Genetic parameters of postnatal mortality in Danish Holstein calves

Genetic evaluation for stillbirth and preweaning mortality in Australian dairy cattle

The welfare of calves is important to both farmers and consumers. Practices that increase the proportion of calves born alive and enable them to thrive through to weaning contribute to improved sustainability. Stillbirths (SB) are calvings where the calf dies at birth or within 24 h after birth. Preweaning mortality (PWM) refers to calves that die after the first day of life but before weaning based on termination data. Both SB and PWM are binary traits characterized by low heritability. Data collection for these traits is incomplete, compared with traits such as milk yield in cows. Despite these challenges, genetic variation can be measured and used to produce breeding tools, such as EBVs, to reduce calf mortality over time. The aim of this study was to compare the performance of various linear models to predict SB and PWM traits in Holstein and Jersey cattle and evaluate their applicability for industry-wide use in the Australian dairy industry. Calving records from around 2.25 million Holstein and Jersey dams were obtained from DataGene's Central Data Repository from the year 2000 onward, to calculate genetic parameters. About 7% of calves were recorded as SB in the period from 2000 to 2021 (n = 1.48 million calvings). The prevalence of PWM was much lower than SB during the same period at 2% (n = 0.89 million calves). Genetic parameters were estimated for SB direct, SB maternal, and PWM using bivariate linear models with calving ease (CE) as the second trait in the model. The heritability of these calf traits was low and varied between 1% and 5% depending on the breed, trait, and model. In Holstein cattle, heritabilities were 2% for PWM and SB direct and 1% for SB maternal, whereas in Jersey cattle heritabilities were 5% for PWM, 2% for SB direct, and 1% for SB maternal. The genetic trends for both SB direct and SB maternal in Holstein cattle indicate improvement in both traits, whereas there was no apparent increase or decrease in PWM in the past 2 decades. The coefficient of genetic variation for SB direct and PWM was between 11.7% and 23.0% in Holstein and Jersey cattle, demonstrating considerable genetic variation in calf survival traits as a first step to using genetic selection to increase the proportion of calves born alive and calves weaned. A focus on improved calf and calving recording practices is expected to increase the reliability of genetic predictions.

Risk Factor Analysis and Genetic Parameter Estimation for Pre-Weaning Mortality Traits in Boer, Spanish, and Crossbred Goat Kids

The objectives of this study were to evaluate fixed risk factors associated with PWM and to estimate genetic parameters for PWM. A total of 927 birth records from a mixed population of purebred and crossbred Boer and Spanish goats born between 2016 and 2023 at the International Goat Research Center (IGRC) were used for this study. Four binary traits were studied: D0-3 (death within 3 days after birth), D4-60 (death between 4 and 60 days), D61-90 (death between 61 and 90 days), and D0-90 (death within 90 days). Logistic regression models were used to evaluate the risk factors associated with PWM traits. Bayesian threshold models and Gibbs sampling were used to estimate the genetic parameters. Birth weight, season, litter size, sex, dam age, breed, and heterosis were found to be significantly associated with at least one of the PWM traits. Heritability estimates were 0.263, 0.124, 0.080, and 0.207, for D0-3, D4-60, D61-90, and D0-90, respectively. The genetic correlations between the studied traits ranged from 0.892 (D0-3 and D0-90) to 0.999 (D0-3 and D61-90). These results suggest that PWM in goats is influenced by both non-genetic and genetic factors and can be reduced by management, genetic selection, and crossbreeding approaches.

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.

Risk factors and genetic parameter estimates for preweaning survival of Fogera calves

This study utilised mortality records of 1 043 Fogera calves maintained at Andassa Livestock Research Center from 1984 to 2021 to investigate the factors that influence survival and estimate genetic parameters for the preweaning survival of Fogera calves. Survival was defined as the probability of surviving in a given length of time. Survival analysis was done using the Weibull proportional hazard model with Survival Kit version 6.1 software. Genetic variance and heritability estimates were estimated using the sire model. The proportion of right-censored calves up to 1, 4, and 8 months of age was 90.8, 87.8, and 83.5%, respectively. Around 55.8% of all deaths (16.5%) occurred up to one month of age. In addition to birth year, sex, season, and weight at birth were the most important risk factors for calf mortality. The heritability estimates for the survival of calves at 1, 4, and 8 months of age were 0.26 ± 0.14, 0.22 ± 0.13, and 0.38 ± 0.18, respectively. Moderate heritability was estimated at the age of eight months, implying that the inclusion of survival traits in the selection criteria and inclusion in the breeding goal will enhance the preweaning survival rate of calves. Similarly, higher differences in estimated breeding values of sires for survival suggest that the selection of sires with higher estimated breeding values could improve the survival potential of calves. The decreased genetic trend of 3.34% year-1 for the survival potential of Fogera calves during the study periods suggested that survival traits should be included in the breeding goal to reduce the mortality rate.

Genetic parameters for dairy calf and replacement heifer wellness traits and their association with cow longevity and health indicators in Holstein cattle

High mortality and involuntary culling rates cause great economic losses to the worldwide dairy cattle industry. However, there is low emphasis on wellness traits in replacement animals (dairy calves and replacement heifers) during their development stages in modern dairy cattle breeding programs. Therefore, the main objectives of this study were to estimate genetic parameters of wellness traits in replacement cattle (replacement wellness traits) and obtain their genetic correlations with 12 cow health and longevity traits in the Chinese Holstein population. Seven replacement wellness traits were analyzed, including birth weight, survival from 3 to 60 d (Sur1), survival from 61 to 365 d (Sur2), survival from 366 d to the first calving (Sur3), calf diarrhea, calf pneumonia, and calf serum total protein (STP). Single and bivariate animal models were employed to estimate (co)variance components using the data from 189,980 Holstein cattle. The genetic correlations between replacement wellness traits and cow longevity, health traits were calculated by employing bivariate models, including 6 longevity traits and 6 health traits (clinical mastitis, metritis, ketosis, displaced abomasum, milk fever, and hoof health or hoof disease). The estimated heritabilities (± SE) were 0.335 (± 0.008), 0.088 (± 0.005), 0.166 (± 0.006), 0.102 (±0 .006), 0.048 (± 0.003), 0.063 (± 0.004), and 0.170 (± 0.019) for birth weight, Sur1, Sur2, Sur3, pneumonia, diarrhea, and STP, respectively. The majority of the genetic correlations among the 7 replacement wellness traits were negligible. The genetic correlations among Sur1, Sur2, and Sur3 ranged from 0.112 (Sur1 and Sur3) to 0.445 (Sur1 and Sur2) when fitting a linear model (estimates in the observed scale), and from 0.560 (Sur1 and Sur3) to 0.773 (Sur1 and Sur2) when fitting a threshold model (estimates in the liability scale). The genetic correlations between replacement wellness and cow longevity were low (absolute value lower than 0.30), but some of them were significantly different from zero. Compared with other replacement wellness traits, Sur3 and STP had relatively high genetic correlations with cow longevity. Replacement wellness traits are heritable and can be improved through direct genetic and genomic selection. The results from the current study will contribute for better balancing dairy cattle breeding goals to genetically improve dairy cattle wellness in the period from birth to first calving.

Reliabilities of Genomic Prediction for Young Stock Survival Traits Using 54K SNP Chip Augmented With Additional Single-Nucleotide Polymorphisms Selected From Imputed Whole-Genome Sequencing Data

This study investigated effects of integrating single-nucleotide polymorphisms (SNPs) selected based on previous genome-wide association studies (GWASs), from imputed whole-genome sequencing (WGS) data, in the conventional 54K chip on genomic prediction reliability of young stock survival (YSS) traits in dairy cattle. The WGS SNPs included two groups of SNP sets that were selected based on GWAS in the Danish Holstein for YSS index (YSS_SNPs, n = 98) and SNPs chosen as peaks of quantitative trait loci for the traits of Nordic total merit index in Denmark–Finland–Sweden dairy cattle populations (DFS_SNPs, n = 1,541). Additionally, the study also investigated the possibility of improving genomic prediction reliability for survival traits by modeling the SNPs within recessive lethal haplotypes (LET_SNP, n = 130) detected from the 54K chip in the Nordic Holstein. De-regressed proofs (DRPs) were obtained from 6,558 Danish Holstein bulls genotyped with either 54K chip or customized LD chip that includes SNPs in the standard LD chip and some of the selected WGS SNPs. The chip data were subsequently imputed to 54K SNP together with the selected WGS SNPs. Genomic best linear unbiased prediction (GBLUP) models were implemented to predict breeding values through either pooling the 54K and selected WGS SNPs together as one genetic component (a one-component model) or considering 54K SNPs and selected WGS SNPs as two separate genetic components (a two-component model). Across all the traits, inclusion of each of the selected WGS SNP sets led to negligible improvements in prediction accuracies (0.17 percentage points on average) compared to prediction using only 54K. Similarly, marginal improvement in prediction reliability was obtained when all the selected WGS SNPs were included (0.22 percentage points). No further improvement in prediction reliability was observed when considering random regression on genotype code of recessive lethal alleles in the model including both groups of the WGS SNPs. Additionally, there was no difference in prediction reliability from integrating the selected WGS SNP sets through the two-component model compared to the one-component GBLUP.

Genomic evaluation of dairy heifer livability

Differences in breeds and sire lines suggest the presence of a genetic component for heifer livability (HLIV). Genomic evaluation for this trait can increase profitability and improve animal health and welfare. Evaluations for HLIV were examined from 3,362,499 calf data records from heifers of all breeds born from 2009 to 2016. Data were obtained from the national cooperator database maintained by the Council on Dairy Cattle Breeding (https://www.uscdcb.com/). The total number of deaths reported was 134,753 (4.01%), which included herds with death loss between 1.5 and 25.5%. Age at death was evaluated and ranged from >2 d of age until the heifer left the herd, with a maximum of 18 mo of age. Records were not included until 3 yr after the birthdate so that live status of contemporaries could be confirmed by a calving date for those animals. Deaths observed until 2 d after birth were considered to be a stillbirth rather than a failure of HLIV. The scale used for analysis of HLIV was 0 (died) or 100 (live), and the heritability estimate was 0.7% based on sire model with restricted maximum likelihood estimation. Genomic predicted transmitting abilities for Holstein ranged from -1.6% to +1.6% with a standard deviation of 0.5%, and genomic predicted transmitting abilities for Jersey ranged from -0.5% to +0.5% with a standard deviation of 0.2%. The mean overall death loss was about 4%. Reliabilities of genomic predictions for young animals averaged 46% for Holsteins and 30% for Jerseys, and corresponding traditional parent average reliabilities averaged 16% and 12%, respectively. Correlations of HLIV were 0.44 with productive life, 0.18 to 0.22 with yield traits, and 0.29 with early first calving on proven Holstein bulls. The HLIV trait had a favorable genetic trend in recent years, likely because of the indirect selection associated with the correlated traits. The trait HLIV should receive 1% of emphasis on the Lifetime Net Merit index, resulting in economic progress worth $50,000/yr. By encouraging more comprehensive recording on calf mortality, the reliabilities of genetic predictions could increase significantly.

A 44-kb deleted-type copy number variation is associated with decreasing complement component activity and calf mortality in Japanese Black cattle

BACKGROUND

Calf mortality generally occurs in calves prior to weaning, which is a serious problem in cattle breeding. Several causative variants of monogenic Mendelian disorders in calf mortality have been identified, whereas genetic factors affecting the susceptibility of calves to death are not well known. To identify variants associated with calf mortality in Japanese Black cattle, we evaluated calf mortality as a categorical trait with a threshold model and performed a genome-wide copy number variation (CNV) association study on calf mortality.

RESULTS

We identified a 44-kb deleted-type CNV ranging from 103,317,687 to 103,361,802 bp on chromosome 5, which was associated with the mortality of 1-180-day-old calves. The CNV harbored C1RL, a pseudogene, and an IncRNA localized in the C1R and C1S gene cluster, which is a component of the classical complement activation pathway for immune complexes for infectious pathogens. The average complement activity in CNVR_221 homozygotes at postnatal day 7 was significantly lower than that of wild-type animals and heterozygotes. The frequency of the risk allele in dead calves suffering from diarrhea and pneumonia and in healthy cows was 0.35 and 0.28, respectively (odds ratio = 2.2, P = 0.016), suggesting that CNVR_221 was associated with the mortality of Japanese Black calves suffering from an infectious disease.

CONCLUSIONS

This study identified a deleted-type CNV associated with the mortality of 1-180-day-old calves. The complement activity in CNVR_221 homozygotes was significantly lower than that in heterozygotes and wild type animals. The frequency of the risk allele was higher in dead calves suffering from an infectious disease than in healthy cows. These results suggest that the existence of CNVR_221 in calves could be attributed to a reduction in complement activity, which in turn leads to susceptibility to infections. Thus, the risk allele could serve as a useful marker to reduce the mortality of infected Japanese Black calves.

Improving the accuracy of predictions for cow survival by multivariate evaluation model

Context Cow survival measures the ability of cows to survive from the current to subsequent lactation. In addition to economic gain, genetic selection for survival could improve animal welfare by increasing the adaptability and resilience of the cows to both environmental and health challenges. However, survival is a complex trait because it results from a diverse range of reasons for culling of cows from the herd. Consequently, the accuracy of genetic predictions of direct survival are often low. Aims Our aim was to increase the accuracy of predictions of survival in Holstein and Jersey sires by including important predictor traits in multi-trait evaluation models. Methods Phenotypic and genetic correlations between survival trait deviations (TDs) and 35 routinely measured traits (including milk yield, fertility and type traits) were estimated using bivariate sire models. Survival TDs for 538 394 Holstein and 63 839 Jersey cows were used in our study; these cows or their close relatives also had milk, fertility and type traits records between 2002 and 2019. These genetic parameters were required to assess the potential usefulness of predictor traits for the prediction of survival. Key results Survival was genetically correlated with milk, fat and protein yields, overall type, composite mammary system and fertility TDs in both Holstein and Jersey. Further, most of the type traits related to feet and legs, and rump, were also correlated with survival TDs in Jersey. For sires, the accuracy of predictions for survival increased by 0.05 for Holsteins (from 0.54 to 0.59) and for Jerseys (from 0.48 to 0.53) through the use of multivariate models compared with univariate models. Conclusions Survival was genetically associated with traits affecting voluntary and involuntary culling and when included in multi-trait genetic evaluation models, they moderately improved the accuracy of genetic prediction of survival. Implications Predictor traits can be used to increase the accuracy of predictions of survival through the use of multi-trait models. The inclusion of breed-specific predictor traits should be considered, especially for Jerseys in genetic evaluations of survival.

Genetic parameters of passive transfer of immunity for US organic Holstein calves

Passive transfer of immunity is important for calf health and survival. The objectives of this study were to estimate genetic parameters for calf passive transfer of immunity through producer-recorded serum total protein (STP) and to determine associations with other routinely evaluated traits in organic Holstein calves (n = 16,725) that were born between July 2013 to June 2018; a restricted subset (n = 7,518) of calves with known Holstein maternal grandsires was analyzed separately. Producers measured STP on farm, and STP was extracted from farm management software. Failure of passive transfer of immunity (FPT) was declared for calves with STP ≤5.2 g/dL. Calves that had the opportunity to reach 1 yr of age were recorded as either staying in the herd or leaving the herd (STAY365). Univariate and threshold models were fitted for STP and FPT, respectively, and included the fixed effects of herd-year-month of birth, calf age in days at STP measurement, dam age in years, and random effects of animal and birthdate within herd. Model effects for STAY365 included the fixed effects of herd-year-month of birth and random effects of animal and birthdate within herd. Multivariate analyses of STP with FPT or STAY365 were conducted to determine the genetic correlation between traits and STP was also regressed on gestation length. Heritability estimates of STP were 0.06 and 0.08 for full and restricted data, respectively. Heritability estimates for FPT were 0.04 and 0.06 for full and restricted data, respectively. The genetic correlation between STP and FPT was near unity. Heritability estimates for STAY365 ranged from 0.08 to 0.11 with genetic correlation estimates between STP and STAY365 ranging from 0.19 and 0.25. Approximate genetic correlations were estimated for sires (n = 302 and n = 256 for full and restricted data, respectively) with at least 10 daughters for STP and predicted transmitting abilities for health, calving traits, and production. Positive approximate genetic correlations were estimated for STP with cow livability, productive life, net merit dollars, and milk yield; favorable approximate genetic correlations were observed for daughter and sire calving ease, and sire stillbirth. Longer gestation length was associated with reduced STP genetically and phenotypically. These results suggest that passive transfer as measured through STP is heritable and favorably correlated with current measures of health, calving, and production.

Novel approach to incorporate information about recessive lethal genes increases the accuracy of genomic prediction for mortality traits

The genetic underpinnings of calf mortality can be partly polygenic and partly due to deleterious effects of recessive lethal alleles. Prediction of the genetic merits of selection candidates should thus take into account both genetic components contributing to calf mortality. However, simultaneously modeling polygenic risk and recessive lethal allele effects in genomic prediction is challenging due to effects that behave differently. In this study, we present a novel approach where mortality risk probabilities from polygenic and lethal allele components are predicted separately to compute the total risk probability of an individual for its future offspring as a basis for selection. We present methods for transforming genomic estimated breeding values of polygenic effect into risk probabilities using normal density and cumulative distribution functions and show computations of risk probability from recessive lethal alleles given sire genotypes and population recessive allele frequencies. Simulated data were used to test the novel approach as implemented in probit, logit, and linear models. In the simulation study, the accuracy of predicted risk probabilities was computed as the correlation between predicted mortality probabilities and observed calf mortality for validation sires. The results indicate that our novel approach can greatly increase the accuracy of selection for mortality traits compared with the accuracy of predictions obtained without distinguishing polygenic and lethal gene effects.

Estimation of genetic parameters for young stock survival in beef x dairy crossbred calves

Young stock survival is a trait of crucial importance in cattle breeding as calf mortality leads to economic losses and represents an animal welfare issue. The aim of this study was to estimate genetic parameters and sire breeding values for young stock survival in beef x dairy crossbred calves. Two traits were analysed with a univariate animal model: young stock survival between 1 to 30 days and 31 to 200 days after birth. Breed combinations with Belgian Blue sires outperformed all other sire breeds. The lowest survival rates were found for breed combinations with Jersey dams or Blonde d'Aquitaine sires. The results showed low but significant heritabilities (0.045 to 0.075) for both survival traits. Differences in breeding values between sires ranged from -2.5% to 3.5% and from -5.4% to 4.7% survival from 1 to 30 days and 31 to 200 days, respectively. Based on these findings, we concluded that it is feasible to breed for improved young stock survival in beef x dairy crossbred calves. This will hopefully contribute to increasing the survival rate of the calves and reduce economic losses for the farmers.

Factors influencing calf mortality in zebu and crossbred cattle reared under subtropical agroclimatic conditions

Data on birth weight and mortality pattern of Zebu (Sahiwal and Tharparkar) and Crossbred (Holstein Friesian × Tharparkar) cattle spread over 16 years were utilized to analyze the causes of calf mortality and to study the effect of non-genetic factors on calf mortality. Calf mortality was higher in crossbred (27.7%) compared to either Sahiwal (20.7%) or Tharparkar cattle (11.9%). Age group wise analysis revealed maximum mortality within one month age in Zebu cattle, and during 1–3 months age in crossbred cattle. Mortality was higher in calves born during winter, summer and rainy seasons in Sahiwal, crossbred and Tharparkar, respectively. Mortality was higher among male calves compared to female calves. Significantly higher proportion of Sahiwal calves died due to respiratory problems, while general debility was the major reason for calf mortality in crossbred and Tharparkar cattle. Season of birth had highly significant influence within one month age in Sahiwal and crossbred cattle. Influence of all the non genetic factors on calf mortality at various age groups was found to be non significant in Tharparkar cattle. It is inferred that calf mortality was higher in crossbred compared to Zebu cattle and the effect of season of birth and birth weight had a significant effect on calf mortality during first three months age. Among the several causes, respiratory problem was a significant reason for the calf mortality.

Risk factors associated with animal mortality in pasture-based, seasonal-calving dairy and beef herds

Animal mortality is indicative of animal health and welfare standards, which are of growing concern to the agricultural industry. The objective of the present study was to ascertain risk factors associated with mortality at multiple life stages in pasture-based, seasonal-calving dairy and beef herds. Males and females were stratified into seven life stages based on age (0 to 2 d, 3 to 7 d, 8 to 30 d, 31 to 182 d, 183 to 365 d, 366 to 730 d, and 731 to 1,095 d) whereas females with ≥1 calving event were further stratified into five life stages based on cow parity number (1, 2, 3, 4, and 5). Mortality was defined as whether an animal died during each life stage; only animals that either survived the entire duration or died during a life stage were considered. The data, following edits, consisted of 4,404,122 records from 1,358,712 animals. Multivariable logistic regression was used to estimate the logit of the probability of mortality in each life stage separately. The odds of a young animal (i.e., aged ≤ 1,095 d) dying was generally greater if veterinary assistance was required at their birth relative to no assistance (odds ratio [OR]: 3.10 to 31.85), if the animal was a twin relative to a singleton (OR: 1.46 to 2.31) or if the animal was male relative to female (OR: 1.14 to 6.15). Moreover, the odds of a cow (i.e., females with ≥1 calving event) dying were greater when she required veterinary assistance at calving (OR: 2.69 to 7.55) compared with a cow that did not require any assistance, if she produced twin relative to singleton progeny (OR: 1.59 to 2.03) or male relative to female progeny (OR: 1.09 to 1.20). Additionally, the odds of a first or second parity cow dying when she herself had received veterinary assistance at birth were only 0.63 to 0.66 times that of a cow that was provided no assistance at birth. For both young animals and cows, the odds of dying generally increased with herd size, whereas animals residing in expanding herds had lower odds of dying. Results from the present study indicate that the risk factors associated with mortality in pasture-based, seasonal-calving herds are similar to those reported in literature in confinement, nonseasonal-calving herds. Moreover, the present study identifies that these risk factors are similar in both dairy and beef herds, yet the magnitude of the association often differs and also changes with life stage.

A missense mutation in TUBD1 is associated with high juvenile mortality in Braunvieh and Fleckvieh cattle

Background

Haplotypes with reduced or missing homozygosity may harbor deleterious alleles that compromise juvenile survival. A scan for homozygous haplotype deficiency revealed a short segment on bovine chromosome 19 (Braunvieh haplotype 2, BH2) that was associated with high juvenile mortality in Braunvieh cattle. However, the molecular genetic underpinnings and the pathophysiology of BH2 remain to be elucidated.

Results

The frequency of BH2 was 6.5 % in 8,446 Braunvieh animals from the national bovine genome databases. Both perinatal and juvenile mortality of BH2 homozygous calves were higher than the average in Braunvieh cattle resulting in a depletion of BH2 homozygous adult animals (P = 9.3x10⁻¹²). The analysis of whole-genome sequence data from 54 Braunvieh animals uncovered a missense mutation in TUBD1 (rs383232842, p.H210R) that was compatible with recessive inheritance of BH2. The availability of sequence data of 236 animals from diverse bovine populations revealed that the missense mutation also segregated at a low frequency (1.7 %) in the Fleckvieh breed. A validation study in 37,314 Fleckvieh animals confirmed high juvenile mortality of homozygous calves (P = 2.2x10⁻¹⁵). Our findings show that the putative disease allele is located on an ancestral haplotype that segregates in Braunvieh and Fleckvieh cattle. To unravel the pathophysiology of BH2, six homozygous animals were examined at the animal clinic. Clinical and pathological findings revealed that homozygous calves suffered from chronic airway disease possibly resulting from defective cilia in the respiratory tract.

Conclusions

A missense mutation in TUBD1 is associated with high perinatal and juvenile mortality in Braunvieh and Fleckvieh cattle. The mutation is located on a common haplotype likely originating from an ancient ancestor of Braunvieh and Fleckvieh cattle. Our findings demonstrate for the first time that deleterious alleles may segregate across closed cattle breeds without recent admixture. Homozygous calves suffer from chronic airway disease resulting in poor growth performance and high juvenile mortality. The respiratory manifestations resemble key features of diseases resulting from impaired function of airway cilia.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2742-y) contains supplementary material, which is available to authorized users.

Effect of infrared lamps to ameliorate cold stress in Vrindavani calves

Aim:

This study was conducted to determine the effect of infrared lamps to ameliorate cold stress in Vrindavani (Holstein Friesian × Brown Swiss × Jersey × Hariana) calves.

Materials and Methods:

For the present investigation, ten newborn Vrindavani calves were randomly divided into two groups (G₁ and G₂) of five each. The experiment was conducted from 2^nd November to 8^th February when the environmental temperature was at the lowest. The calves of G₁ were provided with no additional protection while the calves of G₂ were protected against the cold weather by providing heat using the infrared lamps. The body weight (kg) of the calves was recorded at weekly interval. The blood samples collected within 6 h of birth and then at fortnightly interval were analyzed for packed cell volume (PCV, %), hemoglobin (Hb, g/dl). Besides, the serum biochemical parameters, viz., Total serum protein (TSP, g/l), albumin (g/l), globulin (g/l), albumin globulin ratio (A:G) and important stress parameters, viz., triiodothyronine (T₃, ng/ml), thyroxine (T₄, ng/ml) and cortisol (ng/ml) were also estimated.

Results:

The calves of G₂ showed higher body weight gain as compared to G₁. The differences were found to be highly significant (p<0.01). The calves in G₁ showed comparatively higher values of PCV and Hb and the differences were found to be significant (p<0.05) on 45^th day for PCV and highly significant (p<0.01) on 60^th day for PCV and on 45^th day for Hb. The values of TSP and albumin were comparatively higher in calves of G₁ as compared to G₂ and the differences were highly significant (p<0.01) on 45^th day for both TSP and albumin and significant (p<0.05) on 60^th day for albumin. Significantly (p<0.01) higher values of cortisol and T₄ were observed on 15 and 45^th day in calves of G₁ as compared to G₂. The T₃ levels were also found higher in calves of G₁ than G₂ and the differences were significant (p<0.05) on 15 and 30^th day and highly significant (p<0.01) on 45^th day of the study.

Conclusion:

Based on the results, it could be concluded that the infrared lamps are efficient in providing favorable microclimate and hence can be effectively used in calf shed to protect newborn calves from adverse conditions of winter and to improve their body growth performance.

Genetic evaluation of calf and heifer survival in Iranian Holstein cattle using linear and threshold models

Calf and heifer survival are important traits in dairy cattle affecting profitability. This study was carried out to estimate genetic parameters of survival traits in female calves at different age periods, until nearly the first calving. Records of 49,583 female calves born during 1998 and 2009 were considered in five age periods as days 1-30, 31-180, 181-365, 366-760 and full period (day 1-760). Genetic components were estimated based on linear and threshold sire models and linear animal models. The models included both fixed effects (month of birth, dam's parity number, calving ease and twin/single) and random effects (herd-year, genetic effect of sire or animal and residual). Rates of death were 2.21, 3.37, 1.97, 4.14 and 12.4% for the above periods, respectively. Heritability estimates were very low ranging from 0.48 to 3.04, 0.62 to 3.51 and 0.50 to 4.24% for linear sire model, animal model and threshold sire model, respectively. Rank correlations between random effects of sires obtained with linear and threshold sire models and with linear animal and sire models were 0.82-0.95 and 0.61-0.83, respectively. The estimated genetic correlations between the five different periods were moderate and only significant for 31-180 and 181-365 (r(g) = 0.59), 31-180 and 366-760 (r(g) = 0.52), and 181-365 and 366-760 (r(g) = 0.42). The low genetic correlations in current study would suggest that survival at different periods may be affected by the same genes with different expression or by different genes. Even though the additive genetic variations of survival traits were small, it might be possible to improve these traits by traditional or genomic selection.

Genetic parameters of postnatal mortality and birth weight in Japanese Black calves

Postnatal mortality (PM) of calves is an economically important trait, because a high mortality rate of calves decreases farm income and significantly increases production costs. In spite of the economic importance of PM, genetic studies on PM have been scarce for Japanese Black cattle. The objectives of this study were to estimate the direct and maternal heritability for PM using a Bayesian threshold model with Gibbs sampling in Japanese Black cattle. The original data consisted of 43 723 records of animals born from January 2005 to June 2006. Four binary traits of mortality were considered: D1-14, D15-60, D61-180 and D1-180 with numbers indicating the period of risk in days after birth. Direct heritabilities for PM ranged from 0.12 to 0.31 and maternal heritabilities for PM were lower than the direct heritabilities and ranged from 0.02 to 0.16. Direct genetic correlations between D1-14 and D15-60, between D15-60 and D61-180, and between D1-14 and D61-180 were 0.501, 0.689 and 0.062, respectively. Direct genetic correlations of birth weight with D1-14, D15-60, D61-180 and D1-180 were 0.089, 0.482, 0.434 and 0.394, respectively. These results indicated that different genes were responsible for early and late PM and early PM (D1-14) can be genetically reduced without influencing birth weight.

Understanding the genetics of survival in dairy cows

Premature mortality and culling causes great wastage in the dairy industry, as a large number of heifers born never become productive or are culled before their full lactation potential is reached. The objectives of this study were to characterize survival and estimate genetic parameters for alternative longevity traits that considered (1) the survival of replacement heifers and (2) functional longevity of milking cows in the UK Holstein Friesian population, using combined information from the British Cattle Movement Service and milk recording organizations. Mortality of heifers was highest in the first month of life and was proportionately highest in calves born during winter months. Heifer mortality tended to decrease with age until about 16 mo onward; it then gradually increased, expected to be associated with culls due to reproductive failure or problems during pregnancy and calving. In milking cows, days of productive life (DPL) was analyzed as an alternative to the current trait lifespan score. Cows that died in 2009 on average lived for 6.8 yr with an average production of 4.3 yr. Heritability estimates were low for both heifer and cow survival and were ~0.01 and ~0.06, respectively. The positive genetic correlation between heifer survival with lifespan score (0.31) indicates that bulls that sire daughters with longer productive lives are also likely to have calves that survive and become replacement heifers. However, the magnitude of the genetic correlation suggests that survival in the rearing period and the milking herd are different traits. Genetic correlations were favorable between DPL with somatic cell count and fertility traits indicating that animals with a longer productive life tend to have lower somatic cell count, a shorter calving interval, fewer days to first service, and require fewer inseminations. However, an antagonistic relationship existed between DPL with milk and fat yield traits.

Estimation of genetic parameters for measures of calf survival in a population of Holstein heifer calves from a heifer-raising facility in New York State

The objectives of this study were to estimate the genetic parameters of survival to weaning and survival to exit for a population of Holstein calves from New York State, as well as to associate the estimated breeding values determined in the current study with traits from ongoing genetic evaluations used in Canada and the United States. Data were recorded for 7,372 heifer calves at a commercial rearing facility in New York State from arrival at 1 to 7 d of age for the duration of stay at the facility (on average, heifers departed the facility 1 mo before calving). Performance and disease up to weaning and mortality before and after weaning were recorded. Analyzed data were limited to daughters of sires with at least 10 calves originating from farms that had sent a minimum of 5 calves to be raised at the facility. As such, calves from 264 sires and 36 herds were studied using 2 statistical methods. The first method, calf survival, used a Weibull proportional hazards model, with survival defined as age at culling, death, or censoring. The second method, a 2-trait sire model, included survival from arrival to weaning (SUV1) and survival from weaning to exit (SUV2). Both models included fixed effects of arrival weight, serum total protein, weaning weight, season and year of birth, and calving ease score. Herd and sire were included as random effects. Significant associations among all fixed effects and calf survival were observed. In general, very light or heavy weight at arrival, low total protein, low weaning weight, and difficult birth increased risk of mortality for calves. The heritability of survival from the first method was 0.063. The heritabilities from the linear model were 0.001 for SUV1 and 0.036 for SUV2. The genetic correlation between SUV1 and SUV2 was 0.58. Genetic variance was close to zero for survival of calves to weaning, but was greater for survival after weaning through the growing period. Breeding values were estimated for SUV1 and SUV2 and correlated with routinely evaluated traits from Canadian and US genetic evaluations. Significant associations between genetic evaluations for survival traits and routinely evaluated traits in Canada and the United States were found, in particular with conformation body traits, somatic cell score, fertility, and longevity.

Genetic analysis of calf and heifer losses in Danish Holstein

Mortality in dairy cattle is not only relevant with regard to economic losses but also to animal health and welfare. Thus, the aim of this investigation was to explore the genetic background of postnatal mortality in calves and replacement heifers in different age groups until first calving in Danish Holsteins. Records of Danish Holstein heifer calves born in the years 1998 to 2007 were extracted from the Danish Cattle database (Danish Cattle, Skejby, Denmark). The following periods (P) were defined for analyses: P1=d 1 to 30, P2=d 31 to 180, P3=d 181 to 365, P4=d 366 until the day before first calving or a maximum age of 1,200 d if no calving was reported, and the full period P5=d 1 until the day before first calving or a maximum age of 1,200 d if no calving was reported. Records of animals slaughtered or exported within a defined period were set to missing for this and following periods, whereas their records were kept for preceding periods. After further data editing, more than 840,000 calves and heifers born in the years 1998 to 2007 were investigated. Mortality rates were 3.23, 2.66, 0.97, 1.92, and 9.36% for the defined periods P1 to P5, respectively. For the estimation of genetic parameters, linear and threshold sire models were applied. Effects accounted for were the random effects herd × year × season and sire as well as the fixed effects year × month, number of dam's parity (parities >5 were set to 5), calf size, and calving ease. In total, the pedigree consisted of 4,643 sires and 20,821 animals. Heritabilities for the linear model were low, ranging from 0.006 (P3) to 0.042 (P5). Heritabilities estimated by threshold models showed a wider range, from not significantly different from zero for periods with low frequencies to 0.082 for P1. The mortality rate until first calving was higher than the stillbirth rate. Genetic and phenotypic variation seemed to be sufficiently high to genetically improve the trait calf and heifer mortality. Hence, a routine genetic evaluation would be valuable for monitoring and for selecting fitter animals in the Danish Holstein cattle population.

The ontogeny of cross-sex genetic correlations: an analysis of patterns

The independent evolution of males and females is typically constrained by shared genetic variance. Despite substantial research, we still know little about the evolution of cross-sex genetic covariance and its standardized measure, the cross-sex genetic correlation (r(MF)). In particular, it is unclear if r(MF) tend to vary with age. We compiled 28 traits for which ontogenetic trends in r(MF) were documented. Decreases in r(MF) with age were observed significantly more often than increases and the mean effect size for the relationship between r(MF) and age was large and negative. This suggests that sexual dimorphism (SD) may typically evolve more readily for phenotypes expressed later in ontogeny and that evolutionary inferences related to the evolution of SD should be limited to the ontogenetic stage at which r(MF) was estimated. Knowledge about ontogenetic variation in r(MF) should help improving our understanding of evolutionary patterns related to SD and the resolution of intralocus sexual conflicts.

Short communication: Genetic analysis of respiratory disease in Norwegian Red calves

A genetic analysis of respiratory disease (RD) in Norwegian Red calves was conducted. This is the first genetic study of calf diseases based on data from the Norwegian health recording system, and RD was chosen because it is the most frequent disease in calves. Records on absence or presence of RD before 180 d of age for 250,212 calves (progeny of 728 Norwegian Red artificial insemination sires) were analyzed with a threshold model. A total of 0.7% of the calves had veterinary treatment of RD before 180 d of age. Heritability of RD in the underlying scale was 0.05, with a 95% credibility interval from 0.02 to 0.09. The "worst" sire had a predicted probability of RD that was more than twice as high as that of the "best" one (1.15 vs. 0.44%). Their 95% credibility intervals for predicted probability of RD, however, overlapped. With improved and more extensive recording of calf diseases, the precision in genetic evaluation of sires could increase considerably. The frequency of RD is very low in the Norwegian Red population at present, so there is not much scope for genetic improvement. However, this study indicates that reasonably precise genetic evaluation of sires for resistance to RD could be feasible.

Estimation of Genetic Parameters for Perinatal Sucking Behavior of Italian Brown Swiss Calves

Brown Swiss breeders sometimes experience difficulties in feeding calves because of the weak sucking ability of the calves in the early days of life. For the welfare of the calves, they should be suckled by their dams or should aggressively ingest colostrum immediately after birth. The composition of colostrum changes rapidly during the first few days of lactation, and the ability of calves to absorb the Ig decreases quickly as well. The aim of this study was to increase our knowledge of environmental and genetic components affecting the sucking response, to evaluate the possibility of selecting for this trait. Sucking ability was recorded in 3 categories (drank from the milk bucket nipple or bottle without help, drank with help, did not drink) at 5 post-natal meals (6, 12, 24, 48, and 72 h from birth). Records were analyzed with 2 different models: a single-trait threshold sire model, in which all observations were analyzed as a single trait with 5 levels, and a multiple-trait threshold liability sire model, in which meal-by-meal observations were analyzed as 5 different binary traits. Management procedures, the interval between birth and meals, parity, and season of birth were environmental factors affecting the variability in sucking ability. The heritability estimate for the single-trait analysis was 0.14, whereas heritabilities for the multiple-trait analysis were 0.26, 0.22, 0.21 0.12, and 0.13 for the first, second, third, fourth, and fifth meal, respectively. Estimated genetic correlations among traits were high (0.82 to 0.99). This study suggests the possibility of selection based on sucking ability. Future collection of larger data sets on the sucking response of calves in the first 2 meals after birth would increase the accuracy of genetic parameter estimates.

Genetic and nongenetic influences on vigor at birth and preweaning mortality of purebred and high percentage Brahman calves

The objectives of this study were to assess the risk associated with proportion Brahman inheritance, cow age, dystocia, and birth date weather conditions on calf vigor at birth (n = 3,253) and preweaning mortality (n = 3,631), and to estimate heritabilities for these traits. Calves that had poor vigor at birth and calves that died before weaning were coded 1, and those that had adequate birth vigor or survived to weaning were coded 0. Traits were analyzed using GLM. Year (1951 to 2002), cow age, calfgender, minimum temperature on date of birth (two levels: < 5.6 degrees C; or > 5.6 degrees C), and occurrence of dystocia were main effects in models. The proportion of Brahman inheritance in calves was modeled as a covariate. Males had greater odds of poor birth vigor (odds ratio = 1.44, 95% confidence interval = 1.14 to 1.82). The odds of death before weaning for steers relative to heifers approached significance (P = 0.07; odds ratio 1.41, 95% confidence interval 0.97 to 2.04). Calves born to young (3-yr-old) or very old (13 yr or older) cows had greater (P < 0.05) odds of poor vigor and death before weaning than calves of 5-yr-old cows. Calves with difficult births had 2.59 times greater odds of poor birth vigor (95% confidence interval 1.40 to 4.79) and 12.9 times greater odds of death before weaning (95% confidence interval 8.14 to 20.39) than calves born with no dystocia. Calves born on days with minimum temperatures of 5.6 degrees C or less had greater odds of poor vigor (odds ratio 1.97, 95% confidence interval 1.50 to 2.59) and of death before weaning (odds ratio 1.64, 95% confidence interval 1.27 to 2.13) than did calves born on days with higher minimums. The occurrence of rainfall on date of birth did not influence calf vigor at birth or preweaning mortality (P > 0.85). Purebred Brahman calves had 24.7 times greater odds (95% confidence interval 8.23 to 73.97) of poor vigor than 2/3 Brahman calves. The regression coefficient estimate for fraction of Brahman inheritance approached significance (P = 0.07) for preweaning mortality. Estimates of direct and maternal heritability were 0.09 +/- 0.05 and 0.10 +/- 0.04 for birth vigor, and 0.06 +/- 0.05 and 0.09 +/- 0.04, respectively, for preweaning mortality. Some exploitable genetic variation exists for these traits, but management of other factors may yield more immediate improvement than selection.