis of these genes demonstrated one “IS-Clustered genes” composed of 85 among 246 genes. This “IS-Clustered genes” contains 12 cancer genes (14.1%) with high significantly proportion. Notably, with 55 among 99 cattle tested (55.6%) harboring ISs within this cluster, suggesting its crucial involvement in BLV-induced pathogenesis. Furthermore, integrated analysis of known lymphoma- and IS-related genes and the 85 “IS-Clustered genes” showed that key genes formed a shared cluster, indicating a potential “common EBL-associated cluster.” These findings provide important insights into the role of BLV integration in EBL development and may contribute to elucidating its molecular mechanisms underlying onset of EBL. In addition, these findings may also aid in the development of therapeutic strategies and facilitate early diagnosis. Full article

The review deals with the current knowledge on the global panzootic spread of highly pathogenic avian influenza viruses (HPAIVs), with an emphasis on the H5N1 clade 2.3.4.4b virus. It describes the viral structure, replication, pathotypes and molecular determinants of host range, including sialic-acid receptor usage and key genetic mammalian-adaptation markers (PB2-E627K and PB2-D701N mutations). The host spectrum nowadays extends from wild waterfowl and poultry including seabirds, terrestrial and marine mammals and, based largely on experimental studies or molecular detection, reptiles, amphibians, and fish. Recently, the H5N1 clade 2.3.4.4b virus has shown marked tropism for lactating mammary epithelium in dairy cattle, with virions shed in raw milk. The review reports epidemiology, geographical expansion, clinical presentation, pathogenesis and pathology, diagnosis, immune responses and vaccination approaches across species. It also analyses European Union (EU) and Italian regulatory frameworks, surveillance strategies and biosecurity measures from a One-Health perspective. The review highlights how climate change, wildlife–livestock interfaces, intensive farming and global trade favor viral persistence and genomic reassortment and concludes by stressing strategic actions to limit further host adaptation and panzootic/pandemic risks. Full article

Influenza D virus (IDV), an emerging orthomyxovirus with zoonotic potential, infects diverse hosts, causes respiratory disease, and remains poorly characterized in China despite its global expansion. From October 2023 to January 2025, we collected 563 nasal swabs from cattle across 28 farms in Jilin Province, Northeast China, and identified seven IDV-positive samples (1.2%), recovering two viable isolates (JL/YB2024 and JL/CC2024). Full-genome sequencing revealed complete, stable seven-segment genomes with high nucleotide identity (up to 99.9%) to contemporary Chinese D/Yamagata/2019 strains and no evidence of reassortment. Maximum-likelihood and time-resolved Bayesian phylogenies of 231 global hemagglutinin-esterase-fusion (HEF) sequences placed the Jilin isolates within the East Asian D/Yamagata/2019 clade and traced their most recent common ancestor to approximately 2017 (95% highest posterior density: 2016–2018), suggesting a cross-border introduction likely associated with regional cattle movement. No IDV was detected in parallel surveillance of swine, underscoring cattle as the principal reservoir and amplifying host. Bayesian skyline analysis demonstrated a marked decline in global IDV genetic diversity during 2020–2022, coinciding with livestock-movement restrictions imposed during the COVID-19 pandemic. Collectively, these findings indicate that IDV circulation in China is sporadic and geographically localized, dominated by the D/Yamagata/2019 lineage, and shaped by multiple independent incursions rather than a single emergence. Both the incorporation of IDV diagnostics into routine bovine respiratory disease surveillance and cattle-import quarantine programs, and the adoption of a One Health framework to monitor potential human spillover and future viral evolution, were recommend. Full article

In 2020, a dairy farm in northwest Germany reported several cows with severe respiratory disease, fever, and reduced milk production. Multiple direct and indirect diagnostic methods were used to identify the cause of the disease. However, the pathogens detected could not be correlated with the severity of the clinical symptoms, so further diagnostic steps were taken. Blood and nasal swab samples were examined using next-generation sequencing (NGS) as part of a metagenomic analysis. For the first time in Germany, Hepacivirus bovis genotype 2 was detected. Real-time RT-PCR assays confirmed the presence of BovHepV genotypes 1 and 2 in the herd between 2020 and 2023. Analyses of complete and partial genome sequences demonstrated the presence of different virus variants in the herd over several years. In addition, the sequence data indicated that cattle can be reinfected with viruses belonging either to different BovHepV subtypes or to the same subtype. Although no direct link could be established between the detection of bovine hepaciviruses and the observed clinical symptoms, the PCR and sequence data obtained provide valuable insights into the epidemiology and pathogenesis of BovHepV infections. Full article

Enterotoxigenic Escherichia coli (ETEC)-induced neonatal calf diarrhea (NCD) causes significant economic losses to the cattle industry; therefore, understanding its antibiotic resistance is crucial for developing targeted prevention and treatment strategies. However, reports on antibiotic resistance in bovine ETEC are currently limited. This study conducted whole-genome sequencing (WGS) and antimicrobial susceptibility testing on ETEC F5- and F5-F41-positive strains isolated from neonatal calf diarrhea samples in Inner Mongolia, China. The results showed that both ETEC F5- and ETEC F5-F41-positive strains are multidrug-resistant, containing ceftriaxone (CRO), ceftazidime (CAZ)) and ciprofloxacin (CIP), which are listed as the highest priority critically important antimicrobial (HP-CIAs) by the World Health Organization (WHO). Combined analysis using the Comprehensive Antibiotic Resistance Database (CARD) and ResFinder 4.1 predictive analysis revealed that the chromosomes and plasmids of the 2 ETEC-positive strains contained 11 classes of antibiotic resistance genes, with the top 3 categories in terms of the number of resistance genes being aminoglycosides, β-lactamases, and chloramphenicols. In addition, various bacterial efflux pumps, including RND, MFS, SMR, and the ABC efflux pump family, were detected. A total of 74 antimicrobial resistance genes were identified in the 2 strains, belonging to 5 categories of drug resistance mechanisms; the antimicrobial resistance phenotype was consistent with the genotype. This study provides a reference for the prevention and treatment of diarrhea caused by ETEC. Full article

This study identified genomic regions associated with carcass traits and primal cut yields in Hanwoo cattle using weighted single-step genome-wide association study (WssGWAS). A total of 50,227 carcass records and genomic data from 23,573 animals with 45,057 single-nucleotide polymorphisms were analyzed. Heritability estimates were 0.24 for carcass weight, 0.22 for eye muscle area, 0.31 for backfat thickness, and 0.36 for marbling score, while those for primal cut yields ranged from 0.02 to 0.26. For carcass traits, candidate genes were identified for carcass weight (XKR4 2.35%, COBL 1.26%), eye muscle area (LCORL 1.56%, TGFBR2 1.49%), backfat thickness (ATG7 1.27%, MYPN 1.33%), and marbling score (TWIST2 1.16%, BMP4 1.14%). For primal cut yields, the chromosome 6 region containing WDR1 was commonly identified across six traits and the chromosome 4 region containing CACNA2D1 across five traits; the chromosome 28 region containing SIRT1 explained the highest genetic variance (6.46%) for striploin. These pleiotropic regions are potential targets for genomic selection to improve production efficiency and carcass value in Hanwoo. Full article

Antimicrobial resistance (AMR) in foodborne pathogens poses a major threat to global public health and food safety. Using 9393 U.S. isolates of Salmonella enterica, Campylobacter jejuni, and Escherichia coli/Shigella collected from poultry, cattle, and swine between 2015 and 2025 and archived in the NCBI Pathogen Isolates Browser, we applied multivariate statistical analysis to characterize antimicrobial resistance patterns in isolates showing resistance to one to six antimicrobials (AMR-1 to AMR-6). Six antimicrobials—tetracycline, streptomycin, sulfisoxazole, ampicillin, nalidixic acid, and ciprofloxacin—were identified through PCA-guided clustering and frequency profiling as the principal axes of co-resistance across pathogens. Tetracycline emerged as a foundational driver of multidrug resistance, while C. jejuni contributed almost exclusively to single-drug resistance and Salmonella enterica dominated higher-order AMR categories, reflecting species-specific ecological and genomic constraints. Gene analyses revealed a progressive, modular accumulation of resistance determinants, led by efflux pumps (mdsA, mdsB), tetracycline genes (tetA/B/O), aminoglycoside-modifying enzymes, sulfonamide genes (sul1/sul2), quinolone resistance determinants (gyrA, acrF, mdtM), and β-lactamases (bla_EC, bla_OXA, bla_CTX). Together, these results demonstrate that multidrug resistance in U.S. foodborne pathogens evolves through coordinated gene–drug–pathogen interactions rather than isolated events, underscoring the need for integrated surveillance and targeted stewardship strategies focused on the dominant antimicrobials and high-risk foodborne pathogens. Full article

The Xinjiang Brown cattle (XJBC) is one of China’s five major dual-purpose dairy and beef breeds. Analyzing the genetic diversity of the Xinjiang Brown cattle population lays the theoretical groundwork for identifying and conserving its genetic resources. This study employed the Illumina Bovine SNP 150K chip to analyze genetic diversity, inbreeding coefficient, kinship, and genetic distance in a population of 750 Xinjiang Brown cattle from three breeding farms in Xinjiang. Genetic diversity was assessed by calculating minimum allele frequency (MAF), observed heterozygosity (Ho), expected heterozygosity (He), polymorphic information content (PIC), and linkage disequilibrium (LD). Population structure was analyzed using PCA. ROH was calculated to derive ROH-based inbreeding coefficients, pedigree-based inbreeding coefficients (F_PED) were estimated using CFC software for comparison, and candidate genes within high-frequency ROH regions in Xinjiang Brown cattle were identified. A G matrix was constructed to analyze population kinship. Results revealed 94,173 high-quality SNP loci in Xinjiang Brown cattle, with an average MAF of 0.276, PIC of 0.376, Ho of 0.345, and He of 0.376. Breeding farm 3 exhibited the fastest LD decay, indicating relatively high genetic diversity across Xinjiang Brown cattle populations, with farm 3 demonstrating greater diversity. The IBS genetic distance was 0.313. The G matrix results aligned with the IBS distance matrix, both indicating close kinship among some individuals within the Xinjiang Brown cattle population. The ranges for average F_PED and average F_ROH across farms were 0.0017–0.0189 and 0.0609–0.0878, respectively. Short ROH segments (0.5–2 Mb) constituted the largest proportion (51.31%) of all ROHs. Within high-frequency ROH enrichment regions, 61 genes, including LCORL, FAM110B, NR4A1, and PER2, were identified as potentially associated with economic traits in Xinjiang Brown cattle. These findings provide relevant marker sites for genomic selection in Xinjiang Brown cattle and lay a theoretical foundation for subsequent research. Full article

Reproductive traits are essential in dairy cattle breeding, and improving body conformation is considered beneficial for reproductive performance. This study systematically analyzed the genetic relationships between six key conformation traits—stature (ST), body depth (BD), loin strength (LS), rump angle (RA), rump width (RW), bone quality (BQ)—and reproductive performance in 1631 Jersey cattle from China. Heritability estimates for conformation traits ranged from 0.05 to 0.62. We identified significant phenotypic and genetic correlations between conformation and reproductive traits, and regression analyses confirmed the predictive value of conformation traits for reproductive outcomes. Genome-wide association studies detected 24 significant SNPs associated with ST, RW, RA, and BQ. Subsequent bioinformatics analysis revealed seven candidate genes (AZIN1, OR2H1, HS6ST3, ERCC4, KCNH5, KRT19, KRT35) involved in embryonic development and estrous cycle regulation. Notably, incorporating six SNPs, which are linked to these candidate genes, into genomic prediction models significantly improved the accuracy for predicting Age at First Calving (AFC) and Gestation Length (GL). These results elucidate the shared genetic basis of conformation and reproduction, providing theoretical support for using conformation traits in marker-assisted selection to enhance reproductive efficiency in Jersey cattle. Full article

Conservation programmes for two local dairy cattle breeds—Latvian Brown old type (BV) and Latvian Blue (LZ)—commenced in 2004. The aim of this study was to evaluate genetic diversity in the BV and LZ local cattle populations using SNP data. This study was based on genotype data from 96 BV and 75 LZ cows and 20 BV and 18 LZ bulls. The SNPs were determined using the GGP 100K bovine SNP BeadChip. Quality control (QC) and genotype data analysis were performed using PLINK v1.9. The observed heterozygosity was moderate, at around 0.4, for both breeds. Inbreeding coefficients were estimated based on homozygosity runs (F_ROH) to compare recent and ancient inbreeding in the BV and LZ populations. Therefore, the ROH segments were divided into segments with the four classes (1–4 Mb, 4–8 Mb, 8–16 Mb, and above 16 Mb). Shorter ROH regions (ROH < 4 Mb) predominated in the genome. ROH regions with lengths above 16 Mb covers 4–6% of the genome in BV and 11% in LZ population. The average inbreeding coefficient for approximately three generations (F_ROH>16) was 2.30% and 4.87% for BV and LZ cows (p < 0.05), respectively, and 2.59% and 3.85% for BV and LZ bulls, respectively. This study demonstrates that inbreeding has increased from generation to generation (F_ROH>16 is higher compared with F_ROH<16) in both populations. The level of current inbreeding in LZ is higher compared with that in the BV breed. The overall level of inbreeding in the BV and LZ populations is low, but there is a high level of inbreeding among a few animals. The impact of inbreeding on cow productivity has been observed in the LZ and BV cow populations. As a result, breeding organisations need to monitor and control the level of inbreeding and prevent the loss of genetic diversity in these animal populations. Breeders should minimize mating among close relatives; introduce genetically unrelated animals, use pedigree, and genomic information in controlling rates of inbreeding. Full article

Background/Objectives: Understanding the genetic basis of growth and fat deposition is crucial for improving beef productivity in Kalmyk cattle, a breed well adapted to the extreme climatic conditions of Kazakhstan. The present study aimed to determine the effects of single-nucleotide polymorphisms (SNPs) in the CRTC2 and ELOVL6 genes on intramuscular fat content and to evaluate their associations with growth and meat quality traits in 18-month-old Kalmyk heifers raised under different environmental conditions. Methods: A total of 400 clinically healthy Kalmyk heifers (200 from LLP “Qazaq Asyldary” and 200 from LLP “Agrofirma Turikpen”) were examined. All animals originated from closed breeding herds, and only unrelated individuals without common ancestors to the third generation were included. Zootechnical measurements— live weight, withers height, chest depth, chest girth, and body length—were performed twice by a trained specialist. Backfat thickness and musculus longissimus dorsi depth were measured postmortem. Blood samples were collected for genomic DNA extraction using the GeneJET purification kit, and DNA quality was assessed by Nanodrop, Qubit, and agarose gel electrophoresis. Target fragments of CRTC2 and ELOVL6 were amplified (150–200 bp) and sequenced on an ABI 3500 system. SNP identification, allele frequencies, and genotyping were performed by alignment to the Bos taurus ARS-UCD1.2 reference genome. Statistical analyses were conducted in RStudio using linear and mixed models with “farm” as a random effect. Results: Only one informative polymorphism, g.133528A>G in ELOVL6, was detected. Three genotypes (AA, AG, GG) were observed, with the heterozygous AG genotype showing significantly higher live weight, greater body length, and improved linear measurements compared to AA and GG. No significant associations were detected with backfat thickness or muscle depth. The g.133528A>G polymorphism in ELOVL6 positively influences growth traits without increasing fatness, aligning with the naturally lean phenotype of Kalmyk cattle. Conclusions: The AG genotype may serve as a promising marker for selecting faster-growing animals in marker-assisted breeding programs. Full article

Bovine ketosis represents a critical metabolic challenge in modern dairy production, primarily affecting high-yielding cows during the periparturient period. The disorder arises from severe negative energy balance (NEB), where energy demands exceed supply, triggering substantial mobilization of adipose tissue and hepatic accumulation of non-esterified fatty acids (NEFAs). This stress overwhelms hepatic oxidative capacity, leading to incomplete fatty acid oxidation and excessive ketone body production—primarily β-hydroxybutyrate (BHB), acetoacetate, and acetone. While genomics enables the identification of candidate genes and genetic variations influencing ketosis susceptibility, metabolomics provides comprehensive, multi-matrix metabolic signatures across blood, milk, urine, and tissues, often revealing predictive biomarkers in the dry period and pre-clinical stage. This review provides a comprehensive overview of ketosis etiology, emphasizing the roles of NEB, fat mobilization, hormonal dysregulation, and oxidative stress. We systematically examine candidate genes, signaling pathways, and the diverse metabolomic profiles underlying disease pathogenesis, and discuss current prevention strategies focusing on periparturient nutritional management and therapeutic interventions. Understanding these integrated molecular and metabolic mechanisms offers valuable insights for developing targeted breeding programs and precision management approaches to enhance metabolic health and economic efficiency in dairy cattle. Full article

The remaining problems in pig farming may no longer be solved with traditional methods. The search for genetic variants associated with desired characteristics and involvement of animals with superior genetics in breeding programs is rarely effective for polygenic traits and pleiotropic genes. The lack of diversity in the germplasm also limits the use of breeding, but some beneficial mutations that did not occur naturally can be introduced manually via genome editing methods. Mutations discovered in other species, such as cattle, can be reproduced in pigs. Traits that were previously pursued for centuries might be achieved by genome editing in a few years. Enormous progress has been made in producing pigs resistant to viruses and in increasing meat productivity and quality. But there are still pressing problems such as lameness and damaging behaviors that probably cannot be solved without genome editing techniques. Their wider application is complicated by the requirement for large amounts of biomaterial, surgical manipulations and cell culture, as well as by the shift towards biomedical research. This review concentrates on the main achievements and challenges in pig agricultural genetics that can be addressed by genome editing. Full article

Kongshan cattle is an indigenous breed from Sichuan Province, China, characterized by their excellent meat quality, high fertility, strong disease resistance, and remarkable environmental adaptability. However, their genomic diversity has not been systematically studied. In this work, we performed whole-genome sequencing of 30 Kongshan cattle from a breeding farm and integrated these data with 113 representative commercial and indigenous cattle breeds worldwide to investigate their population structure and genetic diversity. We further analyzed the ancestral contributions to the development of the breed. The population structure revealed that Kongshan cattle possess four types of ancestral components: East Asian indicine (0.5974), East Asian taurine (0.3464), European taurine (0.0483), and Indian indicine (0.0079). The population also exhibits high nucleotide diversity, second only to pure East Asian indicine cattle. We inferred the ancestry of each variable site in the genome and, in combination with integrated haplotype score analysis, identified candidate genes related to meat quality (ME1, ENPP2, GPD2, PDZRN4, and TMTC2), immunity (MCM6, MAP3K6, PIP4K2A, CDC6, CDC25B, PTAFR, ZC3H10, and NEK6), and environmental adaptability (KCNJ15, BECN1, AOC2, DUSP5, and ST3GAL4). These findings provide valuable insights into the evolutionary history and ancestral origins of Kongshan cattle and contribute to the broader understanding, conservation, and sustainable utilization of indigenous Chinese cattle genetic resources. Full article

Bovine viral diarrhea (BVD) is a highly infectious disease with a global distribution caused by the bovine viral diarrhea virus (BVDV), primarily affecting cattle. Dairy farms play a central role in the persistence and spread of BVDV in Italy, making control strategies and genetic studies essential to reduce its circulation. This work aimed to identify and characterize the genotype and subgenotype of BVDV infecting cattle in a specific area of Sardinia. Ten BVDV Sardinian strains were isolated and sequenced from the blood of infected cattle collected into EDTA tubes during outbreaks between 2018 and 2024. Then, to characterize the isolates, phylogenetic and variant analyses were performed on the entire collection of BVDV genomes available to date in GenBank. All Sardinian isolates were assigned to the BVDV-1b subgenotype. Except for two divergent strains, the isolates clustered into a distinct monophyletic clade characterized by 61 exclusive variants absent in all other analyzed sequences. These findings point to the existence of a distinct Sardinian genomic signature. Moreover, among these mutations, 19 missenses distributed on genes encoding the E1, E2, Core, NS3, NS4B and NS5A proteins could have a relevant functional impact, given the role these proteins play in the virus life cycle and in interaction with the host. Full article