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ABSTRACT: The large-scale recording of traits such as feed efficiency (FE) and methane emissions (ME) for use in genetic improvement programs is complex, costly, and time-consuming. Therefore, heritable traits that can be continuously recorded in dairy herds and are correlated with FE and ME traits could provide useful information for genetic evaluation. Rumination time has been suggested to be associated with FE, methane production (MeP; ME in g/d), and production traits at the phenotypic level. Therefore, the objective of this study was to investigate the genetic relationships among rumination time (RT), FE, methane and production traits using 7,358 records from 656 first-lactation Holstein cows. The estimated heritabilities were moderate for RT (0.45 ± 0.14), MeP (0.36 ± 0.12), milk yield (0.40 ± 0.08), fat yield (0.29 ± 0.06), protein yield (0.32 ± 0.07), and energy-corrected milk (0.28 ± 0.07), but were low and nonsignificant for FE (0.15 ± 0.07), which was defined as the residual of the multiple linear regression of DMI on energy-corrected milk and metabolic body weight. A favorable negative genetic correlation was estimated between RT and MeP (−0.53 ± 0.24), whereas a positive favorable correlation was estimated between RT and energy-corrected milk (0.49 ± 0.11). The estimated genetic correlation of RT with FE (−0.01 ± 0.17) was not significantly different from zero but showed a trend of a low correlation with dry matter intake (0.21 ± 0.13). These results indicate that RT is genetically associated with MeP and milk production traits, but high standard errors indicate that further analyses should be conducted to verify these findings when more data for RT, MeP, and FE become available.

Interest in dairy cow health continues to grow as we better understand health’s relationship with production potential and animal welfare. Over the past decade, efforts have been made to incorporate health traits into national genetic evaluations. However, they have focused on the mature cow, with calf health largely being neglected. Diarrhoea and respiratory disease comprise the main illnesses with regard to calf health. Conventional methods to control calf disease involve early separation of calves from the dam and housing calves individually. However, public concern regarding these methods, and growing evidence that these methods may negatively impact calf development, mean the dairy industry may move away from these practices. Genetic selection may be a promising tool to address these major disease issues. In this review, we examined current literature for enhancing calf health through genetics and discussed alternative approaches to improve calf health via the use of epidemiological modelling approaches, and the potential of indirectly selecting for improved calf health through improving colostrum quality. Heritability estimates on the observed scale for diarrhoea ranged from 0.03 to 0.20, while for respiratory disease, estimates ranged from 0.02 to 0.24. The breadth in these ranges is due, at least in part, to differences in disease prevalence, population structure, data editing and models, as well as data collection practices, which should be all considered when comparing literature values. Incorporation of epidemiological theory into quantitative genetics provides an opportunity to better determine the level of genetic variation in disease traits, as it accounts for disease transmission among contemporaries. Colostrum intake is a major determinant of whether a calf develops either respiratory disease or diarrhoea. Colostrum traits have the advantage of being measured and reported on a continuous scale, which removes the issues classically associated with binary disease traits. Overall, genetic selection for improved calf health is feasible. However, to ensure the maximum response, first steps by any industry members should focus efforts on standardising recording practices and encouragement of uploading information to genetic evaluation centres through herd management software, as high-quality phenotypes are the backbone of any successful breeding programme.

ABSTRACT: Feed efficiency has become an increasingly important research topic in recent years. As feed costs rise and the environmental impacts of agriculture become more apparent, improving the efficiency with which dairy cows convert feed to milk is increasingly important. However, feed intake is expensive to measure accurately on large populations, making the inclusion of this trait in breeding programs difficult. Understanding how the genetic parameters of feed efficiency and traits related to feed efficiency vary throughout the lactation period is valuable to gain understanding into the genetic nature of feed efficiency. This study used 121,226 dry matter intake (DMI) records, 120,500 energy-corrected milk (ECM) records, and 98,975 metabolic body weight (MBW) records, collected on 7,440 first-lactation Holstein cows from 6 countries (Canada, Denmark, Germany, Spain, Switzerland, and the United States), from January 2003 to February 2022. Genetic parameters were estimated using a multiple-trait random regression model with a fourth-order Legendre polynomial for all traits. Weekly phenotypes for DMI were re-parameterized using linear regressions of DMI on ECM and MBW, creating a measure of feed efficiency that was genetically corrected for ECM and MBW, referred to as genomic residual feed intake (gRFI). Heritability (SE) estimates varied from 0.15 (0.03) to 0.29 (0.02) for DMI, 0.24 (0.01) to 0.29 (0.03) for ECM, 0.55 (0.03) to 0.83 (0.05) for MBW, and 0.12 (0.03) to 0.22 (0.06) for gRFI. In general, heritability estimates were lower in the first stage of lactation compared with the later stages of lactation. Additive genetic correlations between weeks of lactation varied, with stronger correlations between weeks of lactation that were close together. The results of this study contribute to a better understanding of the change in genetic parameters across the first lactation, providing insight into potential selection strategies to include feed efficiency in breeding programs.

ABSTRACT: Directly measuring individual cow energy balance is not trivial. Other traits such as body condition score (BCS) and BCS change (ΔBCS) can, however, be used as an indicator of cow energy status. Body condition score is a metric used worldwide to estimate cow body reserves, but the estimation of ΔBCS was, until now, conditional on the availability of multiple BCS assessments. The aim of the present study was to estimate ΔBCS from milk mid-infrared (MIR) spectra and days in milk (DIM) in intensively fed dairy cows using statistical prediction methods. Daily BCS was interpolated from cubic splines fitted through the BCS records and daily ΔBCS was calculated from these splines. The ΔBCS records were merged with milk MIR spectra recorded on the same week. The dataset comprised 37,077 ΔBCS phenotypes across 9,403 lactations from 6,988 cows in 151 herds based in Quebec, Canada. Partial least squares regression (PLSR) and a neural network (NN) were then used to estimate ΔBCS from (1) MIR spectra only, (2) DIM only, or (3) MIR spectra and DIM together. The ΔBCS data in both the first 120 and 305 DIM of lactation were used to develop the estimates. Daily ΔBCS had a standard deviation of 4.40 × 10−3 BCS units in the 120-d dataset and of 3.63 × 10−3 BCS units in the 305-d dataset. A 4-fold cross-validation was used to calibrate and test the prediction equations. External validation was also conducted using more recent years of data. Irrespective of whether based on the first 120 or 305 DIM, or when MIR spectra only, DIM only or MIR spectra and DIM were jointly used as prediction variables, NN produced the lowest root mean square error (RMSE) of cross-validation (1.81 × 10−3 BCS units and 1.51 × 10−3 BCS units, respectively, using the 120-d and 305-d dataset). Relative to predictions for the entire 305 DIM, the RMSE of cross-validation was 15.4% and 1.5% lower in the first 120 DIM when using PLSR and NN, respectively. Predictions from DIM only were more accurate than those using just MIR spectra data but, irrespective of the dataset and of the prediction model used, combining DIM information with MIR spectral data as prediction variables reduced the RMSE compared with the inclusion of DIM alone, albeit the benefit was small (the RMSE from cross-validation reduced by up to 5.5% when DIM and spectral data were jointly used as model features instead of DIM only). However, when predicting extreme ΔBCS records, the MIR spectral data were more informative than DIM. Model performance when predicting ΔBCS records in future years was similar to that from cross-validation demonstrating the ability of MIR spectra of milk and DIM combined to estimate ΔBCS, particularly in early lactation. This can be used to routinely generate estimates of ΔBCS to aid in day-to-day individual cow management.

ABSTRACT: Heat stress is a prominent issue in livestock production, even for intensively housed dairy herds in Canada. Production records and meteorological data can be combined to assess heat tolerance in dairy cattle. The overall aim of this study was to evaluate the possibility of genetic evaluation for heat tolerance in Canadian dairy cattle. The 2 specific objectives were (1) to estimate the genetic parameters for milk, fat, and protein yield for Holsteins while accounting for high environmental heat loads, and (2) to determine if a genotype-by-environment interaction causes reranking of top-ranked sires between environments with low and high heat loads. A repeatability test-day model with a heat stress function was used to evaluate the genetic merit for milk, fat, and protein yield under heat stress and at thermal comfort for first parity in 5 regions in Canada. The heat stress function for each trait was defined using a specific temperature-humidity index (THI) threshold. The purpose of this function was to quantify the level of heat stress that was experienced by the dairy cattle. The estimated genetic correlation between the general additive genetic effect and the additive effect on the slope of the change in the trait phenotype for milk, fat, and protein yield ranged from −0.16 to −0.30, −0.20 to −0.44, and −0.28 to −0.42, respectively. These negative correlations imply that there is an antagonistic relationship between sensitivity to heat stress and level of production. The heritabilities for milk, fat, and protein yield at 15 units above the THI threshold ranged from 0.15 to 0.27, 0.11 to 0.15, and 0.11 to 0.15, respectively. Finally, the rank correlations between the breeding values from a repeatability model with no heat stress effect and the breeding values accounting for heat stress for the 100 top-ranked bulls indicated possible interaction between milk production traits and THI, resulting in substantial reranking of the top-ranked sires in Canada, especially for milk yield. This is the first study to implement weather data from the NASA POWER database in a genetic evaluation of heat tolerance in dairy cattle. The NASA POWER database is a novel alternative meteorological resource that is potentially more reliable and consistent and with broader coverage than weather station data increasing the number of animals that could be included in a heat stress evaluation.

ABSTRACT: Weather station data and test-day production records can be combined to quantify the effects of heat stress on production traits in dairy cattle. However, meteorological data sets that are retrieved from ground-based weather stations can be limited by spatial and temporal data gaps. The National Aeronautics and Space Administration Prediction of Worldwide Energy Resources (NASA POWER) database provides meteorological data over regions where surface measurements are sparse or nonexistent. The first aim of this study was to determine whether NASA POWER data are a viable alternative resource of weather data for studying heat stress in Canadian Holsteins. The results showed that average, minima, and maxima ambient temperature and dewpoint temperature as well as 4 different types of temperature-humidity index (THI) values from NASA POWER were highly correlated to the corresponding values from weather stations (regression R2 > 0.80). However, the NASA POWER values for the daily average, minima, and maxima wind speed and relative humidity were poorly correlated to the corresponding weather station values (regression R2 = 0.10 to 0.49). The second aim of this study was to quantify the influence of heat stress on Canadian dairy cattle. This was achieved by determining the THI values at which milk, protein, and fat yield started to decline due to heat stress as well as the rates of decline in these traits after the respective thresholds, using segmented polynomial regression models. This was completed for both primiparous and multiparous cows from 5 regions in Canada (Ontario, Quebec, British Columbia, the Prairies, and the Atlantic Maritime). The results showed that all production traits were negatively affected by heat stress and that the patterns of responses for milk, fat, and protein yields to increasing THI differed from each other. We found 3 THI thresholds for milk yield, 1 for fat yield, and 2 for protein yield. All thresholds marked a change in rate of decrease in production yield per unit THI, except for the first milk yield threshold, which marked a greater rate of increase. The first thresholds for milk yield ranged between 47 and 50, the second thresholds ranged between 61 and 69, and the third thresholds ranged between 72 and 76 THI units. The single THI threshold for fat yield ranged between 48 and 55 THI units. Finally, the first and second thresholds ranged between 58 and 62 THI units and 72 and 73 THI units for protein yield, respectively.

Methane emission is not included in the current breeding goals for dairy cattle mainly due to the expense and difficulty in obtaining sufficient data to generate accurate estimates of the relevant traits. While several models have been developed to predict methane emission from milk spectra using reference methane data obtained by the respiration chamber, SF6 and sniffer methods, the prediction of methane emission from milk mid-infrared (MIR) spectra using reference methane data collected by the GreenFeed system has not yet been explored. Methane emission was monitored for 151 cows using the GreenFeed system. Prediction models were developed for daily and average (for the trial period of 12 or 14 days) methane production (g/d), yield (g/kg DM intake (DMI)) and intensity (g/kg of fat- and protein-corrected milk) using partial least squares regression. The predictions were evaluated in 100 repeated validation cycles, where animals were randomly partitioned into training (80%) and testing (20%) populations for each cycle. The best performing model was observed for average methane intensity using MIR, parity and DMI with validation coefficient of determination (R2val) and RMSE of prediction of 0.66 and 4.7 g/kg of fat- and protein-corrected milk, respectively. The accuracy of the best models for average methane production and average methane yield were poor (R2val = 0.28 and 0.12, respectively). A lower accuracy of prediction was observed for methane intensity and production (R2val = 0.42 and 0.17) when daily records were used while prediction for methane yield was comparable to that for average methane yield (R2val = 0.16). Our results suggest the potential to predict methane intensity with moderate accuracy. In this case, prediction models for average methane values were generally better than for daily measures when using the GreenFeed system to obtain reference methane emission measurements.

Abstract Background Optimization of an RNA-Sequencing (RNA-Seq) pipeline is critical to maximize power and accuracy to identify genetic variants, including SNPs, which may serve as genetic markers to select for feed efficiency, leading to economic benefits for beef production. This study used RNA-Seq data (GEO Accession ID: PRJEB7696 and PRJEB15314) from muscle and liver tissue, respectively, from 12 Nellore beef steers selected from 585 steers with residual feed intake measures (RFI; n = 6 low-RFI, n = 6 high-RFI). Three RNA-Seq pipelines were compared including multi-sample calling from i) non-merged samples; ii) merged samples by RFI group, iii) merged samples by RFI and tissue group. The RNA-Seq reads were aligned against the UMD3.1 bovine reference genome (release 94) assembly using STAR aligner. Variants were called using BCFtools and variant effect prediction (VeP) and functional annotation (ToppGene) analyses were performed. Results On average, total reads detected for Approach i) non-merged samples for liver and muscle, were 18,362,086.3 and 35,645,898.7, respectively. For Approach ii), merging samples by RFI group, total reads detected for each merged group was 162,030,705, and for Approach iii), merging samples by RFI group and tissues, was 324,061,410, revealing the highest read depth for Approach iii). Additionally, Approach iii) merging samples by RFI group and tissues, revealed the highest read depth per variant coverage (572.59 ± 3993.11) and encompassed the majority of localized positional genes detected by each approach. This suggests Approach iii) had optimized detection power, read depth, and accuracy of SNP calling, therefore increasing confidence of variant detection and reducing false positive detection. Approach iii) was then used to detect unique SNPs fixed within low- (12,145) and high-RFI (14,663) groups. Functional annotation of SNPs revealed positional candidate genes, for each RFI group (2886 for low-RFI, 3075 for high-RFI), which were significantly (P

Feed represents a substantial proportion of production costs in the dairy industry and is a useful target for improving overall system efficiency and sustainability. The objective of this study was to develop methodology to estimate the economic value for a feed efficiency trait and the associated methane production relevant to Canada. The approach quantifies the level of economic savings achieved by selecting animals that convert consumed feed into product while minimizing the feed energy used for inefficient metabolism, maintenance and digestion. We define a selection criterion trait called Feed Performance (FP) as a 1 kg increase in more efficiently used feed in a first parity lactating cow. The impact of a change in this trait on the total lifetime value of more efficiently used feed via correlated selection responses in other life stages is then quantified. The resulting improved conversion of feed was also applied to determine the resulting reduction in output of emissions (and their relative value based on a national emissions value) under an assumption of constant methane yield, where methane yield is defined as kg methane/kg dry matter intake (DMI). Overall, increasing the FP estimated breeding value by one unit (i.e. 1 kg of more efficiently converted DMI during the cow’s first lactation) translates to a total lifetime saving of 3.23 kg in DMI and 0.055 kg in methane with the economic values of CAD $0.82 and CAD $0.07, respectively. Therefore, the estimated total economic value for FP is CAD $0.89/unit. The proposed model is robust and could also be applied to determine the economic value for feed efficiency traits within a selection index in other production systems and countries.

The massive improvement in food production, as a result of effective genetic selection combined with advancements in farming practices, has been one of the greatest achievements of modern agriculture. For instance, the dairy cattle industry has more than doubled milk production over the past five decades, while the total number of cows has been reduced dramatically. This was achieved mainly through the intensification of production systems, direct genetic selection for milk yield and a limited number of related traits, and the use of modern technologies (e.g., artificial insemination and genomic selection). Despite the great betterment in production efficiency, strong drawbacks have occurred along the way. First, across-breed genetic diversity reduced dramatically, with the worldwide use of few common dairy breeds, as well as a substantial reduction in within-breed genetic diversity. Intensive selection for milk yield has also resulted in unfavorable genetic responses for traits related to fertility, health, longevity, and environmental sensitivity. Moving forward, the dairy industry needs to continue refining the current selection indexes and breeding goals to put greater emphasis on traits related to animal welfare, health, longevity, environmental efficiency (e.g., methane emission and feed efficiency), and overall resilience. This needs to be done through the definition of criteria (traits) that (a) represent well the biological mechanisms underlying the respective phenotypes, (b) are heritable, and (c) can be cost-effectively measured in a large number of animals and as early in life as possible. The long-term sustainability of the dairy cattle industry will also require diversification of production systems, with greater investments in the development of genetic resources that are resilient to perturbations occurring in specific farming systems with lesser control over the environment (e.g., organic, agroecological, and pasture-based, mountain-grazing farming systems). The conservation, genetic improvement, and use of local breeds should be integrated into the modern dairy cattle industry and greater care should be taken to avoid further genetic diversity losses in dairy cattle populations. In this review, we acknowledge the genetic progress achieved in high-yielding dairy cattle, closely related to dairy farm intensification, that reaches its limits. We discuss key points that need to be addressed toward the development of a robust and long-term sustainable dairy industry that maximize animal welfare (fundamental needs of individual animals and positive welfare) and productive efficiency, while also minimizing the environmental footprint, inputs required, and sensitivity to external factors.

Abstract Background Ketosis in dairy cattle has been shown to cause a high morbidity in the farm and substantial financial losses to dairy farmers. Ketosis symptoms, however, are difficult to identify, therefore, the amount of ketone bodies (mainly β-hydroxybutyric acid, BHB) is used as an indicator of subclinical ketosis in cows. It has also been shown that milk BHB concentrations have a strong correlation with ketosis in dairy cattle. Mid-infrared spectroscopy (MIR) has recently became a fast, cheap and high-throughput method for analyzing milk components. The aim of this study was to perform a genome-wide association study (GWAS) on the MIR-predicted milk BHB to identify genomic regions, genes and pathways potentially affecting subclinical ketosis in North American Holstein dairy cattle. Results Several significant regions were identified associated with MIR-predicted milk BHB concentrations (indicator of subclinical ketosis) in the first lactation (SCK1) and second and later lactations (SCK2) in Holstein dairy cows. The strongest association was located on BTA6 for SCK1 and BTA14 on SCK2. Several SNPs on BTA6 were identified in regions and variants reported previously to be associated with susceptibility to ketosis and clinical mastitis in Jersey and Holstein dairy cattle, respectively. One highly significant SNP on BTA14 was found within the DGAT1 gene with known functions on fat metabolism and inflammatory response in dairy cattle. A region on BTA6 and three SNPs on BTA20 were found to overlap between SCK1 and SCK2. However, a novel region on BTA20 (55–63 Mb) for SCK2 was also identified, which was not reported in previous association studies. Enrichment analysis of the list of candidate genes within the identified regions for MIR-predicted milk BHB concentrations yielded molecular functions and biological processes that may be involved in the inflammatory response and lipid metabolism in dairy cattle. Conclusions The results of this study confirmed several SNPs and genes identified in previous studies as associated with ketosis susceptibility and immune response, and also found a novel region that can be used for further analysis to identify causal variations and key regulatory genes that affect clinical/ subclinical ketosis.

A recently developed methodological approach for determining the greenhouse gas emissions impact of national breeding programs was applied to measure the effects of current and future breeding goals on the emission intensity (EI) of the Canadian dairy industry. Emission intensity is the ratio of greenhouse gas outputted in comparison to the product generated. Traits under investigation affected EI by either decreasing the direct emissions yield (i.e. increasing feed performance), changing herd structure (i.e. prolonging herd life) or through the dilution effect of increased production (i.e. increasing fat yield). The intensity value (IV) of each trait, defined as the change in emissions’ intensity per unit change in each trait, was calculated for each of the investigated traits. The IV trend of these traits was compared for the current and prospective selection index, as well as for a system with and without quota (the supply management policy designed to prevent overproduction). The overall EI of the average genetic merit Canadian dairy herd per breeding female was 5.07 kg CO2eq/kg protein equivalent output. The annual reduction in EI due to the improvement of production traits was −0.027, −0.018 and −0.006 for fat, protein and milk other solids, respectively. The functional traits, herd life and mastitis resistance, had more modest effects (−0.008 and −0.001, respectively). These results are consistent with international studies that identified traits related to production, survival, health and fertility as having the largest impact on the environmental footprint of dairy cattle. Overall, the dairy industry is becoming more efficient by reducing its EI through selection of environmentally favorable traits, with a 1% annual reduction of EI in Canada.

The difficulties and costs of measuring individual feed intake in dairy cattle are the primary factors limiting the genetic study of feed intake and utilisation, and hence the potential of their subsequent industry-wide applications. However, indirect selection based on heritable, easily measurable, and genetically correlated traits, such as conformation traits, may be an alternative approach to improve feed efficiency. The aim of this study was to estimate genetic and phenotypic correlations among feed intake, production, and feed efficiency traits (particularly residual feed intake; RFI) with routinely recorded conformation traits. A total of 496 repeated records from 260 Holstein dairy cows in different lactations (260, 159 and 77 from first, second and third lactation, respectively) were considered in this study. Individual daily feed intake and monthly BW and body condition scores of these animals were recorded from 5 to 305 days in milk within each lactation from June 2007 to July 2013. Milk yield and composition data of all animals within each lactation were retrieved, and the first lactation conformation traits for primiparous animals were extracted from databases. Individual RFI over 301 days was estimated using linear regression of total 301 days actual energy intake on a total of 301 days estimated traits of metabolic BW, milk production energy requirement, and empty BW change. Pair-wise bivariate animal models were used to estimate genetic and phenotypic parameters among the studied traits. Estimated heritabilities of total intake and production traits ranged from 0.27±0.07 for lactation actual energy intake to 0.45±0.08 for average body condition score over 301 days of the lactation period. RFI showed a moderate heritability estimate (0.20±0.03) and non-significant phenotypic and genetic correlations with lactation 3.5 % fat-corrected milk and average BW over lactation. Among the conformation traits, dairy strength, stature, rear attachment width, chest width and pin width had significant (P

The objectives of this study were to analyze the trend of within-breed genetic diversity and identify major causes leading to loss of genetic diversity in Guernsey breed in three countries. Pedigree files of Canadian (GCN), South African (GSA) and American (GUS) Guernsey populations containing 130 927, 18 593 and 1 851 624 records, respectively, were analyzed. Several parameters derived from the in-depth pedigree analyses were used to measure trends and current levels of genetic diversity. Pedigree completeness index of GCN, GSA and GUS populations, in the most recent year (2007), was 97%, 74% and 79%, respectively, considering four generations back in the analysis. The rate of inbreeding in each population was 0.19%, 0.16% and 0.17% between 2002 and 2007, respectively. For the same period, the estimated effective population size for GCN, GSA and GUS was 46, 57 and 46, respectively. The estimated percentage of genetic diversity lost within each population over the last four decades was 8%, 3% and 5%, respectively. The relative proportion of genetic diversity lost due to random genetic drift in the three populations was 93%, 91% and 86%, respectively. In conclusion, the results suggested that GCN and GUS have lost more genetic diversity than GSA over the past four decades, and this loss is gaining momentum due to increasing rates of inbreeding. Therefore, strategies such as optimum contribution selection and migration of genetic material are advised to increase effective population size, particularly in GCN and GUS.

Health traits are of paramount importance for economic dairy production. Improvement in liability to diseases has been made with better management practices, but genetic aspects of health traits have received less attention. Dairy producers in Canada have been recording eight health traits (mastitis (MAST), lameness (LAME), cystic ovarian disease (COD), left displaced abomasum (LDA), ketosis (KET), metritis (MET), milk fever (MF) and retained placenta (RP)) since April 2007. Genetic analyses of these traits were carried out in this study for the Holstein breed. Edits on herd distributions of recorded diseases were applied to the data to ensure a sufficient quality of recording. Traits were analysed either individually (MAST, LAME, COD) or were grouped according to biological similarities (LDA and KET, and MET, MF and RP) and analysed with multiple-trait models. Data included 46 104 cases of any of the above diseases. Incidence ranged from 2.3% for MF to 9.7% for MAST. MET and KET also had an incidence below 4.0%. Variance components were estimated using four different sire threshold models. The differences between models resulted from the inclusion of days at risk (DAR) and a cow effect, in addition to herd, parity and sire effects. Models were compared using mean squared error statistic. Mean squared error favoured, in general, the sire and cow within sire model with regression on DAR included. Heritabilities on the liability scale were between 0.02 (MET) and 0.21 (LDA). There was a moderate, positive genetic correlation between LDA and KET (0.58), and between MET and RP (0.79).

A new genetic evaluation system for the reproductive performance of dairy cattle has been developed in Canada. The evaluation system includes all traits related to reproductive performance, namely age at first service as a heifer trait, interval from calving to first service for cows and 7 traits each for both heifers and cows (56-days non return rate, interval from first service to conception, number of services to conception, gestation length, direct and maternal calving ease, direct and maternal calf survival and direct and maternal calf size). The model of analysis is a 16-trait animal model with different fixed effects according to the analyzed trait. Two indices for daughter fertility and calving performance have been developed. The impact of including the two indices in the national selection index was assessed.

The objective of this study was to investigate genetic merit of return over feed (ROF), which is a herd profit index defined by CanWest Dairy Herd Improvement as a difference between milk income and feed cost. A multiple-trait (MT) model and random regression model (RRM) were used. The traits analyzed in MT were rearing cost and ROF of the first three lactations. In RRM, a cumulative ROF was fitted as function of age and rearing cost was treated as a correlated trait. Variance components were estimated within a Bayesian framework by Gibbs sampling using a subsample of data. Breeding values were then estimated for 3 041 078 animals using records of 1 951 893 cows. Estimates of heritability for rearing cost from MT and RRM were 0.23 and 0.22, respectively. ROF per lactation and cumulative ROF were negatively correlated with rearing cost. Estimates of heritability of ROF through the first, second and third lactation from MT were 0.27, 0.10 and 0.08, respectively. Estimates of heritability of ROF from RRM increased with age and ranged from 0.08 through 0.31. Estimated breeding values (EBVs) for ROF from MT and RRM were moderately correlated with official EBV for production traits and the Canadian selection index (Lifetime Profit Index). Herd life EBV had −0.07 and 0.19 correlations with EBVs for ROF from MT and RRM, respectively. From both MT and RRM, small favorable correlations were reported between EBVs for ROF and for bone quality and angularity, whereas low unfavorable correlations were reported with EBV for udder depth, front end and chest width. Majority of correlations between EBVs for ROF and for reproduction traits were near 0, with the exception of EBV for gestation length, calf size and calving ease, where small favorable correlations were reported. The ROF is a good indicator of cow profitability despite the fact that it is a simplified profit index that does not account for animal-specific health and reproductive cost. However, because ROF does not account for differences in heritabilities between components of profit, ROF is not recommended to be used for direct selection for profit.

The shape of individual deviations of milk yield for dairy cattle from the fixed part of a random regression test day model (RRTDM) was investigated. Data were 53,217 TD records for milk yield of 6,229 first lactation Canadian Holsteins in Ontario. Data were fitted with a model that included the fixed effects of herd-testdate, DIM interval nested within age and season of calving. Residuals of the model were then fitted with the following functions: Ali and Schaeffer 5 parameter model, fourth-order Legendre Polynomials, and cubic spline with three, four or five knots. Result confirm the great variability of shape that can be found when individual lactation are modeled. Cubic splines gave better fitting pe4rformances although together with a marked tendency to yield aberrant estimates at the edge of the lactation trajectory.

Abstract Background Pain of musculoskeletal origin is very common in young patients affected by Mucopolysaccharidoses. This scoping review evaluates the evidence for assessment, pharmacological treatment and rehabilitation management for musculoskeletal pain of the latter. Methods A Medline search through PubMed has been performed for studies published in English at least for the past twenty years. Two investigators independently reviewed all search results and extracted those that met the inclusion criteria. Results 29 studies have been selected and analysed in depth, of which 10 related to pain assessment, 11 concerned pharmacological approach, and 8 reported rehabilitation approaches. Conclusion Few data are available in literature concerning the classification and management of pain in children with Mucopolysaccharidoses. Notwithstanding, pain evaluation methods are effectively used to classify pain intensity, according to the age group and communication abilities of young Mucopolysaccharidoses patients. The review emphasizes that drug therapies have a palliative purpose, while rehabilitation reduces musculoskeletal pain and can provide a therapeutic effect on disabilities.

Abstract Background The Mayo Elbow Performance Score (MEPS) is a rating system consisting of four dimensions to evaluate elbow performance. It is a common tool for assessment of elbow impairments worldwide. We determined the validity and reliability of its German version (MEPS-G) after cross-cultural adaptation. Methods Six investigators examined 57 patients with elbow pathologies. The MEPS-G was compared to validated elbow scores such as the German versions of DASH, the Oxford Elbow Score, pain level and subjective elbow performance on a VAS. Inter-rater reliability (IRR) and validity of the score and its dimensions were also reviewed. Verification was performed using the intraclass correlation coefficient (ICC), the prevalence and bias with adjusted Kappa (PABAK) and the Spearman correlation. Results The IRR of the MEPS-G score was moderate (ICC (2.1) = 0.65). The IRR of the four individual dimensions was moderate to high (K PABAK = 0.55 -0.81). Validity for the sum score (r = 0.52–0.65) and the dimensions pain (r = 0.53–0.62), range of motion (r = 0.7) and stability (r = − 0.61) was verified. The function subscale reached insufficient validity (r = 0.15–0.39). Conclusion The MEPS-G is not sufficiently valid, which is consistent with its English version. The patient-based dimensions were a weakness, demonstrating high risk of bias. There is no general recommendation for the utilization of the MEPS-G as outcome measurement for patients with elbow pathologies.

Background: Alexithymia is associated to Eating Disorders (ED) and relevant for their prognosis but it is uncertain if it is ubiquitous, primary, and necessary for ED outburst. Methods: 124 ED outpatients and 80 healthy controls were compared with the Toronto Alexithymia Scale, personality, and psychopathology measures. Alexithymia and the other features are compared between anorexia nervosa (AN), bulimia nervosa (BN) and control groups. Alexithymia-based clusters were explored and compared with controls. Alexithymia traits are correlated with the other features. Results: Difficulty in identifying feelings was ubiquitous in ED subjects. A Non-Alexithymic Cluster (NAC) and an Alexithymic Cluster (ALC) were found with no difference in AN/BN distribution. ALC displays disordered personality and high psychopathology. Self-directiveness and interoceptive awareness were independently related to alexithymia and to depressive feelings. These two features along with depressive features completely accounted for alexithymia variance. Conclusion: Even though the difficulty in identifying feelings is ubiquitous in ED subjects, Alexithymia may not represent a primary trait but a complex dysfunction consequent to co-occurring character immaturity, altered interoceptive awareness, and depressive traits.

Body conformation traits are directly associated with longevity, fertility, health, and workability in dairy cows and have been under direct genetic selection for many decades in various countries worldwide. The main objectives of this study were to perform genome-wide association studies and functional enrichment analyses for fourteen body conformation traits using imputed high-density single nucleotide polymorphism (SNP) genotypes. The traits analyzed include body condition score (BCS), body depth (BD), bone quality (BQ), chest width (CW), dairy capacity (DC), foot angle (FAN), front legs view (FLV), heel depth (HDe), height at front end (HFE), locomotion (LOC), rear legs rear view (RLRV), rear legs side view (RLSV), stature (ST), and a composite feet and legs score index (FL) of Holstein cows scored in Canada. De-regressed estimated breeding values from a dataset of 39,135 North American Holstein animals were used as pseudo-phenotypes in the genome-wide association analyses. A mixed linear model was used to estimate the SNP effects, which ranged from 239,533 to 242,747 markers depending on the trait analyzed. Genes and quantitative trait loci (QTL) located up to 100 Kb upstream or downstream of the significant SNPs previously cited in the Animal QTLdb were detected, and functional enrichment analyses were performed for the candidate genes identified for each trait. A total of 20, 60, 13, 17, 27, 8, 7, 19, 4, 10, 13, 15, 7, and 13 genome-wide statistically significant SNPs for Bonferroni correction based on independent chromosomal segments were identified for BCS, BD, BQ, CW, DC, FAN, FLV, HDe, HFE, LOC, RLRV, RLSV, ST, and FL, respectively. The significant SNPs were located across the whole genome, except on chromosomes BTA24, BTA27, and BTA29. Four markers (for BCS, BD, HDe, and RLRV) were statistically significant when considering a much stricter threshold for the Bonferroni correction for multiple tests. Moreover, the genomic regions identified overlap with various QTL previously reported for the trait groups of exterior, health, meat and carcass, milk, production, and reproduction. The functional enrichment analyses revealed 27 significant gene ontology terms. These enriched genomic regions harbor various candidate genes previously reported as linked to bone development, metabolism, as well as infectious and immunological diseases., Competing Interests: Author TC was employed by the company PEAK. FM was employed by the company Lactanet Canada. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Sousa Junior, Pinto, Cruz, Oliveira Junior, Oliveira, Chud, Pedrosa, Miglior, Schenkel and Brito.)

Background: Structural variants (SVs) such as deletions, duplications, and insertions are known to contribute to phenotypic variation but remain challenging to identify and genotype. A more complete, accessible, and assessable collection of SVs will assist efforts to study SV function in cattle and to incorporate SV genotyping into animal evaluation., Results: In this work we produced a large and deeply characterized collection of SVs in Holstein cattle using two popular SV callers (Manta and Smoove) and publicly available Illumina whole-genome sequence (WGS) read sets from 310 samples (290 male, 20 female, mean 20X coverage). Manta and Smoove identified 31 K and 68 K SVs, respectively. In total the SVs cover 5% (Manta) and 6% (Smoove) of the reference genome, in contrast to the 1% impacted by SNPs and indels. SV genotypes from each caller were confirmed to accurately recapitulate animal relationships estimated using WGS SNP genotypes from the same dataset, with Manta genotypes outperforming Smoove, and deletions outperforming duplications. To support efforts to link the SVs to phenotypic variation, overlapping and tag SNPs were identified for each SV, using genotype sets extracted from the WGS results corresponding to two bovine SNP chips (BovineSNP50 and BovineHD). 9% (Manta) and 11% (Smoove) of the SVs were found to have overlapping BovineHD panel SNPs, while 21% (Manta) and 9% (Smoove) have BovineHD panel tag SNPs. A custom interactive database ( https://svdb-dc.pslab.ca ) containing the identified sequence variants with extensive annotations, gene feature information, and BAM file content for all SVs was created to enable the evaluation and prioritization of SVs for further study. Illustrative examples involving the genes POPDC3, ORM1, G2E3, FANCI, TFB1M, FOXC2, N4BP2, GSTA3, and COPA show how this resource can be used to find well-supported genic SVs, determine SV breakpoints, design genotyping approaches, and identify processed pseudogenes masquerading as deletions., Conclusions: The resources developed through this study can be used to explore sequence variation in Holstein cattle and to develop strategies for studying SVs of interest. The lack of overlapping and tag SNPs from commonly used SNP chips for most of the SVs suggests that other genotyping approaches will be needed (for example direct genotyping) to understand their potential contributions to phenotype. The included SV genotype assessments point to challenges in characterizing SVs, especially duplications, using short-read data and support ongoing efforts to better characterize cattle genomes through long-read sequencing. Lastly, the identification of previously known functional SVs and additional CDS-overlapping SVs supports the phenotypic relevance of this dataset., (© 2024. The Author(s).)

Bovine leukemia virus (BLV) is the causative agent of enzootic bovine leukosis (leukosis) frequently observed in North American dairy herds. Infection with BLV can lead to persistent lymphocytosis and tumors, and is associated with decreased production, immunity and fertility. With no available treatment or vaccine, reducing the prevalence of leukosis through management and culling has not yet been successful. Genetic selection could contribute to permanent improvement in dairy cattle resistance to leukosis. This study aimed to examine the prevalence and impact of leukosis in Canada, and to assess the potential for including leukosis resistance in Canadian national genetic evaluations by characterizing the genetic architecture of leukosis resistance using pedigree and genomic information. A total of 117,349 milk enzyme-linked immunosorbent assay test records on 96,779 Holstein cows from 950 Canadian herds taken between 2007 and 2021 were provided by Lactanet Canada (Guelph, ON, Canada). Each cow was classified as test-positive for leukosis or test-negative for leukosis. Leukosis was present in approximately 77% of herds tested; within those herds, an average of 39% of cows tested were test positive for leukosis. Heritabilities of 0.10 (SE = 0.001) and 0.07 (SE <0.001) were estimated for leukosis resistance using a linear animal model and BLUP or single-step GBLUP methodology, respectively. Breeding value correlations were estimated between leukosis resistance and economically important and phenotypically relevant traits. Most correlations between leukosis resistance and traits already included in Canadian genetic evaluations were favorable, with the exception of somatic cell score. The candidate genes for leukosis resistance identified using a genome-wide association study, were on chromosome 23, with some being part of the major histocompatibility complex. This study showed that genetic evaluation for leukosis resistance is possible, and could be considered for inclusion in Canadian national selection indices., (The Authors. Published by Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

Routine milk samples are commonly subjected to spectroscopic analysis within the mid-infrared (MIR) region of the electromagnetic spectrum to estimate macro-constituents of milk like fat, protein, lactose, and urea content. These spectra, however, can also be used to predict other traits, such as daily body condition score (BCS) change. The objective of the present study was to assess the transferability across countries of equations to predict daily body condition score change (ΔBCS) developed using milk MIR data collected in Ireland and in Canada. Body condition was scored on a scale from 1 (emaciated) to 5 (obese) in both countries. A total of 347,254 BCS records from 80,400 Canadian cows were available along with 73,193 BCS records from 6,572 Irish cows. Partial least squares regression (PLSR) and neural networks (NN) were separately used to predict daily ΔBCS. Two scenarios were studied 1) using Canadian and Irish data combined as the calibration data set to predict daily ΔBCS in Canada and in Ireland separately, and 2) Canadian and Irish data used separately to predict daily ΔBCS in each country separately. These prediction methods were applied to data with and without pretreatment (i.e., first derivative of the spectrum) as well as with and without standardizing daily ΔBCS across countries. For all the scenarios investigated, the correlation between actual and predicted daily ΔBCS when calibrated and validated (using cross-validation) in the same country ranged from 0.92 to 0.94, and from 0.85 to 0.87 for the Canadian and Irish data sets, respectively. When the data from Canada and Ireland were combined in the calibration process to predict daily ΔBCS, the correlations between actual and predicted ΔBCS were ≥ 0.90 and ≥ 0.80 for Canadian and Irish daily ΔBCS, respectively indicating no improvement in predictive ability. Predictive performance when calibrated using just Canadian data and validated using just Irish data was poor, and vice versa. Nonetheless, when developing equations for a country for which a limited database (i.e., 100 records) of gold standard and MIR data were available, predictive performance improved when the limited database was supplemented with the large data set from the other country. In general, for some of the investigated scenarios, standardizing the daily ΔBCS data within country before undertaking the calibration improved prediction accuracy. In conclusion, the benefit of merging data from different countries, at least based on the trait (i.e., daily ΔBCS) and countries (i.e., Ireland and Canada) considered in the present study were limited and, in cases, counter-productive., (© 2024, The Authors. Published by Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

This study aimed to evaluate the impact of copy number variants (CNV) on 13 reproduction and 12 disease traits in Holstein cattle. Intensity signal files containing log R ratio and B allele frequency information from 13,730 Holstein animals genotyped with a 95K SNP panel, and 8,467 Holstein animals genotyped with a 50K SNP panel were used to identify the CNVs. Subsequently, the identified CNVs were validated using whole-genome sequence data from 126 animals, resulting in 870 high-confidence copy number variant regions (CNVR) on 12,131 animals. Out of these, 54 CNVR had frequencies higher than or equal to 1% in the population and were used in the genome-wide association analysis (one CNVR at a time, including the G matrix). Results revealed that 4 CNVR were significantly associated with at least one of the traits analyzed in this study. Specifically, 2 CNVR were associated with 3 reproduction traits (i.e., calf survival, first service to conception, and nonreturn rate), and 2 CNVR were associated with 2 disease traits (i.e., metritis and retained placenta). These CNVR harbored genes implicated in immune response, cellular signaling, and neuronal development, supporting their potential involvement in these traits. Further investigations to unravel the mechanistic and functional implications of these CNVR on the mentioned traits are warranted., (The Authors. Published by Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

Interest in dairy cow health continues to grow as we better understand health's relationship with production potential and animal welfare. Over the past decade, efforts have been made to incorporate health traits into national genetic evaluations. However, they have focused on the mature cow, with calf health largely being neglected. Diarrhoea and respiratory disease comprise the main illnesses with regard to calf health. Conventional methods to control calf disease involve early separation of calves from the dam and housing calves individually. However, public concern regarding these methods, and growing evidence that these methods may negatively impact calf development, mean the dairy industry may move away from these practices. Genetic selection may be a promising tool to address these major disease issues. In this review, we examined current literature for enhancing calf health through genetics and discussed alternative approaches to improve calf health via the use of epidemiological modelling approaches, and the potential of indirectly selecting for improved calf health through improving colostrum quality. Heritability estimates on the observed scale for diarrhoea ranged from 0.03 to 0.20, while for respiratory disease, estimates ranged from 0.02 to 0.24. The breadth in these ranges is due, at least in part, to differences in disease prevalence, population structure, data editing and models, as well as data collection practices, which should be all considered when comparing literature values. Incorporation of epidemiological theory into quantitative genetics provides an opportunity to better determine the level of genetic variation in disease traits, as it accounts for disease transmission among contemporaries. Colostrum intake is a major determinant of whether a calf develops either respiratory disease or diarrhoea. Colostrum traits have the advantage of being measured and reported on a continuous scale, which removes the issues classically associated with binary disease traits. Overall, genetic selection for improved calf health is feasible. However, to ensure the maximum response, first steps by any industry members should focus efforts on standardising recording practices and encouragement of uploading information to genetic evaluation centres through herd management software, as high-quality phenotypes are the backbone of any successful breeding programme., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)