Genetic Selection for Mastitis Resistance

Application of Genomic Selection in Beef Cattle Disease Prevention

Genomic applications in beef cattle disease prevention have gained traction in recent years, offering new strategies for improving herd health and reducing economic losses in the livestock industry. Advances in genomics, including identification of genetic markers linked to disease resistance, provide powerful tools for early detection, selection, and management of cattle resistant to infectious diseases. By incorporating genomic technologies such as whole-genome sequencing, genotyping, and transcriptomics, researchers can identify specific genetic variants associated with resistance to pathogens like bovine respiratory disease and Johne's disease. These genomic insights allow for more accurate breeding programs aimed at enhancing disease resistance and overall herd resilience. Genomic selection, in particular, enables identification of individuals with superior genetic traits for immune function, reducing the need for antibiotic treatments and improving animal welfare. Moreover, precision medicine, powered by genomic data, supports development of tailored health management strategies, including targeted vaccination plans and antimicrobial stewardship. Incorporation of genomic tools in beef cattle management also offers the potential for early disease detection, facilitating proactive interventions that reduce the spread of infections. Despite challenges like cost, data interpretation and integration into current management systems, the potential advantages of genomic applications in disease prevention are substantial. As these technologies advance, they are anticipated to have crucial roles in improving sustainability (by enhancing herd performance), profitability (by improving overall herd longevity), and biosecurity (by decreasing the likelihood of disease outbreaks) of beef cattle production systems worldwide.

Advancing Dairy and Beef Genetics Through Genomic Technologies

The US beef and dairy industries have made remarkable advances in sustainability and productivity through technological advancements, including selective breeding. Yet, challenges persist due to the complex nature of quantitative traits. While the beef industry has progressed in adopting genomic technologies, the availability of phenotypic data remains an obstacle. To meet the need for sustainable production systems, novel traits are being targeted for selection. Additionally, emerging approaches such as genome editing and high-throughput phenotyping hold promise for further genetic progress. Future research should address the challenges of translating functional genomic findings into practical applications, while simultaneously harnessing analytical methods.

Genetic parameters for udder conformation traits derived from Cartesian coordinates generated by robotic milking systems in North American Holstein cattle

Udder conformation is directly related to milk yield, cow health, workability, and welfare. Automatic milking systems (AMS, also known as milking robots) have become popular worldwide, and the number of dairy farms adopting these systems has increased considerably over the past years. In each milking visit, AMS record the location of the 4 teats as Cartesian coordinates in an xyz plan, which can then be used to derive udder conformation traits. Because AMS generate a large amount of data for individual cows per milking visit, they can contribute to an accurate assessment of important traits such as udder conformation without the addition of human classifier errors (in subjective scoring systems). Therefore, the primary objectives of this study were to estimate genomic-based genetic parameters for udder conformation traits derived from AMS records in North American Holstein cattle and to assess the genetic correlation between the derived traits for evaluating the feasibility of multitrait genomic selection for breeding cows that are more suitable for milking in AMS. The Cartesian teat coordinates measured during each milking visit were collected by 36 milking robots in 4,480 Holstein cows from 2017 to 2021, resulting in 5,317,488 records. A total of 4,118 of these Holstein cows were also genotyped for 57,600 SNPs. Five udder conformation traits were derived: udder balance (UB, mm), udder depth (UD, mm), front teat distance (FTD, mm), rear teat distance (RTD, mm), and distance front-rear (DFR, mm). In addition, 2 traits directly related to cow productivity in the system were added to the study: daily milk yield (DY) and milk electroconductivity (EC; as an indicator of mastitis). Variance components and genetic parameters for UB, UD, FTD, RTD, DFR, DY, and EC were estimated based on repeatability animal models. The estimates of heritability (± SE) for UB, UD, FTD, RTD, DFR, DY, and EC were 0.41 ± 0.02, 0.79 ± 0.01, 0.53 ± 0.02, 0.40 ± 0.02, 0.65 ± 0.02, 0.20 ± 0.02, and 0.46 ± 0.02, respectively. The repeatability estimates (± SE) for UB, UD, FTD, RTD, and DFR were 0.82 ± 0.01, 0.93 ± 0.01, 0.87 ± 0.01, 0.83 ± 0.01, and 0.88 ± 0.01, respectively. The strongest genetic correlations were observed between FTD and RTD (0.54 ± 0.03), UD and DFR (-0.47 ± 0.03), DFR and FTD (0.32 ± 0.03), and UD and FTD (-0.31 ± 0.03). These results suggest that udder conformation traits derived from Cartesian coordinates from AMS are moderately to highly heritable. Furthermore, the moderate genetic correlations between these traits should be considered when developing selection subindexes. The most relevant genetic correlations between traits related to cow milk productivity and udder conformation traits were between UD and EC (-0.25 ± 0.03) and between DFR and DY (0.30 ± 0.04), in which both genetic correlations are favorable. These findings will contribute to the design of genomic selection schemes for improving udder conformation in North American Holstein cattle, especially in precision dairy farms.

Associations of the Swiss national reporting system's antimicrobial use data and management practices in dairy cows on tiestall farms

Antimicrobial use (AMU) in Switzerland is above target and requires reduction, especially in dairy cattle. Measuring AMU is pivotal to identifying starting points for AMU reduction, and so are studies investigating its potential drivers in dairy farms worldwide. However, although AMU in dairy farms is high, studies estimating AMU specifically in tiestall farms are scarce. Tiestalls are a common housing system and their prevalence among dairy farms accounts to approximatively 73%, 41%, and 40% in Canada, the United States, and Switzerland, respectively. The objectives of this cross-sectional, retrospective observational study were to estimate AMU using the newly established Swiss national reporting system for AMU in livestock and to identify associated factors on Swiss tiestall dairy farms. We calculated the treatment incidence (TI) by using the European Medicines Agency methodology and their defined daily dose (DDD) and defined course dose (DCD) standards. Data on factors potentially associated with AMU were obtained through personal interviews with farm managers on 221 farms. Retrospectively, during a 1-year period, data on a total of 7,619 treatments were extracted from the national database. Associations between management factors and TI were analyzed using a generalized linear model with gamma distribution. The mean (± SD) overall TI was 5.46 DDD/cow-year (± 4.10 DDD/cow-year). Intramammary treatment during lactation accounted for highest TI (3.24 ± 3.16 DDD/cow-year), whereas dry-cow therapy accounted for lowest TI (0.44 ± 0.49 DCD/cow-year). We found that 5 of the investigated management factors were significantly associated with TI. Organic production (estimate = -2.16; 95% CI = -3.62 to -0.70) and herd size (estimate = -0.81; 95% CI = -1.23 to -0.39) were negatively associated with TI. Specific cow breeds (Brown Swiss estimate = 1.56; 95% CI = 0.45-2.68) and Holstein Friesian (estimate = 1.42; 95% CI = 0.03-2.82; reference: other breeds) and the use of hygienic powders on the lying area (estimate = 1.10; 95% CI = 0.04-2.17) were positively associated with TI. Overall, the Swiss national reporting system is a valuable tool for AMU estimation. Several herd characteristics and management factors were associated with AMU in tiestall farms. Further studies focusing on factors associated with AMU and which are amenable to intervention will help improve stewardship programs and subsequently reduce AMU in dairy cows.

Genes and pathways revealed by whole transcriptome analysis of milk derived bovine mammary epithelial cells after Escherichia coli challenge

Mastitis, inflammation of the mammary gland, is the costliest disease in dairy cattle and a major animal welfare concern. Mastitis is usually caused by bacteria, of which staphylococci, streptococci and Escherichia coli are most frequently isolated from bovine mastitis. Bacteria activate the mammary immune system in variable ways, thereby influencing the severity of the disease. Escherichia coli is a common cause of mastitis in cattle causing both subclinical and clinical mastitis. Understanding of the molecular mechanisms that activate and regulate the host response would be central to effective prevention of mastitis and breeding of cows more resistant to mastitis. We used primary bovine mammary epithelial cell cultures extracted noninvasively from bovine milk samples to monitor the cellular responses to Escherichia coli challenge. Differences in gene expression between control and challenged cells were studied by total RNA-sequencing at two time points post-challenge. In total, 150 and 440 (Padj < 0.05) differentially expressed genes were identified at 3 h and 24 h post-challenge, respectively. The differentially expressed genes were mostly upregulated at 3 h (141/150) and 24 h (424/440) post-challenge. Our results are in line with known effects of E. coli infection, with a strong early inflammatory response mediated by pathogen receptor families. Among the most significantly enriched early KEGG pathways were the TNF signalling pathway, the cytokine-cytokine receptor interaction, and the NF-kappa B signalling pathway. At 24 h post-challenge, most significantly enriched were the Influenza A, the NOD-like receptor signalling, and the IL-17 signaling pathway.

Effects of a mastitis J5 bacterin vaccination on the productive performance of dairy cows: An observational study using propensity score matching techniques

Inferring causal effects between variables when utilizing observational data is challenging due to confounding factors not controlled through a randomized experiment. Propensity score matching can decrease confounding in observational studies and offers insights about potential causal effects of prophylactic management interventions such as vaccinations. The objective of this study was to determine potential causality and impact of vaccination with an Escherichia coli J5 bacterin on the productive performance of dairy cows applying propensity score matching techniques to farm-recorded (e.g., observational) data. Traits of interest included 305-d milk yield (MY305), 305-d fat yield (FY305), 305-d protein yield (PY305), and somatic cell score (SCS). Records from 6,418 lactations generated by 5,121 animals were available for the analysis. Vaccination status of each animal was obtained from producer-recorded information. Confounding variables considered were herd-year-season groups (56 levels), parity (5 levels: 1, 2, 3, 4, and ≥5), and genetic quartile groups (4 levels: top 25% through bottom 25%) derived from genetic predictions for MY305, FY305, PY305, and SCS, as well as for the genetic susceptibility to mastitis. A logistic regression model was applied to estimate the propensity score (PS) for each cow. Subsequently, PS values were used to form pairs of animals (1 vaccinated with 1 unvaccinated control), depending on their PS similarities (difference in PS values of cows within a match required to be <20% of 1 standard deviation of the logit of PS). After the matching process, 2,091 pairs of animals (4,182 records) remained available to infer the causal effects of vaccinating dairy cows with the E. coli J5 bacterin. Causal effects estimation was performed using 2 approaches: simple matching and a bias-corrected matching. According to the PS methodology, causal effects of vaccinating dairy cows with a J5 bacterin on their productive performance were identified for MY305. The simple matched estimator suggested that vaccinated cows produced 163.89 kg more milk over an entire lactation when compared with nonvaccinated counterparts, whereas the bias-corrected estimator suggested that such increment in milk production was of 150.48 kg. Conversely, no causal effects of immunizing dairy cows with a J5 bacterin were identified for FY305, PY305, or SCS. In conclusion, the utilization of PS matching techniques applied to farm-recorded data was feasible and allowed us to identify that vaccination with an E. coli J5 bacterin relates to an overall milk production increment without compromising milk quality.

Genomic Characterization and Initial Insight into Mastitis-Associated SNP Profiles of Local Latvian Bos taurus Breeds

Latvia has two local Bos taurus breeds-Latvian Brown (LBG) and Latvian Blue (LZG)-characterized by a good adaptation to the local climate, longevity, and high fat and protein contents in milk. Since these are desired traits in the dairy industry, this study investigated the genetic background of the LBG and LZG breeds and identified the genetic factors associated with mastitis. Blood and semen samples were acquired, and whole genome sequencing was then performed to acquire a genomic sequence with at least 35× or 10× coverage. The heterozygosity, nucleotide diversity, and LD analysis indicated that LBG and LZG cows have similar levels of genetic diversity compared to those of other breeds. An analysis of the population structure revealed that each breed clustered together, but the overall differentiation between the breeds was small. The highest genetic variance was observed in the LZG breed compared with the LBG breed. Our results show that SNP rs721295390 is associated with mastitis in the LBG breed, and SNPs rs383806754, chr29:43998719CG>C, and rs462030680 are associated with mastitis in the LZG breed. This study shows that local Latvian LBG and LZG breeds have a pronounced genetic differentiation, with each one suggesting its own mastitis-associated SNP profile.

Molecular regulatory mechanism of key LncRNAs in subclinical mastitic cows with folic acid supplementation

BACKGROUND

Folic acid is a water-soluble B vitamin (B9), which is closely related to the body's immune and other metabolic pathways. The folic acid synthesized by rumen microbes has been unable to meet the needs of high-yielding dairy cows. The incidence rate of subclinical mastitis in dairy herds worldwide ranged between 25%~65% with no obvious symptoms, but it significantly causes a decrease in lactation and milk quality. Therefore, this study aims at exploring the effects of folic acid supplementation on the expression profile of lncRNAs, exploring the molecular mechanism by which lncRNAs regulate immunity in subclinical mastitic dairy cows.

RESULTS

The analysis identified a total of 4384 lncRNA transcripts. Subsequently, differentially expressed lncRNAs in the comparison of two groups (SF vs. SC, HF vs. HC) were identified to be 84 and 55 respectively. Furthermore, the weighted gene co-expression network analysis (WGCNA) and the KEGG enrichment analysis result showed that folic acid supplementation affects inflammation and immune response-related pathways. The two groups have few pathways in common. One important lncRNA MSTRG.11108.1 and its target genes (ICAM1, CCL3, CCL4, etc.) were involved in immune-related pathways. Finally, through integrated analysis of lncRNAs with GWAS data and animal QTL database, we found that differential lncRNA and its target genes could be significantly enriched in SNPs and QTLs related to somatic cell count (SCC) and mastitis, such as MSTRG.11108.1 and its target gene ICAM1, CXCL3, GRO1.

CONCLUSIONS

For subclinical mastitic cows, folic acid supplementation can significantly affect the expression of immune-related pathway genes such as ICAM1 by regulating lncRNAs MSTRG.11108.1, thereby affecting related immune phenotypes. Our findings laid a ground foundation for theoretical and practical application for feeding folic acid supplementation in subclinical mastitic cows.

Association of plasma miRNAs with early life performance and aging in dairy cattle

Early life performance traits in dairy cattle can have important influences on lifetime productivity. Poor health and fertility are of great economical and animal welfare concern. Circulating miRNAs have been linked to several livestock traits, including resistance to infection, fertility, and muscle development. This study aimed to identify circulating miRNAs associated with early life performance traits and aging in dairy cattle. Plasma samples from female calves (n = 12) identified retrospectively as differing in health, growth, and fertility outcomes prior to first calving were analyzed using PCR arrays detecting 378 miRNAs. Levels of 6 miRNAs differed significantly in calves with poor growth/fertility relative to controls (t-test: P<0.05). Additionally, general(ized) (non)linear mixed models identified 1 miRNA associated with average daily gain until weaning, 22 with live bodyweight at one year of age, 47 with age at first service, and 19 with number of infections before first calving. Out of 85 distinct miRNAs that were associated with at least one animal trait, 9 miRNAs were validated by RT-qPCR in a larger cohort (n = 91 animals), which included longitudinal plasma samples (calf, heifer, first lactation cow). Significant associations (P<0.05) involving individual miRNAs or ratios between miRNAs and early-life performance traits were identified, but did not retain significance after multiple testing adjustment. However, levels of 8 plasma miRNAs (miR-126-3p, miR-127, miR-142-5p, miR-154b, miR-27b, miR-30c-5p, miR-34a, miR-363) changed significantly with age, most prominently during the calf-to-heifer transition. Comparative RT-qPCR analyses of these miRNAs across 19 calf tissues showed that most were ubiquitously expressed. Online database mining identified several pathways involved in metabolism and cell signaling as putative biological targets of these miRNAs. These results suggest that miR-126-3p, miR-127, miR-142-5p, miR-154b, miR-27b, miR-30c-5p, miR-34a, miR-363 are involved in regulating growth and development from birth to first lactation (~2 years old) and could provide useful biomarkers of aging in cattle.

Neutrophils expressing major histocompatibility complex class II molecules circulate in blood and milk during mastitis and show high microbicidal activity

Bovine mastitis is mainly caused by bacterial infection and is responsible for important economic losses as well as alterations of the health and welfare of animals. The increase in somatic cell count (SCC) in milk during mastitis is mainly due to the influx of neutrophils, which have a crucial role in the elimination of pathogens. For a long time, these first-line defenders have been viewed as microbe killers, with a limited role in the orchestration of the immune response. However, their role is more complex: we recently characterized a bovine neutrophil subset expressing major histocompatibility complex class II (MHC-II) molecules (MHC-II^pos), usually distributed on antigen-presenting cells, as having regulatory capacities in cattle. In this study, our objective was to evaluate the implication of different neutrophils subsets in the mammary gland immunity during clinical and subclinical mastitis. Using flow cytometry, we analyzed the presence of MHC-II^pos neutrophils in blood and in milk during clinical mastitis at different time points of inflammation (n = 10 infected quarters) and during subclinical mastitis, defined as the presence of bacteria and an SCC >150,000 cells/mL (n = 27 infected quarters). Our results show, for the first time, that in blood and milk, neutrophils are a heterogeneous population and encompass at least 2 subsets distinguishable by their expression of MHC-II. In milk without mastitis, we observed higher production of reactive oxygen species and higher phagocytosis capacity of MHC-II^pos neutrophils compared with their MHC-II^neg counterparts, indicating the high bactericidal capacities of MHC-II^pos neutrophils. MHC-II^pos neutrophils are enriched in milk compared with blood during subclinical mastitis but not during clinical mastitis. Moreover, we observed a positive and highly significant correlation between MHC-II^pos neutrophils and T lymphocytes present in milk during subclinical mastitis. Our experiments involved a total of 47 cows (40 Holstein and 7 Normande cows). To conclude, our study opens the way to the discovery of new biomarkers of mastitis inflammation.

Genetic polymorphisms in immune- and inflammation-associated genes and their association with bovine mastitis resistance/susceptibility

Bovine mastitis, the inflammation of the mammary gland, is a contagious disease characterized by chemical and physical changes in milk and pathological changes in udder tissues. Depressed immunity and higher expression of inflammatory cytokines with an elevated milk somatic cell count can be observed during mastitis in dairy cattle. The use of somatic cell count (SCC) and somatic cell score (SCS) as correlated traits in the indirect selection of animals against mastitis resistance is in progress globally. Traditional breeding for mastitis resistance seems difficult because of the low heritability (0.10-0.16) of SCC/SCS and clinical mastitis. Thus, genetic-marker-selective breeding to improve host genetics has attracted considerable attention worldwide. Moreover, genomic selection has been found to be an effective and fast method of screening for dairy cattle that are genetically resistant and susceptible to mastitis at a very early age. The current review discusses and summarizes the candidate gene approach using polymorphisms in immune- and inflammation-linked genes (CD4, CD14, CD46, TRAPPC9, JAK2, Tf, Lf, TLRs, CXCL8, CXCR1, CXCR2, C4A, C5, MASP2, MBL1, MBL2, LBP, NCF1, NCF4, MASP2, A2M, and CLU, etc.) and their related signaling pathways (Staphylococcus aureus infection signaling, Toll-like receptor signaling, NF-kappa B signaling pathway, Cytokine-cytokine receptor, and Complement and coagulation cascades, etc.) associated with mastitis resistance and susceptibility phenotypic traits (IL-6, interferon-gamma (IFN-γ), IL17, IL8, SCS, and SCC) in dairy cattle.

Immune mechanisms, resistance genes, and their roles in the prevention of mastitis in dairy cows

Mastitis is one of the most important diseases of the mammary gland. The increased incidence of this disease in cows is due to the breeding of dairy cattle for higher yields, which is accompanied by an increased susceptibility to mastitis. Therefore, the difficulty involved with preventing this disease has increased. An integral part of current research is the elimination of mastitis in order to reduce the consumption of antibiotic drugs, thereby reducing the resistance of microorganisms and decreasing companies' economic losses due to mastitis (i.e. decreased milk yield, increased drug costs, and reduced milk supply). Susceptibility to mastitis is based on dairy cows' immunity, health, nutrition, and welfare. Thus, it is important to understand the immune processes in the body in order to increase the resistance of animals. Recently, various studies have focused on the selection of mastitis resistance genes. An important point is also the prevention of mastitis. This publication aims to describe the physiology of the mammary gland along with its immune mechanisms and to approximate their connection with potential mastitis resistance genes. This work describes various options for mastitis elimination and focuses on genetic selection and a closer specification of resistance genes to mastitis. Among the most promising resistance genes for mastitis, we consider CD14, CXCR1, lactoferrin, and lactoglobulin.

A Practical Application of Genomic Predictions for Mastitis Resistance in Italian Holstein Heifers

Heifers are a fundamental resource on farms, and their importance is reflected in both farm management and economy. Therefore, the selection of heifers to be reared on a farm should be carefully performed to select only the best animals. Genomic selection is available nowadays to evaluate animals in a fast and economic way. However, it is mainly used on the sire line and on performance traits. Ten farms were selected based on their 5-year records of average somatic cell count and evenly classified into high (>300,000 cells/mL) and low somatic cell count (<150,000 cells/mL). Genomic indexes (regarding both wellness and productive traits) were evaluated in 157 Italian Holstein heifers reared in the selected ten farms (90 from high-cells farms and 67 from low-cells ones). Linear mixed models were fitted to analyze the effects of the abovementioned genomic indexes on related phenotypes. Results have shown that farms classified into low somatic cell count had an overall better animal genomic pool compared to high somatic cell count ones. Additionally, the results shown in this study highlighted a difference in wellness genomic indexes in animals from farms with either a high or a low average somatic cell count. Applying genomic tools directly to heifer selection could improve economic aspects related to herd turnover.

Association of Lactoferrin and Toll-like Receptor 2 Genotypes with Mastitis and Milk Components in Vietnamese Holstein Cattle

Mastitis is one of the most widespread diseases in dairy cows and causes huge losses for the dairy industry. Molecular markers can be used for the quick diagnosis of mastitis infection, consequently reducing the loss caused by this disease. Lactoferrin (LTF) and Toll-like receptor 2 (TLR2) have been suggested as candidate genes for mastitis; however, their associations with the mastitis incidence and milk components have not been reported in Vietnamese Holstein cows. This study examined the association of TLR2 and LTF polymorphisms with subclinical mastitis and milk components in the Holstein breed raised in Vietnam. Among 192 samples, we identified 44 mastitis-positive samples (22.92%). The mastitis significantly reduced the fat and lactose components in milk (p < 0.001) but increased the protein concentration in milk. A total of 94 (49%) and 98 (51%) cows had AA and AB genotypes for the LTF gene, respectively. No significant association was found between the LTF genotypes and the milk component traits or mastitis incidence (p > 0.05). The interaction between LTF and mastitis incidence was significantly associated with the protein percentage (p = 0.01). A total of 78, 76, and 38 cows had genotypes GG, GT, and TT for the TLR2 gene, respectively. TLR2 genotypes were not significantly associated with mastitis incidence (p > 0.05) but were significantly associated with pH value (p = 0.03). The interaction between TLR2 and mastitis incidence was significantly associated with the fat (p = 0.02) and protein percentage (p = 0.04). Further studies are required to confirm the roles of LTF and TFL2 in mastitis in the Holstein breed in Vietnam.

Understanding the genomic architecture of clinical mastitis in Bos indicus

This study elucidated potential genetic variants and QTLs associated with clinical mastitis incidence traits in Bos indicus breed, Sahiwal. Estimated breeding values for the traits (calculated using Bayesian inference) were used as pseudo-phenotypes for association with genome-wide SNPs and further QTL regions underlying the traits were identified. In all, 25 SNPs were found to be associated with the traits at the genome-wide suggestive threshold (p ≤ 5 × 10^-4) and these SNPs were used to define QTL boundaries based on the linkage disequilibrium structure. A total of 16 QTLs were associated with the trait EBVs including seven each for clinical mastitis incidence (CMI) in first and second lactations and two for CMI in third lactation. Nine out of sixteen QTLs overlapped with the already reported QTLs for mastitis traits, whereas seven were adjudged as novel ones. Important candidates for clinical mastitis in the identified QTL regions included DNAJB9, ELMO1, ARHGAP26, NR3C1, CACNB2, RAB4A, GRB2, NUP85, SUMO2, RBPJ, and RAB33B genes. These findings shed light on the genetic architecture of the disease in Bos indicus, and present potential regions for fine mapping and downstream analysis in future.

Nuclear magnetic resonance spectroscopy to investigate the association between milk metabolites and udder quarter health status in dairy cows

Nuclear magnetic resonance spectroscopy was applied to investigate the association between milk metabolome and udder quarter health status in dairy cows. Mammary gland health status was defined by combining information provided by traditional somatic cell count (SCC) and differential SCC (DSCC), which expresses the percentage of neutrophils and lymphocytes over total SCC. Quarter milk samples were collected in triplicate (d 1 to 3) from 10 Simmental cows, 5 defined as cases and 5 defined as controls according to SCC levels at d 0. A total of 120 samples were collected and analyzed for bacteriology, milk composition, SCC, DSCC, and milk metabolome. Bacteriological analysis revealed the presence of mostly coagulase-negative staphylococci in quarter milk samples of cows defined as cases. Nuclear magnetic resonance spectra of all quarter samples were first analyzed using the unsupervised multivariate approach principal component analysis, which revealed a specific metabolomic fingerprint of each cow. Then, the supervised cross-validated orthogonal projections to latent structures discriminant analysis unquestionably showed that each cow could be very well identified according to its milk metabolomic fingerprint (accuracy = 95.8%). The comparison of 12 different models, built on bucketed 1-dimensional NOESY spectra (noesygppr1d, Bruker BioSpin) using different SCC and DSCC thresholds, corroborated the assumption of improved udder health status classification ability by joining information provided by both SCC and DSCC. Univariate analysis performed on the 34 quantitated metabolites revealed lower levels of riboflavin, galactose, galactose-1-phosphate, dimethylsulfone, carnitine, hippurate, orotate, lecithin, succinate, glucose, and lactose, and greater levels of lactate, phenylalanine, choline, acetate, O-acetylcarnitine, 2-oxoglutarate, and valine, in milk samples with high somatic cells. In the 5 cases, results of the udder quarter with the highest SCC compared with its symmetrical relative were in line with quarter-level findings. Our study suggests that increased SCC is associated with changes in milk metabolite fingerprint and highlights the potential use of different metabolites as novel indicators of udder health status and milk quality.

MILK LIPIDS AND SUBCLINICAL MASTITIS

This article deals with the process of obtaining quality raw milk by analyzing its lipid composition. The lipid composition of raw milk depends on many factors, among which, first of all, is the species, the composition of the diet and the physiological state of the breast. In recent years, a large amount of data has accumulated on the fluctuations of certain lipid parameters of milk depending on the type, age, lactation, diet, time of year, exercise, animal husbandry technology, physiological state of the lactating organism in general and breast status in particular. Factors of regulation of fatty acid composition of raw milk: genetically determined parameters of quality and safety; fatty acid composition of the diet; synthesis of fatty acids by microorganisms of the digestive tract; synthesis of fatty acids in the breast; physiological state of the breast. The milk of each species of productive animals has its own specific lipid profile and is used in the formulation of certain dairy products to obtain the planned technological and nutritional parameters. Diagnosis of productive animals for subclinical mastitis involves the use of auxiliary (thermometry, thermography, electrical conductivity) and laboratory research methods: counting the number of somatic cells; use of specialized tests; microbiological studies of milk; biochemical studies of milk. The biochemical component in the diagnosis of subclinical forms of mastitis is underestimated. An increase in body temperature implies an increase in the intensity of heat release during the oxidation of substrates, sometimes due to a decrease in the intensity of synthesis of energy-intensive compounds. There are simply no other sources of energy in the body. The situation is the same with certain parts of the metabolism, which are aimed at the development of protective reactions to the etiological factor aimed at the defeat of the breast. That is why the biochemical composition of breast secretions in the absence of clinical signs of mastitis undergoes biochemical changes and the task of scientists is to develop mechanisms for clear tracking of such changes, identification of animals with subclinical forms of mastitis and effective treatment.

Comparison of machine learning methods to predict udder health status based on somatic cell counts in dairy cows

Bovine mastitis is one of the most important economic and health issues in dairy farms. Data collection during routine recording procedures and access to large datasets have shed the light on the possibility to use trained machine learning algorithms to predict the udder health status of cows. In this study, we compared eight different machine learning methods (Linear Discriminant Analysis, Generalized Linear Model with logit link function, Naïve Bayes, Classification and Regression Trees, k-Nearest Neighbors, Support Vector Machines, Random Forest and Neural Network) to predict udder health status of cows based on somatic cell counts. Prediction accuracies of all methods were above 75%. According to different metrics, Neural Network, Random Forest and linear methods had the best performance in predicting udder health classes at a given test-day (healthy or mastitic according to somatic cell count below or above a predefined threshold of 200,000 cells/mL) based on the cow’s milk traits recorded at previous test-day. Our findings suggest machine learning algorithms as a promising tool to improve decision making for farmers. Machine learning analysis would improve the surveillance methods and help farmers to identify in advance those cows that would possibly have high somatic cell count in the subsequent test-day.

Advances in therapeutic and managemental approaches of bovine mastitis: a comprehensive review

Mastitis (intramammary inflammation) caused by infectious pathogens is still considered a devastating condition of dairy animals affecting animal welfare as well as economically incurring huge losses to the dairy industry by means of decreased production performance and increased culling rates. Bovine mastitis is the inflammation of the mammary glands/udder of bovines, caused by bacterial pathogens, in most cases. Routine diagnosis is based on clinical and subclinical forms of the disease. This underlines the significance of early and rapid identification/detection of etiological agents at the farm level, for which several diagnostic techniques have been developed. Therapeutic regimens such as antibiotics, immunotherapy, bacteriocins, bacteriophages, antimicrobial peptides, probiotics, stem cell therapy, native secretory factors, nutritional, dry cow and lactation therapy, genetic selection, herbs, and nanoparticle technology-based therapy have been evaluated for their efficacy in the treatment of mastitis. Even though several strategies have been developed over the years for the purpose of managing both clinical and subclinical forms of mastitis, all of them lacked the efficacy to eliminate the associated etiological agent when used as a monotherapy. Further, research has to be directed towards the development of new therapeutic agents/techniques that can both replace conventional techniques and also solve the problem of emerging antibiotic resistance. The objective of the present review is to describe the etiological agents, pathogenesis, and diagnosis in brief along with an extensive discussion on the advances in the treatment and management of mastitis, which would help safeguard the health of dairy animals.

Efficacy Prediction of Four Pharmaceutical Formulations for Intramammary Administration Containing Aloe vera (L.) Burm. f. Combined With Ceftiofur or Cloxacillin in Lactating Cows as an Alternative Therapy to Treat Mastitis Caused by Staphylococcus aureus

Synergy or additive effect between Aloe vera (L.) Burm.f. and beta-lactam (β-lactam) antibiotics has been reported against Staphylococcus aureus, one of the most important etiological agents of cow mastitis. The goal of the present study was to predict the efficacy of intramammary formulations containing the Aloe vera gel extract in the combination with cloxacillin or ceftiofur at low concentrations in lactating cows as an alternative therapy. Each quarter of 20 healthy Holstein Friesian lactating cows were treated with a single dose of one of the following formulations, corresponding to one of these treatment groups: A1, A2, A3, and A4. A1 and A2 contained cloxacillin at 0.25 and 0.5 mg/ml, whereas A3 and A4 contained ceftiofur 0.25 and 0.5 mg/ml, respectively. In addition, all formulations contained 600 mg/ml of an alcoholic extract of Aloe vera. Milk samples were taken at predefined time points. Antibiotics and aloin (active compound of Aloe vera) concentrations were assessed by liquid chromatography mass spectrometry system (LC-MS/MS). Pharmacokinetic profiles were obtained, and the efficacy index, the fraction of dosing interval in which the antimicrobial concentration remains above the minimum inhibitory concentrations (MICs) (T > MIC) for each formulation, was calculated considering MIC values against Staphylococcus aureus ATCC 29213 as obtained for the combination Aloe vera + antibiotic and aloin concentration in the extract. Mammary gland safety assessment was performed for each combination. Values of the main efficacy index for this study, T > MIC (h) for Aloe vera were 23.29, 10.50, 27.50, and 13.89, whereas for cloxacillin or ceftiofur were 19.20, 10.9, 19.74, and 15.63, for A1, A2, A3, and A4, respectively. Only A1 and A3 reached aloin and antibiotic recommended values as predictors of clinical efficacy for cloxacillin, ceftiofur, and aloin (50, 70, and 60%, respectively), assuming a dose interval of 24 h. The efficacy index values obtained suggest that A1 and A3 might be an effective therapy to treat bovine mastitis caused by S. aureus after a single dose. Nevertheless, further trials in S. aureus mastitis clinical cases are mandatory to confirm the efficacy of Aloe vera formulations.

Identification of SNPs Associated with Somatic Cell Score in Candidate Genes in Italian Holstein Friesian Bulls

Mastitis is an infectious disease affecting the mammary gland, leading to inflammatory reactions and to heavy economic losses due to milk production decrease. One possible way to tackle the antimicrobial resistance issue stemming from antimicrobial therapy is to select animals with a genetic resistance to this disease. Therefore, aim of this study was to analyze the genetic variability of the SNPs found in candidate genes related to mastitis resistance in Holstein Friesian bulls. Target regions were amplified, sequenced by Next-Generation Sequencing technology on the Illumina® MiSeq, and then analyzed to find correlation with mastitis related phenotypes in 95 Italian Holstein bulls chosen with the aid of a selective genotyping approach. On a total of 557 detected mutations, 61 showed different genotype distribution in the tails of the deregressed EBVs for SCS and 15 were identified as significantly associated with the phenotype using two different approaches. The significant SNPs were identified in intergenic or intronic regions of six genes, known to be key components in the immune system (namely CXCR1, DCK, NOD2, MBL2, MBL1 and M-SAA3.2). These SNPs could be considered as candidates for a future genetic selection for mastitis resistance, although further studies are required to assess their presence in other dairy cattle breeds and their possible negative correlation with other traits.

Heritability of Teat Condition in Italian Holstein Friesian and Its Relationship with Milk Production and Somatic Cell Score

In spite of the impressive advancements observed on both management and genetic factors, udder health still represents one of most demanding objectives to be attained in the dairy cattle industry. Udder morphology and especially teat condition might represent the first physical barrier to pathogens' access. The objectives of this study were to investigate the genetic component of teat condition and to elucidate its relationship with both milk yield and somatic cell scores in dairy cattle. Moreover, the effect of selection for both milk yield and somatic cell scores on teat condition was also investigated. A multivariate analysis was conducted on 10,776 teat score records and 30,160 production records from 2469 Italian Holstein cows. Three teat scoring traits were defined and included in the analysis. Heritability estimates for the teat score traits were moderate to low, ranging from 0.084 to 0.238. When teat score was based on a four-classes ordinal scoring, its genetic correlation with milk yields and somatic cell score were 0.862 and 0.439, respectively. The scale used to classify teat-end score has an impact on the magnitude of the estimates. Genetic correlations suggest that selection for milk yield could deteriorate teat health, unless more emphasis is given to somatic cell scores. Considering that both at national and international level, the current selection objectives are giving more emphasis to health traits, a further genetic deterioration in teat condition is not expected.

Role of the JAK-STAT Pathway in Bovine Mastitis and Milk Production

Simple Summary

The cytokine-activated Janus kinase (JAK)—signal transducer and activator of transcription (STAT) pathway has an important role in the regulation of immunity and inflammation. In addition, the signaling of this pathway has been reported to be associated with mammary gland development and milk production. Because of such important functions, the JAK-STAT pathway has been widely targeted in both human and animal diseases as a therapeutic agent. Recently, the JAK2, STATs, and inhibitors of the JAK-STAT pathway, especially cytokine signaling suppressors (SOCSs), have been reported to be associated with milk production and mastitis-resistance phenotypic traits in dairy cattle. Thus, in the current review, we attempt to overview the development of the JAK-STAT pathway role in bovine mastitis and milk production.

Abstract

The cytokine-activated Janus kinase (JAK)—signal transducer and activator of transcription (STAT) pathway is a sequence of communications between proteins in a cell, and it is associated with various processes such as cell division, apoptosis, mammary gland development, lactation, anti-inflammation, and immunity. The pathway is involved in transferring information from receptors on the cell surface to the cell nucleus, resulting in the regulation of genes through transcription. The Janus kinase 2 (JAK2), signal transducer and activator of transcription A and B (STAT5 A & B), STAT1, and cytokine signaling suppressor 3 (SOCS3) are the key members of the JAK-STAT pathway. Interestingly, prolactin (Prl) also uses the JAK-STAT pathway to regulate milk production traits in dairy cattle. The activation of JAK2 and STATs genes has a critical role in milk production and mastitis resistance. The upregulation of SOCS3 in bovine mammary epithelial cells inhibits the activation of JAK2 and STATs genes, which promotes mastitis development and reduces the lactational performance of dairy cattle. In the current review, we highlight the recent development in the knowledge of JAK-STAT, which will enhance our ability to devise therapeutic strategies for bovine mastitis control. Furthermore, the review also explores the role of the JAK-STAT pathway in the regulation of milk production in dairy cattle.

Genome-Wide DNA Methylation Analysis of Mammary Gland Tissues From Chinese Holstein Cows With Staphylococcus aureus Induced Mastitis

Staphylococcus aureus intramammary infection is one of the most common causes of chronic mastitis in dairy cows, whose development may be associated with epigenetic changes in the expression of important host defense genes. This study aimed to construct a genome-wide DNA methylation profile of the mammary gland of Chinese Holstein cows (n = 3) following experimentally induced S. aureus mastitis, and to explore the potential gene regulatory mechanisms affected by DNA methylation during S. aureus mastitis. DNA was extracted from S. aureus-positive (n = 3) and S. aureus-negative (n = 3) mammary gland quarters and subjected to methylation-dependent restriction-site associated DNA sequencing (Methyl-RAD Seq). Results showed that CmCGG/CmCWGG DNA methylation sites were unevenly distributed and concentrated on chromosomes 5, 11, and 19, and within intergenic regions and intron regions of genes. Compared with healthy control quarters, 9,181 significantly differentially methylated (DM) CmCGG sites and 1,790 DM CmCWGG sites were found in the S. aureus-positive quarters (P < 0.05, |log2FC| > 1). Furthermore, 363 CmCGG differently methylated genes (DMGs) and 301 CmCWGG DMGs (adjusted P < 0.05, |log2FC| > 1) were identified. Gene ontology and KEGG enrichment analysis indicated that CmCGG DMGs are involved in immune response pathways, while the CmCWGG DMGs were mainly enriched in gene ontology terms related to metabolism. The mRNAs of 526 differentially methylated CmCGG genes and 124 differentially methylated CmCWGG genes were also significantly differentially expressed (RNA-Seq data) in the same samples, herein denoted differentially methylated and expressed genes (DMEGs) (P < 0.05). Functional enrichment analysis of DMEGs revealed roles related to biological processes, especially the regulation of immune response to diseases. CmCGG DMEGs like IL6R, TNF, BTK, IL1R2, and TNFSF8 enriched in several immune-related GO terms and pathways indicated their important roles in host immune response and their potential as candidate genes for S. aureus mastitis. These results suggest potential regulatory roles for DNA methylation in bovine mammary gland processes during S. aureus mastitis and serves as a reference for future epigenetic regulation and mechanistic studies.

Selection for Favorable Health Traits: A Potential Approach to Cope with Diseases in Farm Animals

Disease is a global problem for animal farming industries causing tremendous economic losses (>USD 220 billion over the last decade) and serious animal welfare issues. The limitations and deficiencies of current non-selection disease control methods (e.g., vaccination, treatment, eradication strategy, genome editing, and probiotics) make it difficult to effectively, economically, and permanently eliminate the adverse influences of disease in the farm animals. These limitations and deficiencies drive animal breeders to be more concerned and committed to dealing with health problems in farm animals by selecting animals with favorable health traits. Both genetic selection and genomic selection contribute to improving the health of farm animals by selecting certain health traits (e.g., disease tolerance, disease resistance, and immune response), although both of them face some challenges. The objective of this review was to comprehensively review the potential of selecting health traits in coping with issues caused by diseases in farm animals. Within this review, we highlighted that selecting health traits can be applied as a method of disease control to help animal agriculture industries to cope with the adverse influences caused by diseases in farm animals. Certainly, the genetic/genomic selection solution cannot solve all the disease problems in farm animals. Therefore, management, vaccination, culling, medical treatment, and other measures must accompany selection solution to reduce the adverse impact of farm animal diseases on profitability and animal welfare.

Identification of novel molecular markers of mastitis caused by Staphylococcus aureus using gene expression profiling in two consecutive generations of Chinese Holstein dairy cattle

Background

Mastitis in dairy cows caused by Staphylococcus aureus is a major problem hindering economic growth in dairy farms worldwide. It is difficult to prevent or eliminate due to its asymptomatic nature and long persistence of infection. Although transcriptomic responses of bovine mammary gland cells to pathogens that cause mastitis have been studied, the common responses of peripheral blood leukocytes to S. aureus infection across two consecutive generations of dairy cattle have not been investigated.

Methods

In the current study, RNA-Seq was used to profile the transcriptomes of peripheral blood leukocytes sampled from S. aureus-infected mothers and their S. aureus-infected daughters, and also healthy non-infected mothers and their healthy daughters. Differential gene expression was evaluated as follows: 1) S. aureus-infected cows versus healthy non-infected cows (S vs. H, which include all the mothers and daughters), 2) S. aureus-infected mothers versus healthy non-infected mothers (SM vs. HM), and 3) S. aureus-infected daughters versus healthy non-infected daughters (SMD vs. HMD).

Results

Analysis of all identified expressed genes in the four groups (SM, SMD, HM, and HMD) showed that EPOR, IL9, IFNL3, CCL26, IL26 were exclusively expressed in both the HM and HMD groups, and that they were significantly (P <  0.05) enriched for the cytokine-cytokine receptor interaction pathway. A total of 17, 13 and 10 differentially expressed genes (DEGs) (FDR P_adj. < 0.1 and |FC| > 1.2) were detected in the three comparisons, respectively. DEGs with P <  0.05 and |FC| > 2 were used for functional enrichment analyses. For the S vs. H comparison, DEGs detected included CCL20, IL13 and MMP3, which are associated with the IL-17 signaling pathway. In the SM vs. HM and SMD vs. HMD comparisons, five (BLA-DQB, C1R, C2, FCGR1A, and KRT10) and six (BLA-DQB, C3AR1, CFI, FCAR, FCGR3A, and LOC10498484) genes, respectively, were involved in the S. aureus infection pathway.

Conclusions

Our study provides insights into the transcriptomic responses of bovine peripheral blood leukocytes across two generations of cattle naturally infected with S. aureus. The genes highlighted in this study could serve as expression biomarkers for mastitis and may also contain sequence variation that can be used for genetic improvement of dairy cattle for resilience to mastitis.

Genotype by environment interaction for somatic cell score in Holstein cattle of southern Brazil via reaction norms

Objective

The objective of this study was to evaluate the genetic behavior of a population of Holstein cattle in response to the variation of environmental temperature by analyzing the effects of genotype by environment interaction (GEI) through reaction norms for the somatic cell score (SCS).

Methods

Data was collected for 67,206 primiparous cows from the database of the Paraná Holstein Breeders Association in Brazil, with the aim of evaluating the temperature effect, considered as an environmental variable, distinguished under six gradients, with the variation range found being 17°C to 19.5°C, over the region. A reaction norm model was adopted utilizing the fourth order under the Legendre polynomials, using the mixed models of analysis by the restricted maximum likelihood method by the WOMBAT software. Additionally, the genetic behavior of the 15 most representative bulls was assessed, in response to the changes in the temperature gradient.

Results

A mean score of 2.66 and a heritability variation from 0.17 to 0.23 was found in the regional temperature increase. The correlation between the environmental gradients proved to be higher than 0.80. Distinctive genetic behaviors were observed according to the increase in regional temperature, with an observed increase of up to 0.258 in the breeding values of some animals, as well as a reduction in the breeding of up to 0.793, with occasional reclassifications being observed as the temperature increased.

Conclusion

Non-relevant GEI for SCS were observed in Holstein cattle herds of southern Brazil. Thus, the inclusion of the temperature effect in the model of genetic evaluation of SCS for the southern Brazilian Holstein breed is not required.

Association of GH, STAT5A, MYF5 gene polymorphisms with milk somatic cell count, EC and pH levels of Holstein dairy cattle

This study was conducted to ivnestigate the associations of GH-AluI, STAT5A-AvaI and MYF5-TaqI gene polymorphisms with milk somatic cell count (SCC), electrical conductivity (EC) and pH levels in Holstein dairy cows. For this purpose, 167 blood and 1670 milk samples of 167 Holstein cows in their 2nd lactation were used. There were significant relationships between GH-AluI genotypes and milk EC (p < 0.001) and between STAT5A-AvaI genotypes and milk EC (p = 0.007), but there were not any significant relationships between MYF5 gene polymorphism and the investigated traits (p > 0.05). The greatest EC values were observed in GH-AluI-LV and STAT5A-AvaI-TT-genotyped individuals. Just because of association of EC with mastitis, it was concluded that present GH-AluI and STAT5A-AvaI polymorphisms could be used in further studies to be conducted to improve mastitis resistance and milk quality traits of Holstein dairy cows.

Bovine mastitis: risk factors, therapeutic strategies, and alternative treatments - A review

Bovine mastitis, an inflammation of the mammary gland, is the most common disease of dairy cattle causing economic losses due to reduced yield and poor quality of milk. The etiological agents include a variety of gram-positive and gram-negative bacteria, and can be either contagious (e.g., Staphylococcus aureus, Streptococcus agalactiae, Mycoplasma spp.) or environmental (e.g., Escherichia coli, Enterococcus spp., coagulase-negative Staphylococcus, Streptococcus uberis). Improving sanitation such as enhanced milking hygiene, implementation of post-milking teat disinfection, maintenance of milking machines are general measures to prevent new cases of mastitis, but treatment of active mastitis infection is dependant mainly on antibiotics. However, the extensive use of antibiotics increased concerns about emergence of antibiotic-resistant pathogens and that led the dairy industries to reduce the use of antibiotics. Therefore, alternative therapies for prevention and treatment of bovine mastitis, particularly natural products from plants and animals, have been sought. This review provides an overview of bovine mastitis in the aspects of risk factors, control and treatments, and emerging therapeutic alternatives in the control of bovine mastitis.

Effects of month of kidding, parity number, and litter size on milk yield of commercial dairy goats in Australia

The aim of this observational study was to identify the influence of key nongenetic factors such as month of kidding, parity, and litter size on milk yield and composition of Australian dairy goats throughout lactation. The study was conducted over 4 consecutive kidding seasons from June 2016 to March 2017. Data from 940 lactations of Saanen goats from a commercial herd were used to observe the effects of month of kidding, parity number, and litter size on total milk yield (L/goat) in early lactation (kidding to 90 d in milk; DIM), mid lactation (91-180 DIM), and late lactation (181-270 DIM), cumulative milk yield (from kidding to 270 DIM; CMY), average lactation length, proportion (%) of does reaching their target lactation length (270 DIM), somatic cell count (SCC), and percentages of milk fat and protein in early lactation. The mean herd responses throughout the entire study were as follows: CMY = 519 L/goat; lactation length = 233 d, with 70% of does reaching 270 DIM; milk fat = 4.2%; milk protein = 2.9%; and SCC = 6.2 × 10⁵ cells/mL. Average milk production peaked in February and was lowest in June (2.4 vs. 1.8 L/goat per day, respectively). Milk yield was affected by month of kidding, parity number, and litter size in all phases of lactation. November kidders had the greatest CMY, and March kidders had the lowest CMY. March kidders had the shortest lactation length and the lowest proportion of does reaching 270 DIM. June kidders had the longest lactation length, whereas September kidders had the highest proportion of does reaching 270 DIM. Maximum milk yield was attained in third parity. Goats in fourth or greater parity had the shortest lactation length, the lowest proportion of does reaching 270 DIM, and the highest SCC. Goats delivering single kids had lower CMY, lower SCC, and higher percentages of fat and protein than does delivering multiple kids. Our findings indicate that milk yield was primarily influenced by month of kidding, and the effects of month of kidding on milk yield were accentuated during mid lactation. However, the effects of month of kidding on milk yield varied significantly among parities.