Search Results (757)

Previous studies have demonstrated that high-yielding dairy cows experience endoplasmic reticulum (ER) stress in the liver during early lactation. To date, most insights into the role of ER stress in metabolism and disease pathophysiology have been derived from rodent and human models. In dairy cattle, however, the specific impact of ER stress on metabolic pathways and its contribution to disease development remain insufficiently characterized. The objective of this study was therefore to investigate the molecular effects of ER stress using a bovine liver cell model (BFH12 cells). ER stress was induced by incubation with Tunicamycin (TM) and Thapsigargin (TG). Molecular responses to ER stress were assessed via a whole-genome array analysis and PCR targeting genes involved in selected metabolic pathways. Incubation with both ER stress inducers resulted in a marked upregulation of genes associated with the unfolded protein response (UPR) within a 4 to 24-h time frame, indicative of the production of robust ER stress in these cells. Unexpectedly, treatment with TM led to a downregulation of numerous genes involved in lipid biosynthesis, including those related to lipogenesis and cholesterol synthesis. Furthermore, incubation with TM and TG induced upregulation of genes involved in fatty acid oxidation and was accompanied by a reduction in intracellular triglyceride concentrations. Genes associated with inflammatory responses were upregulated by both TM and TG, whereas genes encoding antioxidant enzymes were downregulated. Genes involved in ketogenesis did not exhibit a consistent pattern of regulation. Overall, several effects of ER stress previously described in rodent models could not be replicated in this bovine liver cell system. Extrapolating these findings to dairy cows suggests that while ER stress may contribute to hepatic inflammation, it is unlikely to play a significant role in the development of hepatic lipidosis or ketosis. Full article

Milk protein content represents a key economic trait in dairy production, yet the genetic architecture underlying this trait remains unexplored in Romanian dual-purpose cattle breeds. This study conducted a genome-wide association analysis for milk protein content in 313 Romanian Simmental (n = 271) and Romanian Brown (n = 42) cows belonging to the Research and Development Station for Bovine Arad, Romania. Following quality control, 33,531 SNPs were tested for association with protein percentage adjusted for other effects (breed, days in milk, season, year, parity) using linear regression with the first five principal components as covariates to control population stratification. Although no SNP reached genome-wide significance (p < 5 × 10⁻⁸), one SNP achieved significance (p < 2.98 × 10⁻⁵) and seven additional SNPs exceeded the nominal threshold (p < 1 × 10⁻⁴) across six chromosomes. The strongest association (p = 9.56 × 10⁻⁶) mapped to chromosome 25 near C7orf61. Biologically relevant candidate genes included KLF6 on chromosome 13, previously associated with milk traits in Chinese Holstein, and AHCYL1 on chromosome 3, involved in calcium homeostasis. These findings provide initial insights into genomic regions influencing milk protein content in Romanian dual-purpose cattle, though validation in larger cohorts needs to be carried out. Full article

Understanding the genetic regulatory mechanisms of fat accumulation is crucial for improving beef quality. Hanwoo (Korean native cattle) is renowned for its high intramuscular fat (marbling), yet the genetic regulation of adipose gene expression remains insufficiently understood. In this study, we performed expression quantitative trait loci (eQTL) analysis using RNA-Seq data and genotype data from backfat tissue of 75 Hanwoo steers to identify regulatory variants associated with adipose deposition. A total of 25,042 significant cis-eQTL associations (FDR < 0.05) were identified, and 5362 unique top cis-eQTL pairs were retained after gene-wise filtering. Key cis-regulated genes included AGBL1, CACNG1, MYO18B, and DUSP29, which are involved in cytoskeletal organization, muscle development and calcium signaling. Three major cis-regulatory hotspots were located on BTA15 (BTA15:50354741) and BTA21 (BTA21:21526143, and BTA21:21541921). Permutation-based analysis (100,000 iterations) was conducted to control false positives, identifying 12 statistically significant trans-eQTL hotspots (FDR q < 0.05), of which SNP 6:60512276 and SNP 21:17035557 exhibited extensive trans-regulatory activity influencing 429 and 161 genes, respectively. In particular, SNP 21:17035557 acted as a shared cis- and trans-regulatory hub, indicating hierarchical control of adipose gene networks. Functional enrichment analyses revealed significant involvement of cytoskeleton- and calcium-dependent pathways, highlighting the interplay between structural remodeling and metabolic regulation in adipose tissue. These findings provide a comprehensive, system-level view of adipose gene regulation in Hanwoo cattle and highlight candidate molecular targets for genome-assisted and precision breeding. Moreover, this study offers quantitative genomic resources that can support the development of prediction models and decision-support systems for improving carcass traits in Hanwoo breeding programs. Full article

The conservation of agricultural animal resources holds significant importance for addressing future breeding demands and promoting sustainable utilization of regional livestock genetic resources. As one of China’s five major fine cattle breeds, Nanyang cattle exhibit notable characteristics, including strong adaptability and a docile temperament. Through whole-genome comparative analysis of the Nanyang cattle core conservation population and free-ranging populations in mountainous areas, this study systematically investigated the genetic diversity, population structure, and adaptive evolutionary mechanisms of this indigenous Chinese cattle breed. Population structure analysis revealed that both groups belong to a single genetic lineage of Nanyang cattle without significant genetic differentiation; however, the free-ranging population demonstrated a slower linkage disequilibrium decay rate. Combined F_ST and θπ ratio analyses identified 170 positively selected genes, with KEGG enrichment highlighting glutamatergic synapse and African trypanosomiasis immune pathways. PLCB4, as a shared gene across both pathways, may exert pleiotropic functions in environmental adaptation. The core conservation population likely exhibits reduced diversity in neuroplasticity-related genes under artificial selection, whereas the free-ranging population retained more genes associated with environmental adaptation and immune response. These findings provide genomic evidence for formulating differentiated conservation strategies for Nanyang cattle, necessitating balanced co-optimization of production trait breeding and natural adaptability preservation. Full article

Dermatophilosis, caused by the Gram-positive, filamentous bacterium Dermatophilus congolensis, is an important skin disease that adversely affects cattle health and productivity. It also affects other domestic and wild animals and occasionally humans. This review provides a detailed overview of the molecular characteristics and resistome profile of D. congolensis, highlighting recent advances in genomic research. We examine the bacterium’s genome architecture, including its genome size, GC content, gene composition, and phylogenetic placement within the Actinomycetales. Key virulence factors are discussed, including proteolytic enzymes, hyphal invasion, zoospore motility, and the gene products of nasp and agac, emphasizing their roles in tissue invasion, pathogenesis, and diagnostic detection. Furthermore, we analyze resistome, focusing on identified antibiotic resistance genes, diverse resistance mechanisms such as efflux pumps and beta-lactamases, and the contribution of mobile genetic elements to horizontal gene transfer. The implications of these molecular insights for accurate diagnosis, effective treatment, and antibiotic stewardship in cattle production are critically evaluated. Finally, we highlight future research priorities aimed at deepening our understanding of D. congolensis biology and improving strategies for disease control. This review underscores the importance of integrating molecular surveillance with antimicrobial monitoring to safeguard cattle health and promote sustainable livestock management. Full article

Background/Objectives: Morphological defects such as limb malformations, cranial asymmetries, loin deviations, jaw misalignments, and navel irregularities are associated with early culling and reduced productivity in beef cattle. In Bos taurus indicus such as Nellore, the genetic basis of these traits remains poorly characterized. This study aimed to investigate the genetic architecture of six morphological defects in Nellore cattle, namely feet and legs malformation, chamfer asymmetry, fallen hump, loin deviation, jaw misalignment, and navel irregularities, via a genome-wide association study (GWAS) approach tailored for binary traits. Methods: Depending on the trait, the number of genotyped animals analyzed ranged from 3369 to 23,206, using 385,079 SNPs (after quality control). Analyses were conducted using a linear mixed model framework adapted for binary outcomes. Results: Significant associations were identified for four traits: feet and legs, chamfer, hump, and loin. No significant markers were detected for jaw or navel defects, likely due to lower sample sizes and trait incidence. Gene annotation revealed 49 candidate genes related to feet and legs, 4 for chamfer, 4 for hump, and 6 for loin. Conclusions: Candidate genes were enriched for biological functions, including bone remodeling, muscle development, lipid metabolism, and epithelial organization. Overlaps with QTL related to conformation, feed intake, reproductive traits, and carcass quality were also observed. These findings provide novel insights into the genetic control of morphological defects in Nellore cattle and may inform breeding strategies aimed at improving structural soundness. Full article

Fertility is key for calf production. Direct selection for female fertility under field conditions is hindered by low accuracy and selection response. An alternative widely implemented is selection for scrotal circumference (SC), genetically correlated with daughter fertility. This study performed a genome-wide association study (GWAS) to identify genomic regions and candidate loci linked to SC and female fertility in Retinta cattle. A multivariate ssGBLUP was applied using SC records from 1061 bulls, fertility-related traits from 59,254 females and genotypes from 1230 animals using the Axiom™ Bovine Genotyping v3 Array (65k). The ssGWAS revealed 23 1-Mb windows explaining >1% of additive genetic variance for SC, one on chromosome 2 and 22 on chromosome 3. Within these windows, 198 regions spanning 118 protein-coding genes and 80 RNA genes were identified. Several genes, including GSTM3, SPATA1, HFM1, and MSH4, were previously associated with male fertility. Six regions overlapped across male and female traits, containing two protein-coding genes (THSD7B and ENSBTAG00000021755). Identification of genomic markers linked to both female fertility and male SC enables selection of superior animals, improving reproductive efficiency and advancing knowledge of the genomic basis of male–female fertility relationships. Full article

The Krüppel-like factor (KLF) family of transcription regulators plays pivotal roles in adipogenesis, myogenesis, and metabolism. While comprehensively studied in humans and mice, its characterization in cattle remains limited, especially within the skeletal muscle niche. This study aimed to systematically characterize the KLF family in Bos taurus and elucidate its role in breed-specific muscular development. We employed an integrated approach of comparative genomics and single-nucleus RNA sequencing (snRNA-seq) on longissimus dorsi muscle from Angus (ANG, beef breed) and Holstein (HST, dairy breed) cattle. Phylogenomic analysis identified 14 KLF genes, revealing evolutionary conservation and potential functional divergence. snRNA-seq delineated 11 distinct cell populations and uncovered cell-type-specific expression patterns of KLFs. Further machine learning based analysis pinpointed KLF6, KLF9, KLF10, and KLF12 as key global drivers of transcriptional differences between breeds, while KLF6 was identified as a major cell-type-specific contributor in lymphatic endothelial cells. Our work provides a foundational resource for understanding the KLF family in cattle and identifies promising candidate genes for improving meat production traits through molecular breeding. Full article

High non-esterified fatty acids (NEFAs) during negative energy balance in dairy cattle can impair reproduction. While their effects on oocyte maturation and preimplantation embryo development are known, their impact during fertilisation is largely unexplored. This study examined the effects of high NEFA exposure exclusively during in vitro fertilisation (IVF). Bovine oocytes were matured in vitro and fertilised under physiological or high NEFA concentrations. High NEFA concentrations decreased fertilisation, cleavage, and blastocyst rates. Reactive oxygen species production in zygotes was not affected, but blastocysts derived from the High-NEFA group had fewer cells. Spermatozoa exposed to high NEFA concentrations exhibited increased plasma membrane and acrosome damage, higher DNA fragmentation, and reduced mitochondrial membrane potential. The expression of H3K27me3, a repressive histone mark normally erased from fertilisation to embryonic genome activation, was higher in 2-cell than in 4-cell embryos on day 2 after IVF, but only in the High-NEFA group. This delayed H3K27me3 loss, along with increased DNA damage, could partially explain the reduced blastocyst formation observed. In conclusion, high NEFA concentrations can impair pre-implantation embryo development during zygote formation, potentially via effects on both the oocyte and spermatozoon. The latter warrants further investigation using an intracytoplasmic sperm injection model. Full article

The inclusion of meat quality traits in breeding programs is a promising strategy to improve beef by selecting animals based on both growth and meat quality. This study aimed to estimate genetic parameters for average daily gain (ADG) and Warner–Bratzler shear force (WBSF), as well as to perform genome-wide association studies (GWAS) to identify genomic regions and transcription factor (TF) binding sites associated with both traits in Nelore cattle. Genetic parameters were estimated using a bi-trait Bayesian model, and GWAS identified key SNPs explaining over 1% of variance in genomic estimated breeding values. Candidate genes near these SNPs were annotated, TF binding sites predicted, and gene–TF networks constructed. Genetic estimates indicated moderate heritability for ADG, low heritability for WBSF, and a small negative genetic correlation between traits. Genomic regions contained 116 and 151 candidate genes for ADG and WBSF, respectively, with 35 shared between traits. Functional analyses highlighted MYBPC1 and PENK for WBSF, and GHRS and NPY for ADG. TF analysis identified 25 TFs, with 3 key ones highlighted. Gene–TF networks revealed candidates including CAPN1 and LTBP3 for WBSF, and CARM1 and GH1 for ADG. Shared candidate genes identified in the combined network provide valuable insights into the genetic architecture of growth and tenderness in Nelore cattle. Full article

The objective of this study was to evaluate the impact of blending, tuning, and scaling adjustments in ssGBLUP on the accuracy of genomic estimated breeding values (GEBVs) for South African Holstein cattle. The edited dataset included pedigree information for 541,325 animals, 696,413 phenotypic records (milk, protein, and fat yields), and genotypes for 1221 Holstein cattle. The accuracy of GEBVs was evaluated based on different parameter settings for blending (β = 0.05, 0.10, 0.20, 0.30, and 0.40), tuning (τ), and scaling (τ and ω), ranging from 0.60 to 1.00. The results show that ssGBLUP outperformed the traditional pedigree-based approach (ABLUP), with realized accuracies increasing from 0.01 to 0.23 for milk yield, 0.03 to 0.29 for protein yield, and 0.03 to 0.30 for fat yield. Blending with β = 0.30–0.40 slightly increased the accuracy, while tuning adjustments showed limited influence on the prediction results. Scaling factors had a significant influence on accuracy, with ω = 0.60 yielding the highest values (0.26 for milk, 0.32 for protein, and 0.34 for fat). The results of this study show the importance of optimizing the integration of pedigree and genomic information in ssGBLUP to improve the accuracy of genomic predictions, ultimately enhancing selection decisions and genetic progress in South African Holstein cattle. Full article

This study evaluated the diffusion of Listeria monocytogenes (LM) in a beef steak tartare production chain, aiming to (1) evaluate Listeria spp. diffusion in finishing farms supplying beef cattle, (2) evaluate LM prevalence in carcasses, and (3) map LM diffusion in the production plant. A detection rate of 6/76 was observed in the farm, while carcasses after skinning and before refrigeration tested positive in 19/30 and 11/30, respectively. During tartare production, 57/154 meat and 35/191 environmental samples tested positive. A total of 114 LM isolates were characterized via a whole-genome sequencing approach. Five clonal complexes (CCs) and seven sequence types (STs) were identified, with CC9-ST580 being the most prevalent. Four clusters were identified from both the slaughtering and production phases. Genes related to resistance to fosfomycin, quinolones, sulfonamides, lincosamide, and tetracycline were detected. Two hypervirulent strains (CC6-ST6 and CC2-ST145), harboring a full-length inlA, several virulence genes, and stress islands, were detected. Stress Survival Islet 1 was found in almost all the isolates. The wide diffusion of LM in steak tartare requires the management of some critical phases of the production chain (mainly slaughtering); genomic methodologies could be useful in describing the circulation and virulence of LM strains. Full article

The emergence of H5N1 highly pathogenic avian influenza virus (HPAIV) clade 2.3.4.4b in dairy cattle across multiple U.S. states in early 2024 marks a major shift in the virus’s host range and epidemiological profile. Traditionally limited to bird species, the ongoing detection of H5N1 in cattle, a mammalian host not previously considered vulnerable, raises urgent animal and human health concerns about zoonoses and mammalian adaptation. We assessed the feasibility of using commercially available pasteurized milk as a sentinel matrix for the molecular detection and genetic characterization of H5N1 HPAIV. Our aim was to determine whether retail milk could serve as a practical tool for virological monitoring and to evaluate the use of full-length genome segment amplification for extracting genomic sequence information from this highly processed matrix. Our results link HPAIV sequences in store-bought milk to the cattle outbreak and highlight both the potential and the limitations of retail milk as a surveillance window. Together, these findings provide evidence that influenza A virus RNA can be repeatedly detected in retail milk in patterns linked to specific supply chains, with genomic data confirming close relationships with the viruses circulating in cattle. Full article

Genome-wide association studies (GWAS) have been a successful tool for identifying quantitative trait loci (QTL) for economically important traits in dairy cows. However, the availability of QTLs linked to phenotypic traits is limited in the literature. In this study, we used GWAS, haplotype association, and fine-mapping analyses to identify candidate variants associated with milk production, health, and reproductive traits in 380 Chinese Holstein cattle from Southern China using whole-genome sequence data. GWAS identified 91 genome-wide significant signals that were annotated to 63 genes associated with milk production, health, and reproductive traits in dairy cattle. Haplotype association analysis further revealed that eight GWAS signals within three QTLs were associated with milk production and health traits of cows. Fine-mapping analysis revealed that 3 GWAS signals (6_92530313_G_A, 10_17185230_G_A, and 10_17209112_T_G) were the potential causal variants. Several candidate genes, including ANKS1B, IL17RD, CNOT6L, AOC1, and TLE3, have been confirmed to be associated with milk production, health, and reproductive traits in dairy cows. These findings significantly contribute to unraveling the genetic basis of economically important traits in Holstein cattle. Full article

Mixed infections of Mannheimia haemolytica and Mycoplasma bovis are relatively common in bovine respiratory diseases, presenting severe respiratory symptoms and high mortality that severely endanger the cattle industry. In this study, a serotype A1 strain of Mannheimia haemolytica, designated as XJCJMh1, was isolated and identified from the lung tissue of a hybrid Simmental calf infected with Mycoplasma bovis. The pathogenicity of this strain was evaluated using Kunming mice as a model. The results indicated that infection with XJCJMh1 caused pathological manifestations such as pulmonary hemorrhage and edema in mice. Subsequently, the genome of this strain was sequenced and assembled using Illumina sequencing to obtain general genomic features. The genome was annotated and analyzed for gene functions using the Swiss-Prot, NR, GO, COG, KEGG, CAZy, TCDB, and Pfam databases. Additionally, the virulence factors and resistance genes of this strain were annotated using the PHI, VFDB, and CARD databases. The genome of Mannheimia haemolytica XJCJMh1 is 2,595,489 base pairs (bp) in length, with a GC content of 40.93%. Notably, this strain exhibits three distinct genomic islands and contains 98 effectors associated with the type III secretion system (T3SS). The XJCJMh1 strain harbors 74 virulence genes and 45 resistance genes. We annotated the proteins, genes, and associated GO and KEGG pathways of the XJCJMh1 strain; exploring the relationship between these annotations and the strain’s pathogenicity is of considerable value. This study is of great significance for clarifying the pathogenic mechanism and genetic characteristics of the Mannheimia haemolytica strain XJCJMh1 in cattle, and its results provide a scientific reference for analyzing the genomic basis of pathogenicity and drug resistance of Mannheimia haemolytica under co-infection conditions. Full article