Exploratory identification of candidate SNP markers associated with recurrent clinical mastitis in Holstein cattle

Identification of candidate genes for reproductive traits in Chinese Holstein cattle using single-step genome-wide association study.

In dairy farming, reproductive efficiency is vital to both profitability and sustainability. However, years of selective breeding for increased milk yield have adversely affected reproductive potential. This study aimed to pinpoint genomic regions and identify potential candidate genes associated with reproductive traits in Chinese Holstein cattle. In this study, a single-step genome-wide association study (ssGWAS) was conducted using 33,202 phenotypic records from 16,379 animals, 55,244 pedigree records, and genomic data from 1,698 cows. These data were integrated into the ssGWAS analysis, resulting in a total pedigree structure of 21,635 animals. A total of 12 significant markers were identified for calving interval (IC), days open (DO), number of services per conception (NS), and conception rate (CR). Among these significant SNPs, 3 SNPs were for IC, 2 SNPs were for DO, 3 SNPs were for NS, and 4 SNPs were for CR. Several promising candidate genes located near these SNPs have been identified, including SFXN4, B3GAT2, GRK5, PRDX3, and MTHFD1L, highlighting their potential involvement in fertility-related biological processes. Furthermore, functional enrichment analysis identified significant enrichment of pathways associated with cell adhesion and embryonic development, suggesting a potential mechanistic role for DSG family members (DSG1, DSG2, DSG3, and DSG4) in fertility regulation. Collectively, our findings enhance understanding of the complex genetic basis of reproductive traits in dairy cattle and may offer a valuable set of genomic targets for precision breeding of Chinese Holsteins. Integrating these markers into genomic selection programs may contribute to genetic improvements in reproductive efficiency and support the long-term sustainability of dairy production.

Genome-wide association study reveals key genomic regions underlying colostrability in Italian Holstein cattle

Colostrum yield (CY, L) and concentration of immunoglobulin G (IgG, g/L) are important phenotypes to monitor in dairy farms because of their association with the risk of failure of the passive transfer of immunity in the newborn calf. This can occur when the CY of the parturient cow is insufficient or when the IgG concentration is low. Given that both of these traits are heritable, the present study aimed to investigate their genetic determinism by identifying significant genomic regions. A genome-wide association study coupled with an exploratory functional enrichment analysis was carried out to provide preliminary biological context of the detected signals for the ‘colostrability’ defined as the cow’s ability to secrete enough volume (≥ 4 L) of good-quality colostrum (≥ 50 g IgG/L) at calving. Data comprised 960 genotyped Italian Holstein cows with CY recorded within 6 h of calving, together with colostral IgG and total immunoglobulin concentrations. The significant SNPs associated with CY were scattered across BTA3, 5, 10, 11, 21, and 22, with 23 genes on BTA22 either harbouring or flanking significant signals. Apart from some genes already known, part of the significant regions have unclear function. Signals were detected on BTA1, 6, 7, 11, 19, 21, and 25 for IgG concentration, and on BTA6, 7, 11, 21, 23, and 25 for total immunoglobulin concentration. The functional enrichment analysis provided preliminary support for possible involvement of secretory, immune-signalling, and epithelial receptor-related processes. This study confirms the polygenic nature of cows’ ‘colostrability’ being regulated by different genomic regions distributed across the genome. However, exploration of the genomic determinism of CY and immunoglobulin concentration requires larger, independent, and harmonized data, ideally standardized and highly comparable. These findings, although relevant for improving calf health, represent only part of a more complex picture when the goal is selective breeding toward calf health. In addition to dam-related data, including colostrum traits, future studies should integrate calf-related phenotypes associated with failure of passive transfer of immunity, such as intestinal IgG absorption capacity, gut permeability, early-life survival, and health outcomes.

Candidate genomic regions associated with differential clinical response to lumpy skin disease in sahiwal cattle

Metagenomics-based surveillance identifies possible sources of mastitis-associated organisms in organic and conventional dairy farm environments.

Mastitis is one of the most economically significant diseases of the dairy industry. Although farm environments are recognized reservoirs for mastitis pathogens, comprehensive metagenomic comparisons between organic and conventional systems remain limited. We compared the prevalence, diversity, and functional potential of mastitis-associated organisms in one organic and one conventional dairy farm in Texas using shotgun metagenomics. Of 180 samples collected from six environmental sites (teats, liners, parlor floor mats, feed areas, bedding sands, and water troughs), 126 were retained after quality-control exclusions. Taxonomic analysis revealed the prevalence of Pseudomonas fluorescens, Lactococcus garvieae, Escherichia coli, Citrobacter freundii, Enterococcus faecium, and Streptococcus parauberis. Alpha- and beta-diversity analyses indicated similar pathobiome structure between farm types, with niche-specific clustering observed for teat and liner samples. Functional annotation revealed comparable COG category distributions, with toxin-related genes representing the most abundant virulence-associated signatures, followed by lipopolysaccharide synthesis genes; adhesion and capsular polysaccharide genes were relatively more abundant on the organic farm. Metagenome-assembled genomes affiliated with key species confirmed genes related to toxin secretion, lipopolysaccharide biosynthesis, adhesion, and biofilm formation. Collectively, these farms harbored similar mastitis-associated reservoirs but differed in certain virulence-associated signatures, highlighting the need for environment-specific hygiene interventions.

Prevalence of bovine mastitis and antibiotic susceptibility patterns of bacterial isolates in the Jaffna District, Sri Lanka

Bovine mastitis is one of the most economically important infectious diseases affecting the global dairy industry. In the Jaffna district of Northern Sri Lanka, information on mastitis prevalence, bacterial aetiology, and antimicrobial resistance remains limited, constraining evidence-based disease management. To determine the California Mastitis Test (CMT)-based prevalence of bovine mastitis in the Jaffna district, identify causative bacterial pathogens, evaluate antibiotic susceptibility patterns, and assess farm-level risk factors associated with mastitis occurrence. A cross-sectional study was conducted from April to September 2024 across all 15 veterinary ranges of Jaffna district. A total of 200 milk samples from lactating dairy cattle were screened using the CMT. Positive samples were cultured, and bacterial isolates were identified through Gram staining and standard biochemical tests. Antibiotic susceptibility testing was performed using the Kirby-Bauer disk diffusion method against eight antibiotics following CLSI (2021) guidelines, and Multiple Antibiotic Resistance (MAR) indices were calculated. A structured questionnaire administered to 200 farmers collected data on management, breed, hygiene, and milking practices. Associations between risk factors and mastitis occurrence were analysed using chi-square tests and binary logistic regression. The overall prevalence of bovine mastitis was 10.0% (20/200), with all CMT-positive samples yielding bacterial growth. Staphylococcus aureus was the predominant isolate (50%), followed by Streptococcus agalactiae (30%), Escherichia coli (10%), and Klebsiella spp. (10%). Enrofloxacin showed the highest susceptibility (90%; MAR = 0.14), followed by Doxycycline (60%) and Ciprofloxacin (55%), whereas Oxytetracycline exhibited the lowest efficacy (15%; MAR = 0.45). Semi-intensive farming (aOR = 1.72; p  = 0.05), European crossbred cattle (aOR = 3.12; p  < 0.05), milk yield >10 L/day (aOR = 2.45; p  = 0.036), absence of post-milking teat dipping (aOR = 2.67; p  < 0.05), and non-use of gloves during milking (aOR = 2.90; p  < 0.05) were significant risk factors. Bovine mastitis remains a significant challenge in Jaffna district, with S. aureus as the dominant pathogen. Enrofloxacin was the most effective antibiotic, while high resistance to Oxytetracycline highlights concerns regarding antimicrobial resistance. Improved milking hygiene and antibiogram-guided treatment strategies are recommended.

Genome-wide association and selective sweep analyses reveal genetic loci for teat number trait in pigs.

Teat number is a key reproductive trait for the commercial pig industry, as an optimum number enhances weaned piglet survival rate. This study aimed to identify single nucleotide polymorphisms (SNPs) and genomic regions that are associated with teat number in the Large White sow. A total of 1000 French Large White sows were used in an analysis of total, left/right, and maximum unilateral teat number. Environmental factor, Spearman correlation, genome-wide association study (GWAS), linkage disequilibrium, and selective sweep analyses were conducted, with validation performed in a population of 1145 Landrace pigs. Genetic statistics showed that this population's teat number had moderate-low genomic heritability (h2 = 0.17-0.21) and weak negative correlation with weaned piglet litter weight. Parity and season affected teat development. GWAS identified 17 candidate SNPs on SSC 4, 7, and 17. Combined with selective sweep analysis, two key regions on SSC 7 were found, with four teat number-related SNPs, annotated to VRTN, DIO2, NRXN3. These candidate genes are associated with thoracic vertebrae development, hormone regulation during the early stage of teat formation, and nervous system development. These five SNPs showed similar results in the Landrace pig validation population; non-mutant homozygotes had 0.25-1.15 more teats than mutant ones in both populations. This study contributes to the identification of key variant loci associated with teat number-related traits in sows, thereby providing reliable molecular markers and a theoretical basis for marker-assisted selection of sow reproductive performance.