Invited review: A systematic literature review and meta-analysis of mortality and culling in dairy cattle

Exploring herd-level perinatal calf mortality risk factors in eastern Canadian dairy farms

This closed cohort study aimed to identify the associations between dairy calf management practices and herd-level perinatal calf mortality risk. From February 2020 to June 2021, predominantly Holstein dairy farms in Québec (n = 1,832) and New Brunswick (n = 52), Canada, that were registered in the dairy herd improvement program were visited once. A questionnaire covering all aspects of precalving, calving, and colostrum management was administered. Data regarding perinatal mortality were retrieved from the dairy herd improvement program database for each farm for 2021. Perinatal mortality was calculated for each farm as the proportion of calves dead at birth or dying within 24 h after birth. A multivariable negative binomial model was used to assess herd-level factors associated with the risk of perinatal mortality. The final model included the lying surface in the calving area, the typical time to first colostrum intake, typical cow-calf contact time, the proportion of males born, the proportion of assisted calvings, and herd size. Herd-level perinatal mortality risk ranged from 0% to 38.1% (mean ± SE = 7.6% ± 0.1%). A greater proportion of males born, a higher proportion of assisted calvings, and delayed colostrum feeding were associated with increased herd-level perinatal mortality. Factors associated with a decreased herd-level perinatal mortality risk were having a typical cow-calf contact time between 7 and 12 h after calving compared with reduced cow-calf contact time, soft lying surfaces in the calving area compared with concrete and mat-lying surfaces, and an increased number of calvings per year. Our results show that although some of the significant risk factors are not well understood (i.e., calving area lying surface, typical cow-calf contact time), Canadian farmers could focus on the factors under their control (i.e., time to first colostrum feeding, proportion of difficult calvings, males born, and calvings per year) to reduce the risk of perinatal mortality. Future work should focus on qualitative research to understand the dairy farmer motivations and limitations to implementing practices identified in this and other studies to reduce perinatal mortality.

Application of Epidemiological Methods in a Large-Scale Cross-Sectional Study in 765 German Dairy Herds-Lessons Learned

From 2016 to 2020, the "PraeRi" study, conducted by three German veterinary universities, was aimed at enhancing animal health and welfare in dairy farms. With 765 dairy farms visited and 101,307 animals examined, this study provided a basis for improving animal health and welfare. The study population comprised three different regions representing a broad variety of characteristics. To ensure representative estimates, a sample size of 250 farms was determined for each region, employing a stratified sampling plan based on farm size. According to the information provided by the farmers, the most commonly occurring disease in their herds was mastitis without general disorder (14.2% to 16.3% of the herd-depending on the region). For most disorders, prevalence data were lowest for the region South compared with the two remaining regions. Multivariable regression analyses were performed to identify risk factors for various target variables, and the results were communicated through individual reports and benchmarking flyers to participating farmers. The authors encountered challenges in management and communication due to the project's size in terms of personnel, data, and farms examined. Harmonizing data management and hypothesis testing across all involved parties added complexity.

Perinatal mortality in German dairy cattle: Unveiling the importance of cow-level risk factors and their interactions using a multifaceted modelling approach

Perinatal mortality (PM) is a common issue on dairy farms, leading to calf losses and increased farming costs. The current knowledge about PM in dairy cattle is, however, limited and previous studies lack comparability. The topic has also primarily been studied in Holstein-Friesian cows and closely related breeds, while other dairy breeds have been largely ignored. Different data collection techniques, definitions of PM, studied variables and statistical approaches further limit the comparability and interpretation of previous studies. This article aims to investigate the factors contributing to PM in two underexplored breeds, Simmental (SIM) and Brown Swiss (BS), while comparing them to German Holstein on German farms, and to employ various modelling techniques to enhance comparability to other studies, and to determine if different statistical methods yield consistent results. A total of 133,942 calving records from 131,657 cows on 721 German farms were analyzed. Amongst these, the proportion of PM (defined as stillbirth or death up to 48 hours of age) was 6.1%. Univariable and multivariable mixed-effects logistic regressions, random forest and multimodel inference via brute-force model selection approaches were used to evaluate risk factors on the individual animal level. Although the balanced random forest did not incorporate the random effect, it yielded results similar to those of the mixed-effect model. The brute-force approach surpassed the widely adopted backwards variable selection method and represented a combination of strengths: it accounted for the random effect similar to mixed-effects regression and generated a variable importance plot similar to random forest. The difficulty of calving, breed and parity of the cow were found to be the most important factors, followed by farm size and season. Additionally, four significant interactions amongst predictors were identified: breed-calving ease, breed-season, parity-season and calving ease-farm size. The combination of factors, such as secondiparous SIM breed on small farms and experiencing easy calving in summer, showed the lowest probability of PM. Conversely, primiparous GH cows on large farms with difficult calving in winter exhibited the highest probability of PM. In order to reduce PM, appropriate management of dystocia, optimal heifer management and a wider use of SIM in dairy production are possible ways forward. It is also important that future studies are conducted to identify farm-specific contributors to higher PM on large farms.

Effect of Addition of a Mixture of Ethyl Esters of Polyunsaturated Fatty Acid of Linseed Oil to Liquid Feed on Performance and Health of Dairy Calves

This study aimed to determine the effect of supplementing liquid feeds with a mixture of ethyl esters of polyunsaturated fatty acid of linseed oil (EEPUFA; α-linolenic acid-64.5%, linoleic acid-16.1%, and oleic acid-19.4%) on feed intake, body weight gain, feed efficiency, and health of dairy calves. Thirty-six healthy female Holstein-Friesian calves (7 d of age, 41.2 ± 4.0 kg) were assigned to one of two treatment groups (18 calves per group), i.e., control or EEPUFA, and fed liquid feed (whole milk (WM) or milk replacer (MR)) either without or with 10 mL/d of EEPUFA supplementation, respectively, for 56 days (till 63 d of age). Average daily intake of WM and MR was similar between treatments (p = 0.94). Average daily total DM intake and average daily starter feed DM intake were higher for the EEPUFA group (p = 0.05 and p = 0.01, respectively). The average daily body weight gain was also higher for the EEPUFA group (55 g/d; p = 0.03), although final body weight turned out not to be significantly different between groups (75.6 kg vs. 79.0 kg, control vs. EEPUFA, respectively; p = 0.20). Supplementation of liquid feeds with EEPUFA did not affect feed efficiency (p = 0.37) and most of investigated health parameters. However, the percentage of days with diarrhea relative to the number of days receiving treatment was higher in the control group than the EEPUFA group (76 vs. 42, respectively; p = 0.04). Although the results of this preliminary study are promising, further research is needed to establish the dose effect of EEPUFA on the performance and health of calves.

Estimation of genetic parameters of Holstein calf survival

Calf survival is not only an animal welfare issue but also helps to avoid huge losses in economic and genetic material due to calf mortality. Therefore, improving calf survival is essential in dairy breeding. The objective of this study was to explore the factors affecting the survival of Holstein calves in the Ningxia Region and to estimate the genetic parameters of calves using linear models and threshold models. Descriptive statistics were made for 43,847 Holstein calves born from 2018 to 2022 in Ningxia. The number of calves that died at 2-30 d was the highest, the survival rate was the lowest at 451-750 d, followed by 61-180 d and 2-30 d. Studies on the survival rates of calves born in different months have found that calves born in April have the lowest survival rates and calves born in October and December have higher survival rates. Calves born in autumn, third parity, and singleton calves are more likely to survive. The heritability of calf survival traits ranged from 0.002 ~ 0.136. Thus survival is a low heritability trait. Genetic correlation between different survival stages ranged from 0.3991 (2-30 d to 451-750 d) to 0.9985 (361-450 d to 451-750 d), the phenotypic correlation ranged from 0.1476 (2-30 d to 451-750 d) to 0.9582 (361-450 d to 451-750 d). The low genetic correlation between early and late survival suggests that survival in early and late stages may be influenced by different genetic factors. This study is helpful to understand the survival status of Holstein calves and provide a theoretical basis for improving the survival rate of calves.

Application of multiblock analysis to identify key areas and risk factors for dairy cow persistence

The present study analysed the importance of individual variables and different thematic blocks of production areas, management, and herd infectious disease status on cow persistence, characterised by herd on-farm mortality rate (MR), culling rate (CR), and mean age of culled cows (MAofCC) applying multiblock partial least squares (mbPLS) analysis. This study included 120 free-stall dairy herds with ≥ 100 cows. Data on the previous year's predominant cow housing system and management practices were collected, and on-farm measurements and cow scoring were performed. Bulk tank milk (BTM) and heifer blood samples (10 samples per herd) were collected and analysed for antibodies against the selected pathogens. In total, 172 variables were aggregated into 14 thematic blocks. The annual CR, MR, and MAofCC values were calculated for each herd. Thematic blocks with significant impact on cow persistence (included herd MR, CR and MAofCC) were 'infectious diseases' (block importance index out of all blocks = 13.6%, 95% CI 10.3; 20.5), 'fertility management' (16.3%, 95% CI 6.8; 26.9), 'lactating cow management' (11.5%, 95% CI 6.4; 17.8), 'milking' (11.3%, 95% CI 3.2; 17.1), 'herd characteristics' (10.1%, 95% CI 6.3; 14.2), 'close-up period management' (9.7%, 95% CI 2.7; 15.7), 'calving management' (7.9%, 95% CI 3.1; 11.4) and 'disease management' (7.3%, 95% CI 0.2; 12.0). Variable categories with the highest importance in explaining composite outcome including herd MR, CR and MAofCC were rear-end and udder lesions in ≥ 20% of the cows, BTM and heifers seropositive to bovine respiratory syncytial virus, vaccination against bovine herpesvirus 1, twice daily milking and herd location in Northwest region. Larger herd size, higher levels of milk yield, and rearing predominantly Holstein breed cattle were herd factors associated with poorer cow persistency. Grazing cows and having semi-insulated barns were associated with lower CR and MR, respectively. Heat detection and farm pregnancy testing strategies were significant factors in the fertility block. Using disposable dry papers for teat cleaning and not using any wet teat-cleaning tools were risk factors for high MR. A robotic milking system was protective for increased herd MR and CR. A high pre-calving body condition score and poor rear body cleanliness of ≥ 30% of cows were associated with inferior herd persistency outcomes. Calving in group pens with deep litter bedding was associated with a lower CR. Multiblock PLS model is innovative tool that helped to identify most influential farming areas but also single risk factors associated with cow persistency described by multiple parameters.

Prognostic potential of inflammatory markers, oxidative status, thrombocyte indices, and renal biochemical markers in neonatal calf diarrhoea-induced systemic inflammatory response syndrome

The study aimed to assess the prognostic value of inflammatory markers, indicators of oxidative stress, thrombocyte indices, and renal biochemical markers in neonatal calf diarrhoea (NCD) induced by systemic inflammatory response syndrome (SIRS) upon admission. A prospective, observational, and case-control study was conducted on 56 calves diagnosed with NCD. Mean concentrations of interleukin-6 (IL-6), malondialdehyde (MDA), glutathione (GSH), mean platelet volume (MPV), platelet distribution width (PDW), blood urea nitrogen (BUN), and creatinine (Crea) were measured. Furthermore, the neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) were also calculated for SIRS survivors [SIRS (survivor)] and non-survivors [SIRS (non-survivor)] induced by NCD. A prognostic cut-off value for predicting the prognosis of the SIRS's induced by NCD was obtained via receiver operating characteristic (ROC) curve analysis. Upon admission, the SIRS (non-survivor) calves had significantly higher (P < .001) average levels of IL-6, MDA, BUN, Crea, MPV, and PDW compared to the SIRS (survivor) calves and significantly lower (P < .001) average levels of GSH. Despite an apparent increase in the NLR and PLR values of calves diagnosed with SIRS, no significant difference was found between the survival and non-survivor SIRS cases. Positive predictive values (PPVs) for survival were determined as 100 %, 100 %, 80 %, 100 %, 80 %, and 80 %, respectively, using cut-off values of IL-6 (≤259.67 ng/L), MDA (≤2.87 nmol/mL), MPV (≤12.5 fL), PDW (≤34.25 %), BUN (≤168.3 mg/dL), and Crea (≤2.11 mg/dL). The determined threshold values are those obtained upon admission to the hospital. Based on the sensitivity, specificity, and PPVs derived from the ROC analysis, it has been concluded that IL-6, MDA, MPV, PDW, BUN, and Crea are the most relevant biomarkers used for predicting the prognosis of NCD-induced SIRS in calves. Furthermore, it is also noteworthy that IL-6 exhibited the highest effectiveness among all biomarkers.

Genetic parameters and evaluation of mortality and slaughter rate in Holstein and Jersey cows

The longevity of dairy cattle has economic, animal welfare, and health implications and is influenced by the frequency of mortality on the farm and sale for slaughter. In this study cows removed from the herd due to death or slaughter during the lactation were coded 1 and cows that were not terminated were coded 0. Genetic parameters for mortality rates (MR) and slaughter rates (SR) were estimated for Holstein (H) and Jersey (J) breeds by applying both linear (LM) and threshold (TM) sire models using about 1.2 million H and 286,000 J cows. Estimated breeding values (EBV) for MR and SR were predicted using animal models to assess the opportunity for selection and genetic trends. Cow termination data, recorded between 1990 and 2020 on a voluntary basis by Australian dairy farmers, were analyzed. Cow MR has increased from below 1% in the 1990s to 4.1% and 3.6% in recent years in H and J cows, respectively. Most dead cows (∼36%) left the herd before 120 d of lactation, while cows that were slaughtered left the herd toward the end of the lactation. Using the LM, heritability (h2) estimates for MR were lower (1%) than those for SR (2%-3.5%). When h2 were estimated using a TM, the estimates for both traits varied between 4% and 20%, suggesting that the difference in incidence level is one of the reasons for the difference in the h2 values between MR and SR. Early test-day milk yield (MY) and 305-d MY (305-d MY) have unfavorable genetic correlations (0.32-0.41) with MR in both breeds. The genetic correlations of calving interval with MR were stronger (0.54-0.68) than with SR (0.28-0.45) suggesting that poor fertility can serve as an early indicator of poor cow health that may lead to increased risk of death. High early test-day somatic cell count is genetically associated with increased likelihood of slaughter (0.24-0.46), but not with increased likelihood of death. In H, 305-d protein yield (PY) had the strongest genetic correlation (-0.34 to -0.40) with SR whereas in J, both 305-d PY and fat yield showed high genetic (-0.64 to -0.70) and moderate environmental (-0.35 to -0.37) correlations with SR. The genetic correlation of removal from the herd due to death and slaughter was negative (-0.3) in J and zero in H. Strong selection for improved fertility and survival and less selection emphasis for MY, has led to an improvement in the genetic trend for cow MR in H and the trend in J has stabilized. Although genetic evaluations for cow MR are feasible, the reliabilities of the EBV are low and the level of cow MR in Australia are relatively low compared with similar countries. Therefore, genetic evaluation for survival based on mortality and slaughter data could be sufficient in the current selection circumstances where breeding objectives are broadly defined. Nevertheless, all Australian farmers should be encouraged to continue recording mortality and slaughter data for monitoring of the trends and for future development of genetic evaluations.

The evolution of parasite virulence under targeted culling and harvesting in wildlife and livestock

There is a clear need to understand the effect of human intervention on the evolution of infectious disease. In particular, culling and harvesting of both wildlife and managed livestock populations are carried out in a wide range of management practices, and they have the potential to impact the evolution of a broad range of disease characteristics. Applying eco-evolutionary theory we show that once culling/harvesting becomes targeted on specific disease classes, the established result that culling selects for higher virulence is only found when sufficient infected individuals are culled. If susceptible or recovered individuals are targeted, selection for lower virulence can occur. An important implication of this result is that when culling to eradicate an infectious disease from a population, while it is optimal to target infected individuals, the consequent evolution can increase the basic reproductive ratio of the infection, R 0 , and make parasite eradication more difficult. We show that increases in evolved virulence due to the culling of infected individuals can lead to excess population decline when sustainably harvesting a population. In contrast, culling susceptible or recovered individuals can select for decreased virulence and a reduction in population decline through culling. The implications to the evolution of virulence are typically the same in wildlife populations, that are regulated by the parasite, and livestock populations, that have a constant population size where restocking balances the losses due to mortality. However, the well-known result that vertical transmission selects for lower virulence and transmission in wildlife populations is less marked in livestock populations for parasites that convey long-term immunity since restocking can enhance the density of the immune class. Our work emphasizes the importance of understanding the evolutionary consequences of intervention strategies and the different ecological feedbacks that can occur in wildlife and livestock populations.

Graduate Student Literature Review: The problem of calf mortality on dairy farms

Calf mortality can be used as an indicator of animal health and welfare on dairy farms. However, several challenges surround the estimation and reporting of this metric, specifically: (1) lack of records or reliable data, (2) methods of data collection, and (3) inconsistencies in calculation and definitions used. Therefore, despite its importance, the lack of consensus on a definition of calf mortality makes it difficult to compare mortality rates between dairy farms or studies. Monitoring factors associated with calf mortality is vital to create preventative strategies. Although common strategies have been set about how to raise dairy calves and manage dairy calves, discrepancies among studies evaluating factors associated with calf mortality still exist. This review summarizes research on the evaluation of calf mortality and associated risk factors, specifically, the lack of reliable data and standardization of the definition of calf mortality. In addition, current strategies to monitor and prevent calf mortality will be presented in this review.

High risk of dairy cow mortality in early lactation

BACKGROUND

On-farm mortality among dairy cows constitutes a major problem in modern dairy production. Detailed knowledge about when cows die may help guide the prevention of future deaths.

METHODS

Data from 46,927 on-farm dairy cow deaths reported to the Danish Cattle Database were analysed to evaluate the distribution of deaths in relation to time after calving and the effect of parity and breed.

RESULTS

Of all on-farm deaths, 15.2% occurred within 7 days after calving, 32.2% within 30 days and 49.4% within 90 days. Older cows generally died sooner after calving compared to younger cows, and Jersey cows died later than other breeds.

LIMITATIONS

The results are based on a large and reliable dataset but include only data from Danish dairy cows.

CONCLUSION

The distribution of on-farm deaths was very uneven, with a large proportion of deaths occurring during the first few weeks after calving, especially in older cows.

Dutch dairy farmers' perspectives on culling reasons and strategies

Since the abolishment of the milk quota system in Europe in 2014 and the introduction of environmental policies such as the phosphate rights system in the Netherlands, the reasons for culling dairy cows might have changed. The aim of this study was to determine the culling reasons for dairy cattle and to identify farmers' culling strategies and their intentions regarding the alteration of indicated culling strategies. To this end, an online questionnaire was distributed among dairy farmers nationally that resulted in 207 responses. Results showed that the most frequent culling reasons were related to problems with reproduction, udder, and hoof health. Primiparous cows were primarily culled for miscellaneous reasons such as injury, reproduction failure, and low milk yield. Multiparous cows were culled predominantly for reproduction failure, udder health and hoof health reasons. Most respondents indicated that they consider formulating a culling strategy, based on certain rules of thumb regarding the most common reasons for culling. Most farmers also reported that culling decisions on their farms were perceived to be unavoidable, though reproductive culling decisions are primarily voluntary. Most respondents stated that they intended to reduce the culling rate for better economic gain did not intend to alter the amount of replacement stock reared. The applied rules of thumb regarding culling strategies do not seem to have changed since the policy changes in dairy farming. The question remains whether farmers' rules of thumb might have made them unaware of the actual economic consequences of their culling strategies under the altered situation.

A focus group study exploring dairy farmers' perspectives of cull cow management in Ontario, Canada

Introduction

Maintaining the welfare of cull dairy cows from the farm to slaughter is an ongoing challenge for the dairy industry. Recent research suggests that some cull dairy cows within the marketing system are in physical states that are below regulatory standards, and further research is required to determine why these unfit cows are found throughout the journey to abattoirs. Since dairy farms are the origin of these cows, decision making by dairy farmers has been identified as key to preventing cull cows that are considered unfit for transport from entering the marketing system. The objectives of this study were to understand dairy farmers' perspectives on their cull dairy cow management practices, recommendations and requirements of regulations, management tools, and welfare issues.

Methods

Four focus groups with a total of 21 participants were each conducted virtually, video recorded, and transcribed verbatim, with dairy farmers from Ontario, Canada. A thematic analysis of focus group discussions was conducted utilizing deductive reasoning.

Results

There were three themes identified including deciding to cull or not, management of cows being culled, and knowledge and perceptions of cull cow regulations. When making culling decisions, farmers utilize multiple sources of information including personal experiences and values and external referents like veterinarians, family members and other farmers. The welfare of their cows was a high priority but one that was often weighed against the financial outcomes of culling decisions. Finally, most participants considered recent regulatory changes for the management of cows before shipment to be of little importance on their farms.

Discussion

In conclusion, the farmers from this study showed the diversity of considerations they make in culling decisions and the large contribution of animal productivity and economic factors. There was a general lack of knowledge of recent regulatory changes for the shipment of cull cows, and there is room for improving the uptake of new recommendations for culling only cows fit for transportation.

An observational study of ear-tagged calf mortality (1 to 100 days) on Irish dairy farms and associations between biosecurity practices and calf mortality on farms participating in a Johne's disease control program

Postnatal mortality among replacement stock has a detrimental effect on the social, economic, and environmental sustainability of dairy production. Calf mortality rates vary between countries and show differences in temporal trends; most, however, are characterized by high levels of between-farm variability. Explaining this variation can be difficult because herd-level information on management practices relevant to calf health is often not available. The Irish Johne's Control Programme (IJCP) contains a substantial on-farm monitoring program called the Veterinary Risk Assessment and Management Plan (VRAMP). Although this risk assessment is largely focused on factors relevant to the transmission of paratuberculosis, many of its principles are good practice biocontainment policies that are also advocated for the protection of calf health. The objectives of this study were (1) to quantify mortality in ear-tagged Irish dairy calves between 2016 and 2020 using both survival and risk approaches, (2) to determine risk factors for 100-d cumulative mortality hazard in ear-tagged Irish dairy calves between 2016 and 2020, (3) to determine whether 100-d cumulative mortality hazard was higher in ear-tagged calves within herds registered in the IJCP versus those that were not registered in the IJCP and whether there were differences between these cohorts over time, and (4) within IJCP herds, to determine whether VRAMP score or changes in VRAMP score were associated with 100-d cumulative mortality hazard. Excluding perinatal mortality, the overall 100-d cumulative mortality hazard was 4.1%. Calf mortality was consistently underestimated using risk approaches that did not account for calf censoring. Cox proportional hazards models showed that cumulative mortality hazard was greater in male calves; particularly, calves born to Jersey breed dams and those with a beef breed sire. Mortality hazard increased with increasing herd size, was highest in calves born in herds that contract-reared heifers, and lowest in those born in mixed dairy-beef enterprises. Mortality hazard decreased over time with the mortality hazard in 2020 being 0.83 times that of 2016. Mortality hazard was higher in IJCP-registered herds than nonregistered herds (hazard ratio 1.06, 95% CI 1.01-1.12), likely reflecting differences in herds that enrolled in the national program. However, we detected a significant interaction between IJCP status (enrolled vs. not enrolled) and year (hazard ratio 0.96, 95% CI 0.92-1.00), indicating that the decrease in mortality hazard between 2016 and 2020 was greater in IJCP herds versus non-IJCP herds. Finally, increasing VRAMP scores (indicating higher risk for paratuberculosis transmission) were positively associated with increased calf mortality hazard. Postnatal calf mortality rates in Irish dairy herds declined between 2016 and 2020. Our study suggests that implementation of recommended biocontainment practices to control paratuberculosis in IJCP herds was associated with a reduction in calf mortality hazard.

Welfare of dairy cows

This Scientific Opinion addresses a European Commission's mandate on the welfare of dairy cows as part of the Farm to Fork strategy. It includes three assessments carried out based on literature reviews and complemented by expert opinion. Assessment 1 describes the most prevalent housing systems for dairy cows in Europe: tie-stalls, cubicle housing, open-bedded systems and systems with access to an outdoor area. Per each system, the scientific opinion describes the distribution in the EU and assesses the main strengths, weaknesses and hazards potentially reducing the welfare of dairy cows. Assessment 2 addresses five welfare consequences as requested in the mandate: locomotory disorders (including lameness), mastitis, restriction of movement and resting problems, inability to perform comfort behaviour and metabolic disorders. Per each welfare consequence, a set of animal-based measures is suggested, a detailed analysis of the prevalence in different housing systems is provided, and subsequently, a comparison of the housing systems is given. Common and specific system-related hazards as well as management-related hazards and respective preventive measures are investigated. Assessment 3 includes an analysis of farm characteristics (e.g. milk yield, herd size) that could be used to classify the level of on-farm welfare. From the available scientific literature, it was not possible to derive relevant associations between available farm data and cow welfare. Therefore, an approach based on expert knowledge elicitation (EKE) was developed. The EKE resulted in the identification of five farm characteristics (more than one cow per cubicle at maximum stocking density, limited space for cows, inappropriate cubicle size, high on-farm mortality and farms with less than 2 months access to pasture). If one or more of these farm characteristics are present, it is recommended to conduct an assessment of cow welfare on the farm in question using animal-based measures for specified welfare consequences.

Prevalence and Concentration of Mycotoxins in Animal Feed in the Middle East and North Africa (MENA): A Systematic Review and Meta-Analysis

This study seeks a comprehensive meta-analysis of mycotoxin contaminants in animal feed consumed in the Middle East and North Africa (MENA) region. The obtained articles were reviewed, and 49 articles that investigated the contamination of mycotoxins including aflatoxins (AFs), deoxynivalenol (DON), zearalenone (ZEA), T-2 toxin, fumonisins (FUM), and ochratoxin A (OTA), in feed samples or components of animal feed in the MENA region were selected. The titles of the final articles included in the study were meta-analyzed. Necessary information was extracted and categorized from the articles, and a meta-analysis was performed using Stata software. The highest contamination was in dry bread (80%), and Algeria was the most contaminated country (87% of animal feed), with the most mycotoxins contaminating AFs (47%) and FUM (47%). The highest concentration of mycotoxins in animal feed is related to FUM (1240.01 μg/kg). Climate change, economic situation, agricultural and processing methods, the nature of the animal feed, and improper use of food waste in animal feed are among the most critical factors that are effective in the occurrence of mycotoxin contamination in animal feed in MENA. Control of influential factors in the occurrence of contaminations and rapid screening with accurate identification methods to prevent the occurrence and spread of mycotoxin contamination of animal feed seem important.

Necropsy-based study on dairy cow mortality-Underlying causes of death

The worldwide problem of increasing dairy cow mortality is widespread in modern production systems, it causes economic losses, and indicates problems with herd health and welfare. Most studies on causes of dairy cow mortality are limited as they are based on secondary register data, or questionnaires for producers or veterinarians, and neither necropsies nor histopathologic analyses are usually performed. For this reason, no definite causes for dairy cow deaths have been determined making it difficult or impossible to implement effective preventive measures. The objectives of this study were to (1) determine the causes of on-farm mortality of Finnish dairy cows, (2) determine the usefulness of routine histopathologic analysis in bovine necropsies, and (3) assess how reliable producers' perception about the cause of death is. Underlying diagnoses of on-farm deaths were determined through necropsy of 319 dairy cows at an incineration plant. The necropsy data were combined with background information obtained from online questionnaires covering cow and herd records. Mastitis was the most common underlying diagnosis of death (26.6%), followed by digestive disorders (15.4%), other known disorders (13.8%), calving-associated disorders (12.2%), and locomotion disorders (11.9%). The underlying diagnoses of death varied during different stages of lactation and with parity. A large proportion of the study cows (46.7%) died during the first 30 d after calving, and of those, 63.6% died during the first 5 d. A routine histopathologic analysis was performed in every necropsy, and it changed the preliminary gross diagnosis in 18.2% of the cases. Producers' perception about the cause of death agreed with the necropsy-based underlying diagnosis of death in 42.8% of the cases. It was most consistent for mastitis, calving disorders, locomotion diseases, and accidents. In cases where producers had no insights about the cause of death, necropsy revealed the final underlying diagnosis in 88.2% of cases, demonstrating the usefulness of necropsy. Based on our findings, necropsies provide useful and reliable information to develop control programs for cow mortality. Including routine histopathologic analysis in necropsies, more accurate information may be obtained. Furthermore, targeting preventive measures on transitional cows may be most effective, as the number of deaths was highest at this time.

The association of herd performance indicators with dairy cow longevity: An empirical study

The associations between reproductive performance, milk yield and health status with the risk of culling, and thus with a cow's longevity, have been well documented at the individual cow level. Associations at individual cow level may, however, not be valid at herd level due to interrelated herd management aspects and/or policy restrictions. The objective of this study was to explore the association of herd performance indicators with herd-level dairy cow longevity under Dutch production conditions. Longevity was expressed by three different measures, viz. age at culling, lifetime milk production of culled cows and culling rate. The evaluated herd performance indicators included factors on milk production, youngstock rearing, reproduction and health performance as registered on 10 719 Dutch commercial dairy herds during the period 2007-2016. Averaged over herds and the evaluated period, the age of culled milking cows was 2 139 days (5.8 years, SD±298 days), the lifetime milk production of culled cows was 31 238 kg (SD±7,494 kg), and the culling rate was 0.24 (SD±0.08). A mixed linear regression modelling approach was applied to evaluate the association of each of the three longevity measures with the selected herd performance indicators. The results indicated that only four herd performance indictors (herd size, herd expansion, heifer ratio and the proportion of cows with potential subclinical ketosis) shared significant associations with all three longevity variables. Generally, the strength of the associations between each of the evaluated longevity measures and herd performance indicators was only limited. The absence of strong associations between the longevity measures and herd performance indicators reveal that there is potential of extending cattle longevity without affecting the herd performance in terms of milk production, reproduction and health. Moreover, only part of the observed variance in longevity among the herds over time was explained by the herd performance variables, indicating that differences in longevity at herd level may predominantly be determined by other factors, like farmers' attitude and strategic management.

Transcriptional changes detected in fecal RNA from neonatal dairy calves of different breeds following gastrointestinal disease of varying severity

Gastrointestinal (GI) disease is a major health concern in preweaned dairy calves. The objective of this fixed cohort study was to use RNA isolated from preweaned Holstein and Jersey heifer calf feces to study the molecular adaptations to variable clinical GI disease. The study was conducted on a commercial calf ranch in the western U.S. Enrolled calves were assessed twice daily for variations in demeanor, milk intake, and hydration. Fecal consistency scores were recorded at enrollment (day 1), and on the day (day 10) that a fecal sample was collected for differential gene expression (DGE). Calves with diarrhea on either day were classified as having either uncomplicated, localized GI disease (scours), or systemic GI disease (systemic enteritis). Eighty-four calves' fecal RNA was evaluated for DGE, of which 33 calves (n = 20 Holstein; n = 13 Jersey) were consistently healthy. The remaining 51 calves (n = 23 Holstein; n = 28 Jersey) experienced varying severity of GI disease during the sampling window. Genes of interest were related to the inflammatory response (i.e., IFNG, NFKB1, NOD2, TLR2, and TLR4) and cell membrane or cytoplasmic transport (i.e., AQP3, FABP2, KRT8 and SLC5A1). Breed-specific findings indicated that AQP3, IFNG, and TLR4 were upregulated in Holsteins with systemic enteritis, whereas KRT8 was downregulated in systemically affected Jerseys. Holsteins did not appear affected by scours aside from a tendency for DGE of toll-like receptors (TLRs) on the day of diarrhea. However, Jersey calves consistently demonstrated a tendency to upregulate IFNG, NFKB1, and TLR4 when affected with either scours or systemic enteritis. These findings were more pronounced in systemically affected Jersey calves and were observed as a delayed response to both scours and systemic enteritis. These findings support previous observations suggesting that Holstein calves may be better equipped than Jersey calves to rapidly fight pathogen invasion.

Clinical Scoring Systems in the Newborn Calf: An Overview

Simple Summary

Clinical scores are gaining increasing popularity in veterinary medicine thanks to their multiple advantages, which include quickness, ease, and convenience of use. This review discusses the applications of some already-known clinical scores in newborn calf management at birth and during the first weeks of age. Clinical scores are employed to assess newborn calf viability and to diagnose and monitor neonatal calf diarrhea and respiratory diseases, helping the clinician promptly recognize calves needing medical assistance. This review discusses limitations pertaining to their use and encourages efforts towards a greater consistency in definition and validation.

Abstract

A scoring system is an instrument that enables the scorers, including farmers, technicians, and veterinarians, to adopt a systematic approach for diagnosis or monitoring, as it decreases bias and confounding and increases objectivity. Practically, it is a number assigned to a patient that correlates with a probability that a diagnosis can be confirmed or that a specific outcome will follow. This article examines the clinical scores designed or adapted to bovine medicine that aim to assess newborn calf viability and to diagnose and monitor neonatal calf diarrhea and respiratory diseases, helping the clinician promptly recognize calves needing medical assistance. Despite the large number of clinical scores described in the literature, these are still barely used in farm animal practice; possibly, the complexity of the scores and missing recommendations for intervention are reasons for their lack of popularity as well as the crosswise lack of consistency among scores designed for the same purpose. Further research is needed in this regard to increase scores validation and encourage their application in bovine calf neonatology.

Incidence and Treatments of Bovine Mastitis and Other Diseases on 37 Dairy Farms in Wisconsin

The aim of this research was to describe the incidence and treatments of mastitis and other common bovine diseases using one year of retrospective observational data (n = 50,329 cow-lactations) obtained from herd management software of 37 large dairy farms in Wisconsin. Incidence rate (IR) was defined as the number of first cases of each disease divided by the number of lactations per farm. Clinical mastitis (CM) remains the most diagnosed disease of dairy cows. Across all herds, the mean IR (cases per 100 cow-lactations) was 24.4 for clinical mastitis, 14.5 for foot disorders (FD), 11.2 for metritis (ME), 8.6 for ketosis (KE), 7.4 for retained fetal membranes (RFM), 4.5 for diarrhea (DI), 3.1 for displaced abomasum (DA), 2.9 for pneumonia (PN) and 1.9 for milk fever (MF). More than 30% of cows that had first cases of CM, DA, RFM, DI, and FD did not receive antibiotics. Of those treated, more than 50% of cows diagnosed with PN, ME and CM received ceftiofur as a treatment. The IR of mastitis and most other diseases was greater in older cows (parity ≥ 3) during the first 100 days of lactation and these cows were more likely to receive antibiotic treatments (as compared to younger cows diagnosed in later lactation). Cows of first and second parities in early lactation were more likely to remain in the herd after diagnosis of disease, as compared to older cows and cows in later stages of lactation. Most older cows diagnosed with CM in later lactation were culled before completion of the lactation. These results provide baseline data for disease incidence in dairy cows on modern U.S. dairy farms and reinforce the role of mastitis as an important cause of dairy cow morbidity.

Mortality and culling of adult dairy cows in Jordan: A 3-year study (2016-2018) based on a single intensively managed dairy farm

Background and Aim

Dairy cow mortality and culling are important parameters reflecting on cow health, productivity, and welfare as well as important determinants of herd sustainability, growth, and profitability. There are no published reports on the causes and rates of mortality and culling of dairy cows in Jordan. Therefore, the objectives of this study were to determine the most common causes and rates of mortality and culling of adult dairy cows in Jordan using a single well-managed dairy farm as a model over 3 years.

Materials and Methods

Data extracted from the farm management record software over 3 years (January 2016-December 2018) were used in this study. Cow-specific data included the date and month of sale, death or euthanasia, age, parity, reproductive status, and daily milk yield. Cow health-specific data included physical examination findings, presumptive diagnosis, medical or surgical treatments, postmortem findings, and any available laboratory findings. Descriptive analysis was performed to determine means (± standard deviation) and frequencies of various variables using Excel Spreadsheets of Microsoft Word 10.

Results

The 3-year rolling cow population in the farm used in the study was 500 ± 35. The overall mortality and culling rates were 5.9% and 28.5%, respectively. The mean age of died and culled cows was 3 ± 1.2 and 4 ± 1.5 years, respectively. The mortality rates were highest in the colder months (January through April). The most frequent causes of mortality were infectious diseases (28%), followed by non-infectious gastrointestinal diseases (25%), udder and teat diseases (mastitis 22%), and other diseases/accidents (25%). Of the infectious diseases, the most frequently diagnosed were enterotoxemia (12%), tuberculosis (TB) (8%), enteric salmonellosis (7%), and paratuberculosis (1%). The most frequently diagnosed non-infectious gastrointestinal diseases were traumatic reticulitis (11%), vagal indigestion (9%), and abomasal ulcer (5%). The most frequently diagnosed diseases causing mortality involving other body systems were reproductive diseases (acute puerperal metritis 6%), respiratory diseases (pneumonia 5% and pulmonary embolism 1%), metabolic diseases (fatty liver 3%), musculoskeletal diseases (septic arthritis 3% and downer cow syndrome 4%), neurologic diseases (unspecified causes 2%), and finally accidents (electrocution 1%). The most frequent causes of culling were old age/low milk production (39%), followed by the poor reproductive performance (31%), diseases/accidents (24%), and unidentified causes (6%). The most frequent diseases/accidents causing culling were udder diseases (mastitis 32%), followed by non-infectious gastrointestinal diseases (28%) (vagal indigestion [15%], rumen tympany [7%], and abomasal ulcer [6%]), musculoskeletal diseases (23%) (foot and claw diseases [7%], downer cow syndrome [7%], hip luxation [5%], septic arthritis [2%], and gastrocnemius rupture [2%]), respiratory diseases (pneumonia 10%), and finally infectious diseases (9%) (paratuberculosis [3%], hemorrhagic bowel syndrome [2%], and TB [2%]).

Conclusion

Results of this study showed that the majority of deaths and culling of dairy cows in Jordan are due to infectious diseases followed by non-infectious gastrointestinal diseases and mastitis. More efforts aiming at improving biosecurity standards, nutritional management, and mastitis prevention measures are required to limit the impact of disease on farm economy, animal health and productivity, and animal welfare in Jordan.

Cow culling patterns in eight commercial Estonian dairy herds and farmers' behaviour in reporting culling reasons

The present study aimed to reveal the culling-related metrics, identify the culling reason patterns for cows by developing and implementing the cow culling form (CCF), and analyse the concordance of farmers' stated culling reasons with those identified based on the CCF. A CCF was developed to register the disease history and conditions of cows that were related to culling. CCFs were completed by farm managers and veterinarians in eight dairy herds over a one-year period for slaughtered (n = 686) and dead (n = 250) cows. Completed CCFs were interpreted by the study authors to identify underlying, intermediate, influential, and immediate culling reasons. The identified culling reasons were compared to those reported by producers. The mean annual cow culling rate of the study farms was 31.8%, and the average on-farm mortality was 9.3%. Of the 250 cows that died on the farms, 43.6% were euthanised. Only 2% of the cows were slaughtered due to low milk yield. In total, 260 and 119 unique three-reason culling codes were created for slaughtered and dead cows, respectively. Single disease or condition causing slaughter or death of cows was identified in 44.8% and 52.0% of the cases, respectively. Producers' reported culling reasons concurred with the underlying culling reason in 72.6% and 63.6% of slaughtered and dead cows, respectively. A high variety of agreements between the farmers' reported and CCF-based culling codes was identified across single culling reasons. Improved registration of culling reasons is required to support informed herd-based decisions.

Culling and mortality of dairy cows: why it happens and how it can be mitigated

The United Nations estimates that the global population will total 9.7 billion in 2050. Rapid population growth pose a significant obstacle to achieving the Sustainable Development Goals, particularly eradicating hunger and poverty. In view of the expanding population growth, food production ideally should triple to prevent massive food shortages. Sustainable food and nutrition security is the focal point of the dairy industry. Dairy production plays a pivotal role in addressing and advancing global food and nutrition security. It serves as a major source of protein, calcium, and phosphorus in many families in developing countries with a fast-growing population. Consequently, the dairy industry is expected to grow by approximately 26% in the next 10 years and produce an estimated 1077 million tonnes of milk by 2050. However, the growth and distribution of the dairy industry is limited by many factors such as culling and mortality of dairy cows. Several studies highlight reproduction failures, old age, poor milk yield, diseases (mastitis, lameness, and dystocia), and heat stress as some reasons for culling of dairy cows. Hence, this review highlights the factors influencing culling and mortality in dairy production farms, and discusses mitigating measures to limit culling.

Identifying key genes in milk fat metabolism by weighted gene co-expression network analysis

Milk fat is the most important and energy-rich substance in milk, and its content and composition are important reference elements in the evaluation of milk quality. However, the current identification of valuable candidate genes affecting milk fat is limited. IlluminaPE150 was used to sequence bovine mammary epithelial cells (BMECs) with high and low milk fat rates (MFP), the weighted gene co-expression network (WGCNA) was used to analyze mRNA expression profile data in this study. As a result, a total of 10,310 genes were used to construct WGCNA, and the genes were classified into 18 modules. Among them, violet (r = 0.74), yellow (r = 0.75) and darkolivegreen (r =  − 0.79) modules were significantly associated with MFP, and 39, 181, 75 hub genes were identified, respectively. Combining enrichment analysis and differential genes (DEs), we screened five key candidate DEs related to lipid metabolism, namely PI4K2A, SLC16A1, ATP8A2, VEGFD and ID1, respectively. Relative to the small intestine, liver, kidney, heart, ovary and uterus, the gene expression of PI4K2A is the highest in mammary gland, and is significantly enriched in GO terms and pathways related to milk fat metabolism, such as monocarboxylic acid transport, phospholipid transport, phosphatidylinositol signaling system, inositol phosphate metabolism and MAPK signaling pathway. This study uses WGCNA to form an overall view of MFP, providing a theoretical basis for identifying potential pathways and hub genes that may be involved in milk fat synthesis.

Different methods of eubiotic feed additive provision affect the health, performance, fermentation, and metabolic status of dairy calves during the preweaning period

Background

This study aimed to evaluate whether different methods of providing eubiotic feed additives to neonatal calves, during the preweaning period, can improve the calves’ health, performance, ruminal fermentation, and metabolic status. Forty-four (3-day-old) Holstein–Friesian dairy calves (22 female and 22 male) were divided into four treatment groups for the duration of the 8-week trial. The eubiotic feed additive consisted of a combination of probiotic Lactobacillus spp. (multiple-strains at a dose of 250 mg/calf/day) and phytobiotics containing rosmarinic acid, as the main bioactive compound (at a dose of 50 mg/calf/day). The groups were named: CON (control, without eubiotic in either the milk replacer or the starter feed), MR (eubiotic in the milk replacer), SF (eubiotic in the starter feed), MRS (eubiotic in both the milk replacer and the starter feed). The individual intake of starter feed and the fecal scores were measured daily, and body weight and biometric measurements were taken weekly until calves were 56 days of age. Blood samples were collected on day 3 and then every 14 days to determine concentrations of insulin-like-growth-factor-I, β-hydroxybutyrate, non-esterified fatty acids, and blood urea nitrogen. Ruminal fluid was collected on days 28 and 56 for short-chain fatty acids, NH₃-N, and pH measurements.

Results

The body weight of the calves of the MR treatment group was higher compared to all other groups on days 28 and 56. Including the eubiotic feed additive in the milk replacer increased average daily gain, starter intake, and total dry matter intake from day 29 to day 56 and the overall experimental period compared to the CON group. The calves with MR treatment had lower fecal scores from days 3 to 28, a number of parasite oocysts/cysts per gram of feces on day 28, and the occurrences of fecal consistency scores of 3 (mild diarrhea) and 4 (severe diarrhea) were 3.2 and 3.0 times lower, respectively, compared with the CON group. The MR group had higher ruminal concentrations of short-chain-fatty-acids, propionate, and butyrate on day 56 than the CON group. Adding eubiotics into milk replacer resulted in the highest concentrations of blood insulin-like-growth-factor-I and β-hydroxybutyrate from days 29 to 56 and the overall experimental period.

Conclusion

The addition of eubiotic feed additives into the milk replacer can improve health, performance, ruminal fermentation, and biochemical blood indices in dairy calves during the preweaning period.

Interrelationship between diseases and calving season and their impact on reproductive parameters and milk production of tropical dairy cows

The interactions between calving season, the occurrence of retained placenta, intrauterine infections (IUI), and early mastitis, and their effects on the reproductive performance and milk yield of Holstein-Friesian cows in a tropical environment were studied using data from 3320 calvings (1948 cows) from two farms in El Salvador. Based on environmental conditions, season of calving was categorized into: quadrimester 1 (November-February), quadrimester 2 (March-June), and quadrimester 3 (July-October) where quadrimester 2 and 3 had the highest ambient temperature and relative humidity, respectively. Cows were classified into 1, 2, and 3 + parities. The effects of quadrimester and of diseases on days to first service, services per conception, days open, interval between services and 305-day milk yield were studied in separated multivariate regressions. The likelihood of experiencing a disease contingent on the calving season and the likelihood of a cow being culled due to poor fertility associated with experiencing a disease were evaluated using logistic regression. Cows calving in quadrimester 2 and 3 were more likely to suffer from IUI and showed poorer reproduction than cows calving in quadrimester 1. Reproduction was more strongly affected by IUI. Mastitis increased the days to first service, days open, and interval between services. Mastitis and IUI also caused a lower 305-day milk yield. Overall, hotter and more humid conditions lead to higher incidence of disease and poorer reproductive performance. The physiological responses that lead to these phenomena should be further studied to understand the interactions between diseases, environmental conditions and reproduction.

Overview of the practices of on-farm emergency slaughter of cattle in the Nordic countries

On farm mortality is an increasing problem in cattle production systems in the Nordic countries. It represents an economic loss to the farmer and raises questions of sustainability, food waste and animal welfare. On-farm emergency slaughter (OFES) represents, in some situations, an opportunity for a farmer to salvage some of the economic value from an animal that cannot be transported to a slaughterhouse. The basis of the regulation of OFES in the Nordic countries originates largely from legislation from the European Union. However, this review has found that the availability and practice of OFES in the Nordic countries differs considerably. For example, in Norway 4.2% of all cattle slaughter is OFES, whilst in Iceland OFES has never been recorded. National food safety authorities have issued differing regulations and guidelines regarding the suitability of sick and injured animals for OFES. This review shows there is a paucity of data regarding the incidence and reasons for the use of OFES of cattle in the Nordic countries and points out the need for more investigation into this area to improve veterinary education, consumer protection and animal welfare.

Management of calves in commercial dairy farms in Mecklenburg-Western Pomerania, Germany and its impact on calf mortality and prevalence of rotavirus and Cryptosporidium parvum infections in pre-weaned calves

In a cross-sectional study, impact of management in dairy farms on calf mortality rates and prevalence of rotavirus and Cryptosporidium parvum in feces of calves was investigated. Sixty-two commercial dairy herds in Mecklenburg-Western Pomerania, Germany, were stratified selected in 2019. We performed in-person interviews and fecal specimens in samples of all-female calves of age 7 up to 21 days. Management data were documented on farm level. A Multiscreen Ag-ELISA was performed to determine rotavirus and Cryptosporidium parvum. Associations between two calf mortality rates, detection of C. parvum and rotavirus, and predictors were examined with GLM models. In farms with routine vaccination against respiratory diseases, 31-days mortality rate was 4.2% +/-1.26 compared to 7.6% +/-0.97 (p = 0.040) on non-vaccinating farms. Six-months mortality was lower in farms that continued feeding milk to calves during periods of diarrhea compared to farms that did not (6.9% +/-0.8 vs. 12.4% +/-2.3). In case of a routine shifting of calves from the calving box into calf boxes less C. parvum was detected compared to an individual moving of calves (33.3% +/-2.6 vs. 19.6% +/-5.3; p = 0.024). Our model confirms a positive association between occurrence of aqueous feces and frequency of detection of C. parvum (45.4% +/-23.6 vs. 21.4% +/-18.7; p < 0.001). Frequency of detection of rotavirus was lower in farms that reported a defined amount of applicated colostrum per calf than in farms that presented a range of colostrum instead of a defined amount. This study indicates the potential for mitigation of risk factors for mortality in calves.

A review of factors affecting the welfare of dairy calves in pasture-based production systems

Current research on factors affecting the welfare of dairy calves is predominantly based on indoor, year-round calving systems. Calf rearing in these systems differs from that in more seasonal, pasture-based dairy production, meaning that risks to the welfare of dairy calves may not always be comparable between the two systems. The aim of this review was to consolidate the scientific literature relating to calf welfare in pasture-based dairy systems from birth until weaning, allowing for (1) the identification of current and emerging risks to calf welfare and (2) the formation of recommendations to mitigate these risks. Many of the risks to calf welfare discussed in this review are not exclusive to pasture-based dairies. This includes a global trend for increasing perinatal mortalities, a significant number of calves failing to achieve effective passive transfer of immunity, the low uptake of best practice pain relief when calves are disbudded, and the feeding of restricted milk volumes. In addition to these persisting welfare risks, two factors discussed in this review pose an immediate threat to the social license of dairy farming; the separation of cow and calf soon after birth and the management of surplus calves (i.e. calves not needed by the dairy industry). Several recommendations are made to improve the uptake of best-practice calf rearing and progress the development of alternative pasture-based rearing systems that accommodate changing community expectations. These include communication strategies that strengthen farmer beliefs regarding the welfare and productivity benefits achieved by best practice calf rearing and challenge beliefs regarding the associated costs. Farmers should also be encouraged to benchmark their rearing practices through improved record keeping of key rearing inputs and outcomes. Biological research is needed to advise the development of new calf rearing recommendations and the evolution of existing recommendations. Research priorities identified by this review include the effects of dystocia on the neonate and strategies to mitigate these effects, relationships between features of pen design and calf health and welfare, feasibility of dam rearing in large pasture-based dairy systems, and strategies that increase the value of the surplus calf.

Attitudes and personality of farm managers and association with cow culling rates and longevity in large-scale commercial dairy farms

The farmer has the central role in determining cow culling policies on their farm and thus affecting cow longevity. The present study aimed to examine farm managers´ satisfaction, attitudes, personality traits and analyse the associations with dairy cow culling and longevity in large commercial dairy farms. Farm managers of 116 dairy herds rearing at least 100 cows in freestall barns were included. A questionnaire for the farm managers registered personal background information of respondent and included statements capturing their satisfaction, opinions and attitudes regarding dairy cow culling and longevity, farming in general, and a Ten Item Personality Inventory scoring. For each herd, the last 12 months cow culling rate (CR, excluding dairy sale) and herd mean age of culled cows (MAofCC) was obtained from the Estonian Livestock Performance Recording Ltd. A K-mean clustering algorithm was applied to subgroup farm managers based on their attitudes, opinions and personality traits. The yearly mean herd CR was 33.0% and MAofCC was 60.6 months. Farm managers´ were mostly dissatisfied with cow longevity and culling rates in their farms. Dissatisfaction with culling rates and longevity, priority for producing high milk yields over longevity and production-oriented attitude was associated with high culling rates and poor longevity. Farm managers' personality had an effect on herd culling rates and their attitudes explained one third of the variability of culling rates and longevity. Explaining the economic consequences of high culling rates and decreased longevity, improving the visibility of these parameters together with benchmarking could bring these issues into focus.

Birth conditions affect the longevity of Holstein offspring

Studies of dairy cow longevity usually focus on the animal life after first calving, with few studies considering early life conditions and their effects on longevity. The objective was to evaluate the effect of birth conditions routinely collected by Dairy Herd Improvement agencies on offspring longevity measured as length of life and length of productive life. Lactanet provided 712,890 records on offspring born in 5,425 Quebec dairy herds between January 1999 and November 2015 for length of life, and 506,066 records on offspring born in 5,089 Quebec dairy herds between January 1999 and December 2013 for length of productive life. Offspring birth conditions used in this study were calving ease (unassisted, pull, surgery, or malpresentation), calf size (small, medium, or large), and twinning (yes or no). Observations were considered censored if the culling reason was "exported," "sold for dairy production," or "rented out" as well as if the animals were not yet culled at the time of data extraction. If offspring were not yet culled when the data were extracted, the last test-day date was considered the censoring date. Conditional inference survival trees were used in this study to analyze the effect of offspring birth conditions on offspring longevity. The hazard ratio of culling between the groups of offspring identified by the survival trees was estimated using a Cox proportional hazard model with herd-year-season as a frailty term. Five offspring groups were identified with different length of life based on their birth condition. Offspring with the highest length of life [median = 3.61 year; median absolute deviation (MAD) = 1.86] were those classified as large or medium birth size and were also the result of an unassisted calving. Small offspring as a result of a twin birth had the lowest length of life (median = 2.20 year; MAD = 1.69) and were 1.52 times more likely to be culled early in life. Six groups were identified with different length of productive life. Offspring that resulted from an unassisted or surgery calving and classified as large or medium when they were born were in the group with the highest length of productive life (median = 2.03 year; MAD = 1.63). Offspring resulting from a malpresentation or pull in a twin birth were in the group with the lowest length of productive life (median = 1.15 year; MAD = 1.11) and were 1.70 times more likely to be culled early in life. In conclusion, birth conditions of calving ease, calf size, and twinning greatly affected offspring longevity, and such information could be used for early selection of replacement candidates.

Culling and mortality of dairy cows: why it happens and how it can be mitigated

The United Nations estimates that the global population will total 9.7 billion in 2050. Rapid population growth pose a significant obstacle to achieving the Sustainable Development Goals, particularly eradicating hunger and poverty. In view of the expanding population growth, food production ideally should triple to prevent massive food shortages. Sustainable food and nutrition security is the focal point of the dairy industry. Dairy production plays a pivotal role in addressing and advancing global food and nutrition security. It serves as a major source of protein, calcium, and phosphorus in many families in developing countries with a fast-growing population. Consequently, the dairy industry is expected to grow by approximately 26% in the next 10 years and produce an estimated 1077 million tonnes of milk by 2050. However, the growth and distribution of the dairy industry is limited by many factors such as culling and mortality of dairy cows. Several studies highlight reproduction failures, old age, poor milk yield, diseases (mastitis, lameness, and dystocia), and heat stress as some reasons for culling of dairy cows. Hence, this review highlights the factors influencing culling and mortality in dairy production farms, and discusses mitigating measures to limit culling.

Growth performance and mammary gland development of Holstein calves fed milk with 15% solids and treated with growth promoters

The objective of this study was to evaluate growth performance, and mammary gland parenchyma (PAR) development in Holstein female calves fed whole milk combined with milk replacer for 15% total solids (15TS) or only milk (11% TS; 11TS). The effects of zilpaterol hydrochloride (ZH) and an estrogenic implant (EI) on growth performance, serum metabolites, and PAR development in post-weaning calves (63-90 days of age) fed 15TS or 11TS were also investigated. In the first phase, 78 calves were randomly divided into two groups (n = 39/group), 15TS, or 11TS (5 to 8 L/day; starter ad libitum). After weaning, calves were randomly assigned to four treatments, no EI, EI, ZH, and ZH-EI. In phase 1, 15TS calves had greater (P < 0.01) average body weight at weaning than 11TS calves (82.0 ± 5.8 vs. 74.1 ± 5.7 kg). Pre-weaning average daily gain (718 ± 67 vs. 576 ± 64 g/day) was higher (P < 0.01) for 15TS calves than 11TS calves. Feed/gain (1.5 ± 0.3 vs. 1.8 ± 0.3 kg of DMI/kg of gain) was lower (P < 0.01) for 15TS calves than 11TS calves. PAR area (8.8 ± 3.3 vs. 5.0 ± 1.6 cm²) was greater (P < 0.01) for 15TS calves than 11TS calves. No differences (P > 0.10) in average daily gain (986 ± 79 g/day across treatments) were observed in calves receiving ZH, EI, or ZH-EI fed 15TS or 11TS diets previously. However, the PAR area of 15TS calves administered ZH-EI was 2.2 times greater (P < 0.01) than 11TS calves with no ZH and CI. This study demonstrated the benefits of supplying milk with 15% TS for enhancing overall animal growth and PAR development. Further use of ZH and EI during the post-weaning period did improve mammary PAR growth.

The Whole and the Parts—A New Perspective on Production Diseases and Economic Sustainability in Dairy Farming

The levels of production diseases (PD) and the cow replacement rate are high in dairy farming. They indicate excessive production demands on the cow and a poor state of animal welfare. This is the subject of increasing public debate. The purpose of this study was to assess the effect of production diseases on the economic sustainability of dairy farms. The contributions of individual culled cows to the farm’s economic performance were calculated, based on milk recording and accounting data from 32 farms in Germany. Cows were identified as ‘profit cows’ when they reached their individual ‘break-even point’. Data from milk recordings (yield and indicators for PD) were used to cluster farms by means of a principal component and a cluster analysis. The analysis revealed five clusters of farms. The average proportion of profit cows was 57.5%, 55.6%, 44.1%, 29.4% and 19.5%. Clusters characterized by a high proportion of cows with metabolic problems and high culling and mortality rates had lower proportions of profit cows, somewhat irrespective of the average milk-yield per cow. Changing the perception of PD from considering it as collateral damage to a threat to the farms’ economic viability might foster change processes to reduce production diseases.

Dairy farm-workers' knowledge of factors responsible for culling and mortality in the Eastern Cape Province, South Africa

Milk serves as a significant source of protein for many families and aids in combating food insecurity. However, the demand for milk and milk-related products far exceeds the supply. The objective of the study was to evaluate dairy farm-workers' knowledge of factors responsible for culling and mortality of dairy cows in the Eastern Cape Province. Data was collected from 106 dairy farm-workers using a questionnaire. Any correctly answered question by the majority amounted to a point and a zero for incorrectly answered questions. Correct answering by the majority to more than half the questions of a subsection amounted to a pass. A less than 50% pass rate was considered a poor level of knowledge, 51-69% pass rate was considered an average level of knowledge, and anything higher than that was considered a good level of knowledge. Most farm-workers (66.0%) relied on their colleagues for dairy health information. Most dairy farm-workers (49.1%) indicated that lameness, milk fever (56.6%), and mastitis (47.2%) do not lead to culling and mortality of dairy cows. A majority (83%) of farm-workers agreed that reproduction problems, poor milk yield (77.3%), and age (81.1%) are the main reasons for culling dairy cows. The participants had varying perceptions and limited knowledge (28.3%) about the major contributing factors of culling and mortality. The lack of training courses and minimal use of other sources of information such as the internet might contribute to this poor knowledge and perceptions.

Vitamin E and beta-carotene status of dairy cows: a survey of plasma levels and supplementation practices

Culling rate in dairy cattle has increased considerably, thereby reducing cowś longevity and raising sustainability concerns worldwide. In the last decades, feeding systems have changed towards larger inclusion of preserved forages and reduced fresh herbage, which may limit vitamin E and beta-carotene dietary supply to dairy cows. Because of higher oxidative stress, engendered by greater milk production of modern genetics, the requirement for these nutrients is increased. Therefore, this study aimed to assess the current status of vitamin E and beta-carotene of commercial dairy cows. Blood vitamin E and beta-carotene concentrations were measured in 2 467 dairy cows from 127 farms in Belgium, Germany, Iberia and The Netherlands, that were visited once. Five cows were randomly selected per lactation stage per farm: Dry (between 30 and 1 day(s) before calving), Very-early (from calving until 15 days in milk (DIM)), Early (between 16 and 119 DIM), and Mid-late (from 120 DIM onwards). In addition, a survey was conducted to retrieve data on vitamin E and beta-carotene supplementation and feeding practices. Vitamin E and beta-carotene blood concentrations dropped considerably around calving. Among all surveyed cows, more than 75 and 44% were deficient in vitamin E and beta-carotene (i.e., blood concentration below 3.0 and 3.5 mg/l, respectively). Of the Very-early group, more than 97 and 78% of the cows were deficient in vitamin E and beta-carotene, respectively, with respective blood concentrations of 1.15 and 2.71 mg/l, which was significantly lower than the other lactation stages. Vitamin E and beta-carotene blood concentrations, as well as their supplementation levels, significantly varied among countries. Vitamin E and beta-carotene blood concentrations were positively related to the total estimated daily intakes of vitamin E and beta-carotene. Therefore, blood concentrations of vitamin E and beta-carotene depend on their respective level of intake, which is generally below recommendations and varies greatly between countries. Supplementation could contribute to provide cows with adequate amounts of vitamin E and beta-carotene all along the lactation, to ensure their lifetime performance and improve their fertility.

Pre-Weaned Calf Rearing on Northern Irish Dairy Farms: Part 1. A Description of Calf Management and Housing Design

The first few months of life are of great importance to the longevity and lifetime performance of dairy cows. The nutrition, environment and healthcare management of heifer calves must be sufficient to minimise exposure to stress and disease and enable them to perform to their genetic potential. Lack of reporting of farm management practices in Northern Ireland (NI) makes it difficult to understand where issues impacting health, welfare and performance may occur in the rearing process. The objective of this study was to investigate housing design and management practices of calves on 66 dairy farms across NI over a 3-month period and also identify areas that may cause high risk of poor health and performance in dairy calves. An initial survey was used to detail housing and management practices, with two subsequent visits to each farm used to collect animal and housing-based measurements linked to hygiene management, animal health and performance. Large variations in key elements such as weaning criteria and method, calf grouping method used, nutritional feed plane, and routine hygiene management were identified. The specification of housing, in particular ventilation and stocking density, was highlighted as a potential limiting factor for calf health and performance. Lack of measurement of nutritional inputs, hygiene management practices and calf performance was observed. This poses a risk to farmers' ability to ensure the effectiveness of key management strategies and recognise poor calf performance and health.

Seroprevalence of selected endemic infectious diseases in large-scale Estonian dairy herds and their associations with cow longevity and culling rates

Herd culling rates and longevity represent herd health and welfare status as well as farm economic performance. The contribution of endemic circulation of the main cattle pathogens to herd performance has not been previously analysed. The aim of this study was to estimate the herd prevalence of selected endemic bovine pathogens among large commercial dairy herds and to analyse their associations with herd culling rates and longevity. Bulk tank milk (BTM) samples and 10 heifer serum samples were collected from 120 Estonian dairy herds with at least 100 cows, between August 2019 and July 2020. All samples were tested for antibodies against bovine herpesvirus 1 (BHV-1), bovine viral diarrhoea virus (BVDV), bovine respiratory syncytial virus (BRSV), Mycoplasma bovis, Mycobacterium avium spp. paratuberculosis (MAP) and Salmonella Dublin using commercial ELISA. Data on herd size, milk yield, culling rate (CR) and mean age of the culled cows (MAofCC) were collected from the Estonian Livestock Performance Recording Ltd. The apparent herd and animal prevalences were calculated, and linear regression models were used to identify associations between the herd status of six tested pathogens and CR and MAofCC. The herd seroprevalences for antibodies based on BTM and heifer serum sample testing were BHV-1 56.7 % (95 % CI 47.3; 65.7), Mycoplasma bovis 48.3 % (95 % CI 39.1; 57.6), MAP 2.5 % (95 % CI 0.5; 7.1) and S. Dublin 24.2 % (95 % CI 16.8; 32.8) in all tested herds. Excluding vaccinated herds, herds prevalence for BVDV was 27.0 % (95 % CI 19.0; 36.3) and for BRSV 94.7 % (95 % CI 88.1; 98.3). Herd seropositive status for BRSV was associated with lower MAofCC, and herds with BSRV-seropositive youngstock had increased CR. Herds with positive BTM test results for S. Dublin culled cows at an older average age (Coef = 3.79 months, 95 % CI 0.52; 7.07, p = 0.023). MAP-positive herds had somewhat lower herd MAofCC (Coef = -6.18 months, 95 % CI -12.98; 0.63, p = 0.075). There was also a tendency of BVDV-negative herds to have a lower CR than BVDV-positive herds (Coef = -3.03 %, 95 % CI -6.54; 0.49, p = 0.090), and vaccination against BVDV tended to be protective against high CR (Coef = -6.26 %, 95 % CI -12.61; 0.09, p = 0.053 compared to infected herds). This study shows that Estonian large-scale dairy herds are endemically infected with several important cattle pathogens. Most of the studied pathogens influence longevity and culling rates, thus entailing health and economic consequences.

Messenger RNA biomarkers of Bovine Respiratory Syncytial Virus infection in the whole blood of dairy calves

Bovine Respiratory Syncytial Virus (BRSV) is a primary viral cause of Bovine Respiratory Disease (BRD) in young calves, which is responsible for substantial morbidity and mortality. Infection with BRSV induces global gene expression changes in respiratory tissues. If these changes are observed in tissues which are more accessible in live animals, such as whole blood, they may be used as biomarkers for diagnosis of the disease. Therefore, the objective of the current study was to elucidate the whole blood transcriptomic response of dairy calves to an experimental challenge with BRSV. Calves (Holstein–Friesian) were either administered BRSV inoculate (10^3.5 TCID₅₀/ml × 15 ml) (n = 12) or sterile phosphate buffered saline (n = 6). Clinical signs were scored daily and whole blood was collected in Tempus RNA tubes immediately prior to euthanasia, at day 7 post-challenge. RNA was extracted from blood and sequenced (150 bp paired-end). The sequence reads were aligned to the bovine reference genome (UMD3.1) and EdgeR was subsequently employed for differential gene expression analysis. Multidimensional scaling showed that samples from BRSV challenged and control calves segregated based on whole blood gene expression changes, despite the BRSV challenged calves only displaying mild clinical symptoms of the disease. There were 281 differentially expressed (DE) genes (p < 0.05, FDR < 0.1, fold change > 2) between the BRSV challenged and control calves. The top enriched KEGG pathways and gene ontology terms were associated with viral infection and included “Influenza A”, “defense response to virus”, “regulation of viral life cycle” and “innate immune response”. Highly DE genes involved in these pathways may be beneficial for the diagnosis of subclinical BRD from blood samples.

Refining livestock mortality indicators: a systematic review

Background: Livestock mortality impacts farmer livelihoods and household nutrition. Capturing trends in livestock mortality at localised or national levels is essential to planning, monitoring and evaluating interventions and programs aimed at decreasing mortality rates. However, livestock mortality data is disparate, and indicators used have not been standardised. This review aims to assess livestock mortality indicator definitions reported in literature, and define the ages where mortality has greatest impact. Methods: A systematic review was conducted, limited to articles focussed on mortality of cattle, sheep and goats. Peer-reviewed articles in Web of Science until year 2020 were assessed for inclusion of age-based definitions for mortality indicators and data on age distribution of mortality. Indicator definitions for each species were collated and similar terms and age groups most targeted were compared. The cumulative distribution of age at mortality was compared across studies graphically where possible; otherwise, age patterns for mortality were collated. Results: Most studies reported mortality risk rather than rate, and there was little agreement between indicator definitions used in the literature. The most common indicators reported were perinatal and neonatal mortality in cattle, and for perinatal, neonatal and pre-weaning mortality indicators for sheep and goats. Direct comparison of age distribution of mortality was only possible for cattle, which found that approximately 80% of all mortalities within the first 12 months had occurred by six months of age. A significant finding of the study is the variation in age groups for which mortality is reported, which impedes the comparison of mortality risk across studies, particularly for sheep and goats. Conclusions: This study demonstrates the importance and value of standardising mortality risk indicators for general use, including a young stock mortality risk indicator measuring mortality in the highest risk period of birth to six months of age in cattle, sheep and goats.

Evaluation of the association between the introduction of data-driven tools to support calf rearing and reduced calf mortality in dairy herds in the Netherlands

Between 2009 and 2017, calf mortality in the Dutch dairy sector showed a slight but steady increase. The Dutch dairy industry decided to act and supported the development of several data-driven tools that were implemented from 2018 on. The tools informed farmers about their calf mortality rates and stimulated them to improve. The Trend Analysis Surveillance Component of the Dutch cattle Health Surveillance System provided the possibility to evaluate the calf mortality in Dutch dairy herds before and after implementation of these tools. The aim of this study was to evaluate the association between calf mortality and i) all actions that were taken by the Dutch dairy industry to improve the quality of calf rearing and ii) other potential management or environmental factors associated with calf mortality in Dutch dairy herds. Census data from approximately 98 % of all Dutch dairy herds were available from July 2014 until June 2019. Four different calf mortality indicators were defined: perinatal calf mortality risk (i.e., mortality before, during, or shortly after the moment of birth up to the moment of ear-tagging), postnatal calf mortality risk (ear-tagging till 14 d), preweaned calf mortality rate (15 d-55 d) and weaned calf mortality rate (56 d-1 yr.). All data were aggregated to herd and monthly level and were analysed using Population-Averaged Generalized Estimating Equations (PA GEE models) with a Poisson distribution and log link function. When the period before implementation of the tools (2016-2017) was compared to the period thereafter (2018-2019), all four calf mortality indicators decreased. The relative decrease varied from 3 % (postnatal calves) and 10 % (perinatal calves) up to 18 % and 30 % in preweaned and weaned calves, respectively. Registrations of veterinary treatments such as antimicrobial use, vaccinations (calf or cow) and antiparasitic treatments were associated with calf mortality. Additionally, herds with a higher level of metabolic problems in transition cows had a higher calf mortality and also extreme outside temperatures were associated with higher calf mortality. Given that the different tools were implemented nation-wide and a control group was lacking, we could not prove that implementing the different tools caused the reduction in calf mortality. We do however, believe that all the actions and communication towards improvement of calf rearing in dairy herds led to an increased awareness among farmers towards the importance of calf rearing management and therefore a reduction in calf mortality on national level.

Keeping Dairy Cows for Longer: A Critical Literature Review on Dairy Cow Longevity in High Milk-Producing Countries

Simple Summary

The ability of farms to produce milk sustainably is closely related to dairy cow longevity, i.e., the length of productive life. However, longevity is a very complex feature that depends on all the aspects of the lifespan of a cow and there is no standard definition nor metric to measure it. Measuring longevity is important because it influences the profitability and the environmental impact of farms as well as the welfare of the animals. The objectives of this paper were to review metrics used to measure longevity and describe its status among high milk-producing countries. Increasing dairy cow longevity would imply that an animal has an early age at first calving and a long and profitable productive life. Combining age at first calving, length of productive life, and margin over all (available) costs provides a complete evaluation of longevity. This paper also shows that dairy cow longevity has decreased in most high milk-producing countries over time, which confirm the concerns voiced by the dairy industry and other stakeholders. Increasing cow longevity would reduce health costs and increase cow profitability while improving both animal welfare and quality of life, contributing to a more sustainable dairy industry.

Abstract

The ability of dairy farmers to keep their cows for longer could positively enhance the economic performance of the farms, reduce the environmental footprint of the milk industry, and overall help in justifying a sustainable use of animals for food production. However, there is little published on the current status of cow longevity and we hypothesized that a reason may be a lack of standardization and an over narrow focus of the longevity measure itself. The objectives of this critical literature review were: (1) to review metrics used to measure dairy cow longevity; (2) to describe the status of longevity in high milk-producing countries. Current metrics are limited to either the length of time the animal remains in the herd or if it is alive at a given time. To overcome such a limitation, dairy cow longevity should be defined as an animal having an early age at first calving and a long productive life spent in profitable milk production. Combining age at first calving, length of productive life, and margin over all costs would provide a more comprehensive evaluation of longevity by covering both early life conditions and the length of time the animal remains in the herd once it starts to contribute to the farm revenues, as well as the overall animal health and quality of life. This review confirms that dairy cow longevity has decreased in most high milk-producing countries over time and its relationship with milk yield is not straight forward. Increasing cow longevity by reducing involuntary culling would cut health costs, increase cow lifetime profitability, improve animal welfare, and could contribute towards a more sustainable dairy industry while optimizing dairy farmers’ efficiency in the overall use of resources available.

Graduate Student Literature Review: What do we know about the effects of clinical and subclinical hypocalcemia on health and performance of dairy cows?

This narrative literature review summarizes findings regarding the associations of clinical and subclinical hypocalcemia with postpartum health, reproduction, and milk production. To better understand the effects of hypocalcemia, we reviewed clinical and subclinical presentations of the condition and the dynamics of blood Ca concentration in the early postpartum period. We summarize and discuss the associations between hypocalcemia and performance of dairy cows. Up to 50% of dairy cows suffer from at least one disease event in the transition period. The important roles of calcium in muscle contraction and immune function make it a key component of metabolism, inflammation, and defense against infection. Although the effect of clinical hypocalcemia (milk fever) on health and performance is clear, the definition of subclinical hypocalcemia (SCH) and its consequences for health and performance are still ambiguous. Differences in study designs, sampling protocols, Ca concentration thresholds, and sample sizes that may be underpowered for health and reproduction outcomes lead to inconsistent conclusions on the effects of SCH. On current evidence, classification of SCH should be based on at least 2 measurements of blood calcium, using cutpoints supported with relevant data, which may vary depending on the outcome of interest. Arbitrary or poorly supported interpretative thresholds for blood Ca concentrations should be abandoned. Transient SCH appears to be associated with greater milk yield, whereas SCH that is present several days after calving is associated with lesser production and greater disease risk. However, when blood calcium is measured days after calving, primary effects of calcium metabolism may be confounded by feed intake, inflammation, or disease, which might either contribute to or be a consequence of hypocalcemia. Additional research is needed to refine sampling schemes to classify SCH, and to better inform the goals and means of prevention of SCH.

ATAC-Seq identifies regions of open chromatin in the bronchial lymph nodes of dairy calves experimentally challenged with bovine respiratory syncytial virus

Background

Bovine Respiratory Syncytial Virus (BRSV) is a cause of Bovine Respiratory Disease (BRD). DNA-based biomarkers contributing to BRD resistance are potentially present in non-protein-coding regulatory regions of the genome, which can be determined using ATAC-Seq. The objectives of this study were to: (i) identify regions of open chromatin in DNA extracted from bronchial lymph nodes (BLN) of healthy dairy calves experimentally challenged with BRSV and compare them with those from non-challenged healthy control calves, (ii) elucidate the chromatin regions that were differentially or uniquely open in the BRSV challenged relative to control calves, and (iii) compare the genes found in regions proximal to the differentially open regions to the genes previously found to be differentially expressed in the BLN in response to BRSV and to previously identified BRD susceptibility loci. This was achieved by challenging clinically healthy Holstein-Friesian calves (mean age 143 ± 14 days) with either BRSV inoculum (n = 12) or with sterile phosphate buffered saline (PBS) (n = 6) and preparing and sequencing ATAC-Seq libraries from fresh BLN tissues.

Results

Using Diffbind, 9,144 and 5,096 differentially accessible regions (P < 0.05, FDR < 0.05) were identified between BRSV challenged and control calves employing DeSeq2 and EdgeR, respectively. Additionally, 8,791 chromatin regions were found to be uniquely open in BRSV challenged calves. Seventy-six and 150 of the genes that were previously found to be differentially expressed using RNA-Seq, were located within 2 kb downstream of the differentially accessible regions, and of the regions uniquely open in BRSV challenged calves, respectively. Pathway analyses within ClusterProfiler indicated that these genes were involved in immune responses to infection and participated in the Th1 and Th2 pathways, pathogen recognition and the anti-viral response. There were 237 differentially accessible regions positioned within 40 previously identified BRD susceptibility loci.

Conclusions

The identified open chromatin regions are likely to be involved in the regulatory response of gene transcription induced by infection with BRSV. Consequently, they may contain variants which impact resistance to BRD that could be used in breeding programmes to select healthier, more robust cattle.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07268-5.