Journal of Dairy Science最新文献

Identifying genome-enabled methods that provide more accurate genomic prediction is crucial when evaluating complex traits such as dairy cow behavior. In this study, we aimed to compare the predictive performance of traditional genomic prediction methods and deep learning algorithms for genomic prediction of milking refusals (MREF) and milking failures (MFAIL) in North American Holstein cows measured by automatic milking systems (milking robots). A total of 1,993,509 daily records from 4,511 genotyped Holstein cows were collected by 36 milking robot stations. After quality control, 57,600 SNPs were available for the analyses. Four genomic prediction methods were considered: Bayesian least absolute shrinkage and selection operator (LASSO), multiple layer perceptron (MLP), convolutional neural network (CNN), and GBLUP. We implemented the first 3 methods using the Keras and TensorFlow libraries in Python (v.3.9) but the GBLUP method was implemented using the BLUPF90+ family programs. The accuracy of genomic prediction (mean square error) for MREF and MFAIL was 0.34 (0.08) and 0.27 (0.08) based on LASSO, 0.36 (0.09) and 0.32 (0.09) for MLP, 0.37 (0.08) and 0.30 (0.09) for CNN, and 0.35 (0.09) and 0.31(0.09) based on GBLUP, respectively. Additionally, we observed a lower reranking of top selected individuals based on the MLP versus CNN methods compared with the other approaches for both MREF and MFAIL. Although the deep learning methods showed slightly higher accuracies than GBLUP, the results may not be sufficient to justify their use over traditional methods due to their higher computational demand and the difficulty of performing genomic prediction for nongenotyped individuals using deep learning procedures. Overall, this study provides insights into the potential feasibility of using deep learning methods to enhance genomic prediction accuracy for behavioral traits in livestock. Further research is needed to determine their practical applicability to large dairy cattle breeding programs.

Automated milk feeders (AMF) allow farmers to raise calves in groups while generating individual records on milk consumption, drinking speed, and frequency of visits. Calves raised in groups benefit from social interaction, which facilitates learning and adapting to novelty. However, calves in large groups (>12 calves/feeder) experience a higher risk of disease transmission and competition than those housed individually or in smaller groups. Therefore, if group size, grouping strategy, and disease detection are not optimal, the health and performance of calves can be compromised. The objectives of this narrative literature review, from publications available as of February 2023, are to (1) describe the use of AMF in group housing systems for calves and the associated feeding behavior variables they automatically collect, (2) linking feeding behavior collected from AMF to disease risk in calves, (3) describe research on social behavior in AMF systems, and (4) introduce social networks as a promising tool for the study of social behavior and disease transmission in group-housed AMF-fed calves. Existing research suggests that feeding behavior measures from AMF can assist in detecting bovine respiratory disease and enteric disease, which are common causes of morbidity and mortality for preweaning dairy heifers. Automated milk feeder records show reduced milk intake, drinking speed, or frequency of visits when calves are sick. However, discrepancies exist among published research about the sensitivity of feeding behavior measures as indicators of sickness, likely due to differences in feeding plans and disease-detection protocols. Therefore, considering the influence of milk allowance, group density, and individual variation on the analysis of AMF data is essential to derive meaningful information used to inform management decisions. Research using dynamic social networks derived from precision data show potential for the use of social network analysis to understand disease transmission and the effect of disease on social behavior of group-housed calves.

The objective of this study was to investigate the effects of feeding surplus dairy calves a milk replacer (MR) or one of 2 different oral rehydration solutions (ORS) during a midtransportation rest period on metabolic and clinical health indicators, growth, and behavioral outcomes after arrival at a calf-raising facility. Surplus dairy calves (n = 128) were transported in 4 cohorts from February to July 2022 for 12 h to a holding facility, rested for 8 h, then transported for an additional 6 h to a calf-raising facility. Upon arrival at the holding facility, calves were randomly assigned to 1 of 3 treatments: MR (n = 43), a high-sodium ORS developed for diarrhea (ORS-D; n = 43), or a high-potassium ORS developed for transportation (ORS-T; n = 42). The exact age of calves at transportation was unknown; however, all calves were less than 14 d of age. Calf BW at enrollment was 43.9 ± 5.9 kg, 43.7 ± 6.5 kg, and 45.0 ± 4.5 kg for calves fed MR, ORS-D, and ORS-T, respectively. Calves were fed 2.0 L of their treatment twice, once upon arrival and once before leaving the holding facility. At unloading and reloading at the holding facility, calves were weighed and blood samples were obtained. Calves were also health scored at unloading at the holding facility. After arrival at the calf-raising facility, calves were weighed, health scored, and blood samples were taken. Blood samples were collected at 24 and 48 h and BW was recorded at 24 h, 48 h, 72 h, 5 d, 7 d, 14 d, and at 8 wk after arrival at the calf-raising facility. Calves were also health scored daily for 14 d; health scoring included fecal consistency scoring and evaluating the presence or absence of respiratory disease. Lying time, lying bouts, and activity index were measured during transportation and from 3 d relative to transportation using accelerometers. At arrival to the calf-raiser, calves fed ORS-D had higher concentrations of nonesterified fatty acids (NEFA) and BHB than calves fed MR. Furthermore, calves fed ORS-T had higher concentrations of BHB at arrival to the calf raiser compared with calves fed MR. In the 14 d after arrival at the calf-raiser, there was evidence that calves fed ORS-T had a higher proportion of days with diarrhea and respiratory disease compared with those fed MR. During transportation, calves fed ORS-T had a lower activity index than calves fed MR, suggesting that ORS-T calves had lower overall activity. In addition, on the day of transportation (d 0), ORS-T and ORS-D calves had a lower activity index than calves fed MR. There were no treatment effects on growth outcomes. The results of this study suggest that feeding MR rather than an ORS during a midtransportation rest period could minimize fat mobilization and can potentially improve diarrhea and respiratory disease but does not affect growth outcomes after arrival at calf-raisers.

Fertility in dairy cattle has declined as an unintended consequence of single-trait selection for high milk yield. The unfavorable genetic correlation between milk yield and fertility is now well documented; however, the underlying physiological mechanisms are still uncertain. To understand the relationship between these traits, we developed a method that clusters variants with similar patterns of effects and, after the integration of gene expression data, identifies the genes through which they are likely to act. Biological processes that are enriched in the genes of each cluster were then identified. We identified several clusters with unique patterns of effects. One of the clusters included variants associated with increased milk yield and decreased fertility, where the “archetypal” variant (i.e., the one with the largest effect) was associated with the GC gene, whereas others were associated with TRIM32, LRRK2, and U6-associated snRNA. These genes have been linked to transcription and alternative splicing, suggesting that these processes are likely contributors to the unfavorable relationship between the 2 traits. Another cluster, with archetypal variant near DGAT1 and including variants associated with CDH2, BTRC, SFRP2, ZFHX3, and SLITRK5, appeared to affect milk yield but have little effect on fertility. These genes have been linked to insulin, adipose tissue, and energy metabolism. A third cluster with archetypal variant near ZNF613 and including variants associated with ROBO1, EFNA5, PALLD, GPC6, and PTPRT were associated with fertility but not milk yield. These genes have been linked to GnRH neuronal migration, embryonic development, or ovarian function. The use of archetypal clustering to group variants with similar patterns of effects may assist in identifying the biological processes underlying correlated traits. The method is hypothesis generating and requires experimental confirmation. However, we have uncovered several novel mechanisms potentially affecting milk production and fertility such as GnRH neuronal migration. We anticipate our method to be a starting point for experimental research into novel pathways, which have been previously unexplored within the context of dairy production.

Our objectives were to determine the effects of reducing dietary CP concentration on nutrient digestibility, rumen function, N balance, and serum AA concentration for dairy cows in late lactation. At the initiation of the experimental period, we stratified Holstein cows (n = 128; mean ± SD 224 ± 54 DIM) by parity and days pregnant (86 ± 25 d) and assigned them to 1 of 16 pens. For 3 wk, all cows received a covariate diet containing 16.9% CP (DM basis). For the subsequent 12 wk, we assigned pens to 1 of 4 treatments containing 16.2%, 14.4%, 13.4%, or 11.9% CP (DM basis) in a randomized complete block design. Diets were fed as a TMR once daily. To reduce dietary CP, we replaced soybean meal with soybean hulls in the concentrate mix (DM basis). Diet evaluations suggested that several EAA, especially His, limited productivity as dietary CP declined. Digestibility of DM and CP decreased linearly with dietary CP reduction. Digestibility of NDF and potentially digestible NDF tended to respond in a quadratic pattern with the greatest digestibility at intermediate treatments. The reduction in dietary CP did not affect ruminal pH, but ruminal ammonia-N and branched-chain VFA concentrations declined linearly. The concentration of milk urea-N and plasma urea-N, secretion of milk N, and excretions of fecal N, urinary N, urinary urea-N, and unaccounted N decreased linearly with the reduction in dietary CP concentration. Urinary N expressed as a percentage of N intake was unaffected by dietary CP. Serum concentrations of total essential AA and NEAA were unaffected by dietary CP concentration. However, the ratio of essential to NEAA decreased with decreasing dietary CP. Serum 3-methylhistidine concentration increased linearly with decreasing dietary CP concentration, indicating greater skeletal muscle breakdown. Although our trial confirmed that reducing dietary CP decreased absolute excretion of urinary N, diet evaluations suggested that milk protein production decreased as certain essential AA became increasingly limited. Thus, reduced-CP diets have the potential to lessen reactive-N outputs of late-lactation cows, but more research is needed to design diets that minimize deleterious effects on productivity.

Digital dermatitis (DD) is a polybacterial disease endemic to most UK dairy farms. It poses a major financial and welfare threat and is characterized by high incidence and recurrence rates. We aimed to investigate the association between the UK EBV for resistance to digital dermatitis, the digital dermatitis index (DDI), and the frequency of DD, heel horn erosion (HHE), and interdigital hyperplasia (IH) in a population of Holstein dairy cows. We enrolled and genotyped 2,352 cows from 4 farms in a prospective cohort study. Foot lesion records were recorded by veterinary surgeons for each animal at 4 time points during a production cycle, starting at approximately 2 mo before calving and ending in late lactation. Importantly, these records were not used in the calculation of the DDI. Lesion records were matched to the animal's own DDI (n = 2,101) and their sire's DDI (n = 1,812). Digital dermatitis index values in our study population ranged from −1.41 to +1.2 and were transformed to represent distance from the mean expressed in SD. The relationship between the DDI and the presence of DD was investigated using a logistic regression model, with farm, parity, and a farm-parity interaction fitted as covariates. A multivariable logistic regression model was fitted to evaluate the relationship between HHE and DDI with farm fitted as a covariate. Finally, a univariable logistic regression model with DDI as explanatory variable was used to investigate the relationship between IH and DDI. The odds ratio of an animal being affected by DD was 0.69 for 1 SD increase in the animal's DDI (95% CI = 0.63–0.76). The odds of HHE and IH were 0.69 (95% CI = 0.62–0.76) and 0.58 (95% CI = 0.49–0.68) respectively for 1 SD increase in DDI. The adjusted probability of DD was 32% (95% CI = 27–36%) for cows with mean DDI value of 0, while it was 24% (95% CI = 20–29%) in cows with a DDI value of +1. Sire DDI breeding values were standardized in the same way and then binned into terciles creating an ordinal variable representing bulls of high, medium, and low genetic merit for DD resistance. The daughters of low genetic merit bulls were at 2.05 (95% CI = 1.60–2.64), 1.96 (95% CI = 1.53–2.50), and 2.85 (95% CI = 1.64–5.16) times greater odds of being affected by DD, HHE, and IH, respectively, compared with the daughters of high genetic merit bulls. The results of this study highlight the potential of digital dermatitis genetic indexes to aid herd management of DD, and suggest that breeding for resistance to DD, alongside environmental and management control practices, could reduce the prevalence of the disease.

This randomized clinical trial aimed to determine the extent to which injectable micronutrient supplementation at birth can improve intranasal vaccine response by ameliorating oxidative stress in dairy calves from birth to weaning. For this, 120 Holstein heifer calves were enrolled at birth and randomly allocated into one of 4 groups. The 4 groups included 3 commercially available micronutrient supplements (selenium, copper, zinc, and manganese; selenium and vitamin E; and vitamins E, A, and D) and one control (saline). Calves received an intranasal vaccine against the respiratory viruses parainfluenza 3, bovine herpesvirus type 1 (BHV-1), and bovine respiratory syncytial virus (BRSV) within the first week of life. Body weight and hip height (HH) were recorded, and a blood sample and nasal secretion sample were collected at birth before treatment and vaccine administration, as well as weekly until weaning at 8 wk. Health scores, including thoracic ultrasound assessment, were recorded weekly from wk 1 to wk 8. Farm treatment records were collected after the completion of the study. Serum micronutrient concentrations were determined from birth to weaning to identify micronutrient status, and serum blood metabolites were analyzed as markers of nutrient utilization. Redox balance was determined in serum as a ratio of reactive oxygen and nitrogen species to antioxidant capacity, known as the oxidant status index (OSi). Intranasal vaccine response was quantified as anti-BRSV and anti-BHV-1 IgA concentrations in nasal secretions. Linear mixed models with repeated measures were built for micronutrient concentrations, blood metabolites, redox balance, IgA concentrations, BW, and HH. Pre-planned contrasts of the control and supplemented groups were also built for the primary outcome of IgA concentrations. A logistic regression mixed model was built for health events and treatment of disease. Serum selenium concentrations were greater in calves receiving supplements containing Se throughout the first 4 wk of life. However, we did not observe any consistent differences in the other micronutrients. The metabolic biomarkers indicate that supplemented calves had better energy status, as suggested by lower BHB and nonesterified fatty acids concentrations. Supplemented calves showed improved redox balance, as indicated by lower OSi throughout the first week of life. Calves supplemented with antioxidants at birth had higher anti-BRSV IgA than control calves. Our results indicate an improved immune response to vaccines in calves supplemented with antioxidants at birth. However, this did not translate to growth and health performance, as we did not find any differences in average daily gain or incidence of health events throughout the preweaning period. This study provides evidence that improving the antioxidant capacity might improve vaccine response, and further research is required to investigate the appropriate frequency and dose of supplementation to im