Genomic dissection of the correlation between milk yield and various health traits using functional and evolutionary information about imputed sequence variants of 34,497 German Holstein cows.

BACKGROUND: Over the last decades, it was subject of many studies to investigate the genomic connection of milk production and health traits in dairy cattle. Thereby, incorporating functional information in genomic analyses has been shown to improve the understanding of biological and molecular mechanisms shaping complex traits and the accuracies of genomic prediction, especially in small populations and across-breed settings. Still, little is known about the contribution of different functional and evolutionary genome partitioning subsets to milk production and dairy health. Thus, we performed a uni- and a bivariate analysis of milk yield (MY) and eight health traits using a set of ~34,497 German Holstein cows with 50K chip genotypes and ~17 million imputed sequence variants divided into 27 subsets depending on their functional and evolutionary annotation. In the bivariate analysis, eight trait-combinations were observed that contrasted MY with each health trait. Two genomic relationship matrices (GRM) were included, one consisting of the 50K chip variants and one consisting of each set of subset variants, to obtain subset heritabilities and genetic correlations. In addition, 50K chip heritabilities and genetic correlations were estimated applying merely the 50K GRM. RESULTS: In general, 50K chip heritabilities were larger than the subset heritabilities. The largest heritabilities were found for MY, which was 0.4358 for the 50K and 0.2757 for the subset heritabilities. Whereas all 50K genetic correlations were negative, subset genetic correlations were both, positive and negative (ranging from -0.9324 between MY and mastitis to 0.6662 between MY and digital dermatitis). The subsets containing variants which were annotated as noncoding related, splice sites, untranslated regions, metabolic quantitative trait loci, and young variants ranked highest in terms of their contribution to the traits` genetic variance. We were able to show that linkage disequilibrium between subset variants and adjacent variants did not cause these subsets` high effect. CONCLUSION: Our results confirm the connection of milk production and health traits in dairy cattle via the animals` metabolic state. In addition, they highlight the potential of including functional information in genomic analyses, which helps to dissect the extent and direction of the observed traits` connection in more detail.

Highly Pathogenic Avian Influenza A(H5N1) Clade 2.3.4.4b Virus Infection in Domestic Dairy Cattle and Cats, United States, 2024.

We report highly pathogenic avian influenza A(H5N1) virus in dairy cattle and cats in Kansas and Texas, United States, which reflects the continued spread of clade 2.3.4.4b viruses that entered the country in late 2021. Infected cattle experienced nonspecific illness, reduced feed intake and rumination, and an abrupt drop in milk production, but fatal systemic influenza infection developed in domestic cats fed raw (unpasteurized) colostrum and milk from affected cows. Cow-to-cow transmission appears to have occurred because infections were observed in cattle on Michigan, Idaho, and Ohio farms where avian influenza virus-infected cows were transported. Although the US Food and Drug Administration has indicated the commercial milk supply remains safe, the detection of influenza virus in unpasteurized bovine milk is a concern because of potential cross-species transmission. Continued surveillance of highly pathogenic avian influenza viruses in domestic production animals is needed to prevent cross-species and mammal-to-mammal transmission.

Sialic Acid Receptor Specificity in Mammary Gland of Dairy Cattle Infected with Highly Pathogenic Avian Influenza A(H5N1) Virus.

In March 2024, the US Department of Agriculture's Animal and Plant Health Inspection Service reported detection of highly pathogenic avian influenza (HPAI) A(H5N1) virus in dairy cattle in the United States for the first time. One factor that determines susceptibility to HPAI H5N1 infection is the presence of specific virus receptors on host cells; however, little is known about the distribution of the sialic acid (SA) receptors in dairy cattle, particularly in mammary glands. We compared the distribution of SA receptors in the respiratory tract and mammary gland of dairy cattle naturally infected with HPAI H5N1. The respiratory and mammary glands of HPAI H5N1-infected dairy cattle are rich in SA, particularly avian influenza virus-specific SA α2,3-gal. Mammary gland tissues co-stained with sialic acids and influenza A virus nucleoprotein showed predominant co-localization with the virus and SA α2,3-gal. HPAI H5N1 exhibited epitheliotropism within the mammary gland, and we observed rare immunolabeling within macrophages.

Understanding mastitis: Microbiome, control strategies, and prevalence - A comprehensive review.

Mastitis significantly affects the udder tissue in dairy cattle, leading to inflammation, discomfort, and a decline in both milk yield and quality. The condition can be attributed to an array of microbial agents that access the mammary gland through multiple pathways. The ramifications of this ailment are not merely confined to animal welfare but extend to the financial viability of the livestock industry. This review offers a historical lens on mastitis, tracing its documentation back to 1851, and examines its global distribution with a focus on regional differences in prevalence and antimicrobial resistance (AMR) patterns. Specific microbial genes and communities implicated in both mastitis and AMR are explored, including Staphylococcus aureus, Streptococcus agalactiae,Streptococcus dysagalactiae, Streptococcus uberis Escherichia coli, Klebsiella pneumoniae, Mycoplasma bovis, Corynebacterium bovis, among others. These microorganisms have evolved diverse strategies to elude host immune responses and neutralize commonly administered antibiotics, complicating management efforts. The review aims a comprehensive overview of the current knowledge and research gaps on mastitis and AMR, and to highlight the need for a One Health approach to address this global health issue. Such an approach entails multi-disciplinary cooperation to foster judicious antibiotic use, enhance preventive measures against mastitis, and bolster surveillance and monitoring of AMR in pathogens responsible for mastitis.

Prevalence and molecular characterization of extended-spectrum ß-lactamase-producing Escherichia coli isolates from dairy cattle with endometritis in Gansu Province, China.

BACKGROUND: The present study aimed to investigate the prevalence and molecular characterization of extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli (E. coli) isolated from dairy cattle with endometritis in China. The prevalence of ESBL-producing E. coli in sample was detected using ChromID ESBL agar, and genotyping of the ESBL producers was performed by PCR and DNA sequencing. RESULTS: The results revealed that the proportion of positive pathogens tested was 69.76% (180/258) in samples obtained from cows diagnosed with clinical endometritis, with E. coli accounting for 170 out of the 180 positive samples. The infection rate of isolated E. coli was 39.14% (101/258), and co-infections with other pathogens were prevalent. Furthermore, among the 158 E. coli isolates, 50 strains were identified as ESBL producers, with TEM and CTX-M prevalence rates at 78.00% and 32.00%, respectively. Drug sensitivity experiments indicated that 50 isolates of ESBL- producing E. coli were multidrug resistance (MDR), with 48.0% of them exhibiting positive results for both the class 1 integron gene and five gene cassettes associated with resistance to trimethoprim (dfr1 and dfrA17) and aminoglycosides (aadA1, aadA5, and dfrA1), respectively. CONCLUSION: This investigation demonstrated a substantial prevalence and heightened level of antimicrobial resistance among ESBL-producing E. coli isolates derived from dairy cattle infected with endometritis in China.

The possible role of haematophagous flies in the incidence of bovine teat papillomatosis.

The relationship between the incidence of bovine teat papillomatosis and the activity of haematophagous flies was investigated in Japan. A total of 15,737 flies consisting of 33 species were collected by dry ice-baited mosquito net (DMN) trap and a sweep net from udders of cattle. Simulium aokii (Takahasi) of Simuliidae (black flies) was the predominant species, followed by S. tobetsuense Ono and S. iwatense (Shiraki). Simulium aokii had the highest peak in October, followed by September. Numbers of blood spots from the bites per teat in nulliparous cattle were significantly correlated with numbers of S. aokii collected by DMN trap. Numbers of teats with warts and spots of blood from the bites per teat were significantly more abundant in anterior teats than posterior teats. The average incidence of teat papillomatosis in nulliparous cattle was significantly higher than that in parous cattle, and the highest incidence by month was in May, followed by April. Although bovine papillomavirus (BPV) DNA was not detected in flies examined, the presence of black flies and blood spots from their bites were associated with subsequent high incidence of growing warts. In particular, it would pay to give attention to species such as S. aokii that severely attack udders in the present locality. Further investigations for the detection of BPV DNA from flies parasitizing on teats are needed.

Association between prepartum vaginal temperature changes and placenta expulsion time in Holstein dairy cattle.

Retained placenta (RP) adversely affects postpartum productivity and reproduction in dairy cattle. Thus, methods to predict the occurrence of RP before calving would be desirable. Herein, we assessed whether vaginal temperature measurements (which have already been applied to detect calving) could be used to predict the occurrence of RP in cattle. A vaginal temperature recording device was inserted into the vagina of 49 pregnant Holstein-Friesian heifers (n = 16) and cows (n = 33); this device recorded the vaginal temperature every 5 min until the device dropped out at calving. Serum was collected 10 days before the expected calving date. The time points of calving and placental expulsion were identified via video recordings. We further calculated calving duration (temperature decrease to calving) and placenta expulsion time (PE time = calving to placenta expulsion). The PE times were divided into four categories (0-4 h, 4-8 h, 8-12 h, and RP at >12 h), while subsequent analysis revealed that an extension of the PE time dependent on the shortening of the calving duration (P < 0.05). The vaginal temperature patterns also differed in a PE time-dependent manner, and cows with RP did not show any re-elevation of vaginal temperature. Serum analyses indicated an energy deficiency in RP cattle. These results suggest that RP may be detected early as a specific change in the vaginal temperature associated with reproductive hormone secretion.

Prevalence, toxin-genotype distribution, and transmission of Clostridium perfringens from the breeding and milking process of dairy farms.

This study aimed to elucidate the distribution, transmission, and cross-contamination of Clostridium perfringens during the breeding and milking process from dairy farms. The prevalence of 22.3% (301/1351) yielded 494 C. perfringens isolates; all isolates were type A, except for one type D, and 69.8% (345/494) of the isolates carried atyp. cpb2 and only 0.6% (3/494) of the isolates carried cons. cpb2. C. perfringens detected throughout the whole process but without type F. 150 isolates were classified into 94 pulsed-field gel electrophoresis (PFGE) genotypes; among them, six clusters contained 34 PFGE genotypes with 58.0% isolates which revealed epidemic correlation and genetic diversity; four PFGE genotypes (PT57, PT9, PT61, and PT8) were the predominant genotypes. The isolates from different farms demonstrated high homology. Our study confirmed that C. perfringens demonstrated broad cross-contamination from nipples and hides of dairy cattle, followed by personnel and tools and air-introduced raw milk during the milking process. In conclusion, raw milk could serve as a medium for the transmission of C. perfringens, which could result in human food poisoning. Monitoring and controlling several points of cross-contamination during the milking process are essential as is implementing stringent hygiene measures to prevent further spread and reduce the risk of C. perfringens infection.

Unraveling the genetic basis of methane emission in dairy cattle: a comprehensive exploration and breeding approach to lower methane emissions.

Ruminant animals, such as dairy cattle, produce CH4, which contributes to global warming emissions and reduces dietary energy for the cows. While the carbon foot print of milk production varies based on production systems, milk yield and farm management practices, enteric fermentation, and manure management are major contributors togreenhouse gas emissions from dairy cattle. Recent emerging evidence has revealed the existence of genetic variation for CH4 emission traits among dairy cattle, suggests their potential inclusion in breeding goals and genetic selection programs. Advancements in high-throughput sequencing technologies and analytical techniques have enabled the identification of potential metabolic biomarkers, candidate genes, and SNPs linked to methane emissions. Indeed, this review critically examines our current understanding of carbon foot print in milk production, major emission sources, rumen microbial community and enteric fermentation, and the genetic architecture of methane emission traits in dairy cattle. It also emphasizes important implications for breeding strategies aimed at halting methane emissions through selective breeding, microbiome driven breeding, breeding for feed efficiency, and breeding by gene editing.

Assessment of Genomic Diversity and Selective Pressures in Crossbred Dairy Cattle of Pakistan.

Improving the low productivity levels of native cattle breeds in smallholder farming systems is a pressing concern in Pakistan. Crossbreeding high milk-yielding holstein friesian (HF) breed with the adaptability and heat tolerance of Sahiwal cattle has resulted in offspring that are well-suited to local conditions and exhibit improved milk yield. The exploration of how desirable traits in crossbred dairy cattle are selected has not yet been investigated. This study aims to provide the first overview of the selective pressures on the genome of crossbred dairy cattle in Pakistan. A total of eighty-one crossbred, thirty-two HF and twenty-four Sahiwal cattle were genotyped, and additional SNP genotype data for HF and Sahiwal were collected from a public database to equate the sample size in each group. Within-breed selection signatures in crossbreds were investigated using the integrated haplotype score. Crossbreds were also compared to each of their parental breeds to discover between-population signatures of selection using two approaches: cross-population extended haplotype homozygosity and fixation index. We identified several overlapping genes associated with production, immunity, and adaptation traits, including U6, TMEM41B, B4GALT7, 5S_rRNA, RBM27, POU4F3, NSD1, PRELID1, RGS14, SLC34A1, TMED9, B4GALT7, OR2AK3, OR2T16, OR2T60, OR2L3, and CTNNA1. Our results suggest that regions responsible for milk traits have generally experienced stronger selective pressure than others.

Frequency of isolation and phenotypic antimicrobial resistance of fecal Salmonella enterica recovered from dairy cattle in Canada.

Salmonellosis is one of the leading causes of gastrointestinal infections in humans. In Canada, it is estimated that approximately 87,500 cases of salmonellosis occur every year in humans, resulting in 17 deaths. In the United States, it is estimated that 26,500 hospitalizations and 420 deaths occur every year. In dairy cattle, infections caused by nontyphoidal Salmonella enterica can cause mild to severe disease, including enteritis, pneumonia, and septicemia. Our study objectives were to determine the proportion of fecal samples positive for Salmonella in dairy cattle in Canada and determine the resistance pattern of these isolates. We used data collected through the Canadian Dairy Network for Antimicrobial Stewardship and Resistance (CaDNetASR). Pooled fecal samples from preweaning calves, postweaning heifers, lactating cows, and manure storage were cultured for Salmonella, and the isolates were identified using matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Antimicrobial susceptibilities were determined using the minimum inhibitory concentration test, and resistance interpretation was made according to the Clinical and Laboratory Standards Institute. A 2-level, multivariable logistic regression model was built to determine the probability of recovering Salmonella from a sample, accounting for province, year, and sample source. The proportion of farms with at least one positive sample were 12% (17/140), 19% (28/144), and 17% (24/144) for the sampling years 2019, 2020, and 2021, respectively. Out of the 113 Salmonella isolates, 23 different serovars were identified. The occurrence of Salmonella appeared to be clustered by farms and provinces. The most common serovars identified were Infantis (14%) and Typhimurium (14%). Overall, 21% (24/113) of the Salmonella isolates were resistant to at least one antimicrobial. Resistance to tetracycline was commonly observed (17%); however, very limited resistance to category I antimicrobials (categorization according to Health Canada that includes third-generation cephalosporins, fluoroquinolones, polymyxins, and carbapenems) was observed, with one isolate resistant to amoxicillin and clavulanic acid. The proportion of Salmonella isolates resistant to 2 and 3 antimicrobial classes was 3.5% and 8.8%, respectively. Our study provided valuable information on the proportion of fecal samples positive for Salmonella, the serovars identified, and the associated resistance patterns across CaDNetASR herds, at regional and national levels.

Non-linear models of 15N partitioning kinetics in late lactation dairy cows from individually-labeled feed ingredients.

Few studies have examined the N kinetics of individual feeds with stable isotope tracing. We hypothesized that N partitioning to milk and excreta pools as well as the rates of the processes that drive this partitioning would differ for alfalfa silage, corn silage, corn grain, and soybean meal. Feed ingredients were endogenously labeled with 15N and included in 4 diets to create treatments with the same dietary composition and different labeled feed. Diets were fed to 12 late-lactation dairy cows for 4 d (96 h) and feces, urine, and milk collection proceeded during the 4 d of 15N enrichment and for 3 d (80 h) after cessation of label feeding. Nonlinear models of 15N enrichment and decay were fit to milk (MN), urine (UN), and fecal N (FN) in R with the nlme package and feed-specific parameter estimates were compared. The estimated proportions of feed N that were excreted in feces supported our understanding that N from soybean meal and corn grain is more digestible than N from alfalfa and corn silage. Estimates for the N partitioning between milk (MN) and urine (UN) from the 2 concentrate feeds (soybean meal and corn grain) indicated that UN:MN ratios were less than or equal to 1:1 indicating either more or equal nitrogen partitioning to milk compared with urine. It is important to maintain factual accuracy in representing the results rather than implying a desired outcome unsupported by the data. In contrast, UN:MN ratios for forage feeds (corn and alfalfa silage) were > 1:1, indicating more N partitioning to urine than milk. The modeled proportion of total FN that originated from feed N was 82.2% which is in line with previous research using a similar 15N measurement timeframe. However, the proportion of urinary and MN originating from feed N was much lower (60.5% for urine, 57.9% for milk), suggesting that approximately 40% of urinary and MN directly originate from body N sources related to protein turnover.

Invited review: Prevalence, risk factors, treatment, and barriers to best practice adoption for lameness and injuries in dairy cattle-A narrative review.

Lameness and leg injuries are both painful and prevalent across the dairy industry, and are a major welfare concern. There has been a considerable amount of research focused on investigating the risk factors associated with lameness and injuries and how they might be prevented and treated. The objectives of this narrative review were to summarize herd-level prevalence estimates, risk factors, strategies for prevention, control, and treatment of these conditions, and the barriers to best practice adoption for lameness and injuries on dairy farms. There is a relatively high within-herd prevalence of lameness on dairy farms globally, with a recent systematic review estimating the mean prevalence at 22.8%. Similarly, there is a relatively high prevalence of hock injuries, with within-herd estimates ranging from 12% to 81% of cows affected. Knee and neck injuries have been reported to be less common, with 6% to 43% and 1% to 33%, respectively. Numerous risk factors have been associated with the incidence of lameness, notably housing (e.g., access to pasture, bedding depth, bedding type, flooring type, stall design), management (e.g., stall cleanliness, frequency of trimming, holding times, stocking density), and cow-level (e.g., body condition, parity, injured hocks) factors. Risk factors associated with hock injuries can be similarly classified into housing (e.g., bedding type and depth, outdoor access, parlor type, stall design), management (e.g., bedding depth, cleanliness), and cow (e.g., parity, days in milk, lameness) factors. Key preventative approaches for lameness include routine preventative and corrective hoof trimming, improving hoof cushioning and traction through access to pasture or adding rubber flooring, deep-bedded stalls, sand bedding, ensuring appropriate stocking densities, reduced holding times, and the frequent use of routine footbaths. Very little research has been conducted on hock, knee, and neck injury prevention and recovery. Numerous researchers have concluded that both extrinsic (e.g., time, money, space) and intrinsic (e.g., farmer attitude, perception, priorities, and mindset) barriers exist to addressing lameness and injuries on dairy farms. There are many diverse stakeholders in lameness and injury management including the farmer, farm staff, veterinarian, hoof trimmer, nutritionist, and other advisors. Addressing dairy cattle lameness and injuries must, therefore, consider the people involved, as it is these people who are influencing and implementing on-farm decisions related to lameness prevention, treatment, and control.

Genetic and genomic evaluation of age at first calving in Italian Holsteins.

Age at first calving (AFC) represents the nonproductive period of ∼2 yr in Holstein cows, and thus, it has a relevant effect on the cost of rearing replacements in the dairy herd. In the present study, we aimed to evaluate genetic and genomic aspects of AFC in the Italian Holstein population. Data of 4,206,218 heifers with first calving between 1996 and 2020 were used. Age at first calving averaged 26.09 ± 3.07 mo and decreased across years. Heritability was estimated using a linear animal model which included the fixed effects of herd-year-season of birth and classes of gestation length, and the random animal additive genetic effect fitted to a pedigree-based relationship matrix. The EBV and genomically EBV (GEBV) were obtained, and they were standardized to mean 100 and standard deviation 5, where animals above the mean are those contributing to reduce AFC. Heritability estimates of AFC ranged from 0.031 to 0.045. The trend of sires' GEBV was favorable and indicated a reduced AFC across years. Approximate genetic correlations between GEBV of AFC and GEBV of other economically important traits were calculated on a subset of genotyped females born after 2015. Moderate favorable associations of AFC with production traits (0.39-0.51), udder depth (0.40), interval from first to last insemination in heifer (-0.43), and longevity (0.34) were assessed. Overall, the greatest lifetime productive performances and most favorable days open in first lactation were observed when heifers calved at 22 to 23 mo. In contrast, progeny of sires with GEBV of AFC above the mean yielded more milk, fat, and protein in first lactation, and had shorter days open than progeny of sires with GEBV of AFC below the mean. Results suggested that breeding strategies to improve AFC should be pursued, also considering genetic correlations between AFC and traits which are already part of the Italian Holstein breeding objective. The inclusion of AFC in an aggregate index is expected to contribute to enhance farm income.

Milk yield residuals and their link with the metabolic status of dairy cows in the transition period.

The transition period is one of the most challenging periods in the lactation cycle of high-yielding dairy cows. It is commonly known to be associated with diminished animal welfare and economic performance of dairy farms. The development of data-driven health monitoring tools based on on-farm available milk yield development has shown potential in identifying health-perturbing events. As proof of principle, we explored the association of these milk yield residuals with the metabolic status of cows during the transition period. Over 2 yr, 117 transition periods from 99 multiparous Holstein-Friesian cows were monitored intensively. Pre- and postpartum dry matter intake was measured and blood samples were taken at regular intervals to determine ß-hydroxybutyrate, nonesterified fatty acids (NEFA), insulin, glucose, fructosamine, and IGF1 concentrations. The expected milk yield in the current transition period was predicted with 2 previously developed models (nextMILK and SLMYP) using low-frequency test-day (TD) data and high-frequency milk meter (MM) data from the animal's previous lactation, respectively. The expected milk yield was subtracted from the actual production to calculate the milk yield residuals in the transition period (MRT) for both TD and MM data, yielding MRTTD and MRTMM. When the MRT is negative, the realized milk yield is lower than the predicted milk yield, in contrast, when positive, the realized milk yield exceeded the predicted milk yield. First, blood plasma analytes, dry matter intake, and MRT were compared between clinically diseased and nonclinically diseased transitions. MRTTD and MRTMM, postpartum dry matter intake and IGF1 were significantly lower for clinically diseased versus nonclinically diseased transitions, whereas ß-hydroxybutyrate and NEFA concentrations were significantly higher. Next, linear models were used to link the MRTTD and MRTMM of the nonclinically diseased cows with the dry matter intake measurements and blood plasma analytes. After variable selection, a final model was constructed for MRTTD and MRTMM, resulting in an adjusted R2 of 0.47 and 0.73, respectively. While both final models were not identical the retained variables were similar and yielded comparable importance and direction. In summary, the most informative variables in these linear models were the dry matter intake postpartum and the lactation number. Moreover, in both models, lower and thus also more negative MRT were linked with lower dry matter intake and increasing lactation number. In the case of an increasing dry matter intake, MRTTD was positively associated with NEFA concentrations. Furthermore, IGF1, glucose, and insulin explained a significant part of the MRT. Results of the present study suggest that milk yield residuals at the start of a new lactation are indicative of the health and metabolic status of transitioning dairy cows in support of the development of a health monitoring tool. Future field studies including a higher number of cows from multiple herds are needed to validate these findings.

A comprehensive meta-analysis of genetic parameters for resilience and productivity indicator traits in Holstein cattle.

Selection for resilience indicator (RIND) traits in Holstein cattle is becoming an important breeding objective as the worldwide population is expected to be exposed to increased environmental stressors due to both climate change and changing industry standards. However, genetic correlations between RIND and productivity indicator (PIND) traits, which are already being selected for and have the most economic value, are often unfavorable. As a result, it is necessary to fully understand these genetic relationships when incorporating novel traits into selection indices, so that informed decisions can be made to fully optimize selection for both groups of traits. In the past 2 decades, there have been many estimates of RIND traits published in the literature, albeit in small populations. To provide valuable pooled summary estimates, a random-effects meta-analysis was conducted for heritability and genetic correlation estimates for PIND and RIND traits in worldwide Holstein cattle. In total, 926 heritability estimates for 9 PIND and 27 RIND traits, along with 362 estimates of genetic correlation (PIND × RIND traits) were collected. Resilience indicator traits were grouped into the following subgroups: Metabolic Diseases, Hoof Health, Udder Health, Fertility, Heat Tolerance, Longevity, and Other. Pooled estimates of heritability for PIND traits ranged from 0.201 ± 0.05 (energy-corrected milk) to 0.377 ± 0.06 (protein content), while pooled estimates of heritability for RIND traits ranged from 0.032 ± 0.02 (incidence of lameness, incidence of milk fever) to 0.497 ± 0.05 (measures of body weight). Pooled estimates of genetic correlations ranged from -0.360 ± 0.25 (protein content vs. milk acetone concentration) to 0.535 ± 0.72 (measures of fat-to-protein ratio vs. milk acetone concentration). Additionally, out of 243 potential genetic correlations between PIND and RIND traits that could have been reported, only 40 had enough published estimates to implement the meta-analysis model. Our results confirmed that the interactions between PIND and RIND traits are complex, and all relationships should be evaluated when incorporating novel traits into selection indices. This study provides a valuable reference for breeders looking to incorporate RIND traits for Holstein cattle into selection indices.

Inbreeding depression for producer-recorded udder, metabolic, and reproductive diseases in US dairy cattle.

This study leveraged a growing dataset of producer-recorded phenotypes for mastitis, reproductive diseases (metritis and retained placenta), and metabolic diseases (ketosis, milk fever, and displaced abomasum) to investigate the potential presence of inbreeding depression for these disease traits. Phenotypic, pedigree, and genomic information were obtained for 354,043 and 68,292 US Holstein and Jersey cows, respectively. Total inbreeding coefficients were calculated using both pedigree and genomic information; the latter included inbreeding estimates obtained using a genomic relationship matrix and runs of homozygosity. We also generated inbreeding coefficients based on the generational inbreeding for recent and old pedigree inbreeding, for different run-of-homozygosity length classes, and for recent and old homozygous-by-descent segment-based inbreeding. Estimates on the liability scale revealed significant evidence of inbreeding depression for reproductive-disease traits, with an increase in total pedigree and genomic inbreeding showing a notable effect for recent inbreeding. However, we found inconsistent evidence for inbreeding depression for mastitis or any metabolic diseases. Notably, in Holsteins, the probability of developing displaced abomasum decreased with inbreeding, particularly for older inbreeding. Estimates of disease probability for cows with low, average, and high inbreeding levels did not significantly differ across any inbreeding coefficient and trait combination, indicating that although inbreeding may affect disease incidence, it likely plays a smaller role compared with management and environmental factors.

Genome-wide association and functional genomic analyses for various hoof health traits in North American Holstein cattle.

Hoof diseases are a major welfare and economic issue in the global dairy cattle production industry, which can be minimized through improved management and breeding practices. Optimal genetic improvement of hoof health could benefit from a deep understanding of the genetic background and biological underpinning of indicators of hoof health. Therefore, the primary objectives of this study were to perform genome-wide association studies, using imputed high-density genetic markers data from North American Holstein cattle, for 8 hoof-related traits: digital dermatitis, sole ulcer, sole hemorrhage, white line lesion, heel horn erosion, interdigital dermatitis, interdigital hyperplasia, and toe ulcer, and a hoof health index. De-regressed estimated breeding values from 25,580 Holstein animals were used as pseudo-phenotypes for the association analyses. The genomic quality control, genotype phasing, and genotype imputation were performed using the PLINK (version 1.9), Eagle (version 2.4.1), and Minimac4 software, respectively. The functional genomic analyses were performed using the GALLO R package and the DAVID platform. We identified 22, 34, 14, 22, 28, 33, 24, 43, and 15 significant markers for digital dermatitis, heel horn erosion, interdigital dermatitis, interdigital hyperplasia, sole hemorrhage, sole ulcer, toe ulcer, white line lesion disease, and the hoof health index, respectively. The significant markers were located across all autosomes, except BTA10, BTA12, BTA20, BTA26, BTA27, and BTA28. Moreover, the genomic regions identified overlap with various previously reported quantitative trait loci for exterior, health, meat and carcass, milk, production, and reproduction traits. The enrichment analyses identified 44 significant gene ontology terms. These enriched genomic regions harbor various candidate genes previously associated with bone development, metabolism, and infectious and immunological diseases. These findings indicate that hoof health traits are highly polygenic and influenced by a wide range of biological processes.

Antimicrobial resistance of Escherichia coli from dairy farms participating in an antimicrobial stewardship educational program for farm employees.

Antimicrobial use in food-producing animals is under increasing scrutiny due to the potential effect on the selection of antimicrobial-resistant bacteria that may be transmitted to humans by direct contact, with the food chain, or the environment. Novel data monitoring commensal Escherichia coli from dairy farms is essential for understanding antimicrobial resistance (AMR) patterns and their association with herd health management practices. The objectives of this study were to: (1) compare the prevalence of antimicrobial resistance in the E. coli isolates from the hospital, fresh, and mid-lactation pens from 18 conventional dairy farms participating in an educational training program in antimicrobial stewardship practices in California and Ohio, and (2) to characterize the prevalence of antimicrobial resistance of commensal E. coli isolated from pooled fecal pat samples before and 3 mo after participating in the educational training program. Pooled fecal pat samples were collected from the hospital pen, the fresh pen (1 to 5 DIM), and the mid-lactation pens (90 to 150 DIM) on conventional dairies in CA (n = 9) and OH (n = 9). Fecal samples were collected as part of a larger study using a quasi-experimental design that assigned farms to the training intervention group (TG; 6 per state) or the control group (CG; 3 per state). For the TG, farm worker(s) identified as having the task of diagnosis and treatment of adult cows on the farm participated in a training program on antimicrobial stewardship practices. Pooled fecal samples (n = 7) were collected at enrollment and 3 mo after completing the intervention on each of the participating farms (n = 18), followed by culture for E. coli isolation and antimicrobial sensitivity testing using the broth microdilution methodology. Logistic regression models were used to evaluate the association between E. coli antimicrobial resistance patterns with the training intervention and farm-level factors. No effect was observed in the prevalence of resistant isolates between the control and intervention farms after the training was delivered. Isolates from the hospital pens were 2.48 (95% CI: 1.06-6.22, P = 0.03) and 5.61 (95% CI: 1.94-16.91, P < 0.001) times, more likely to be resistant to streptomycin and chloramphenicol, respectively, than isolates from the mid-lactation pens. Our findings indicate there was a higher prevalence of AMR in E. coli associated with the hospital pen within the farm, while the training program for 3 mo did not affect the prevalence of AMR in E. coli on the farms participating in the program. Further research efforts should be conducted to identify factors driving AMR at the pen level, as well as approaches that could be used to reduce the risk of disseminating AMR from sick pens to animals being housed and to other pens on the farm.

Investigating the relationship between fluctuations in daily milk yield as resilience indicators and health traits in Holstein cattle.

Disease-related milk losses directly affect dairy herds' profitability and the production efficiency of the dairy industry. Therefore, this study aimed to quantify phenotypic variability in milk fluctuation periods related to diseases and to explore milk fluctuation traits as indicators of disease resilience. By combining high-frequency daily milk yield data with disease records of cows that were treated and recovered from the disease, we estimated milk variability trends within a fixed period around the treatment day of each record for 5 diseases: udder health, reproductive disorders, metabolic disorders, digestive disorders, and hoof health. The average milk yield decreased rapidly from 6 to 8 d before the treatment day for all diseases, with the largest milk reduction observed on the treatment day. Additionally, we assessed the significance of milk fluctuation periods highly related to diseases by defining milk fluctuations as a period of at least 10 consecutive days in which milk yield fell below 90% of the expected milk production values at least once. We defined the development and recovery phases of milk fluctuations using 3,847 milk fluctuation periods related to disease incidences, and estimated genetic parameters of milk fluctuation traits, including milk losses, duration of the fluctuation, variation rate in daily milk yield, and standard deviation of milk deviations for each phase and their genetic correlation with several important traits. In general, the disease-related milk fluctuation periods lasted 21.19 ± 10.36 d with a milk loss of 115.54 ± 92.49 kg per lactation. Compared with the development phase, the recovery phase lasted an average of 3.3 d longer, in which cows produced 11.04 kg less milk and exhibited a slower variation rate in daily milk yield of 0.35 kg/d. There were notable differences in milk fluctuation traits depending on the disease, and greater milk losses were observed when multiple diseases occurred simultaneously. All milk fluctuation traits evaluated were heritable with heritability estimates ranging from 0.01 to 0.10, and moderate to high genetic correlations with milk yield (0.34 to 0.64), milk loss throughout the lactation (0.22 to 0.97), and resilience indicator (0.39 to 0.95). These results indicate that cows with lower milk losses and higher resilience tend to have more stable milk fluctuations, which supports the potential for breeding for more disease-resilient cows based on milk fluctuation traits. Overall, this study confirms the high effect of diseases on milk yield variability and provides insightful information about their relationship with relevant traits in Holstein cattle. Furthermore, this study shows the potential of using high-frequency automatic monitoring of milk yield to assist on breeding practices and health management in dairy cows.