Genetic analysis of calf survival at different preweaning ages in beef cattle

Bayesian estimates of genetic effects on calf survival in Hardhenu (Bos taurus × Bos indicus) cattle

The aim of the present study is to carry out a risk analysis and Bayesian estimates of genetic effects on calf survival in Hardhenu cattle using data records of 2593 calves born to 102 sires and 790 dams over 25 years. The Bayesian analysis using Gibbs sampling was employed towards threshold animal models to estimate direct and maternal effects on animal survival of studied population. The results showed that mortality from birth to 3 months of age (S1), birth to 6 months of age (S2) and birth to 12 months of age (S3) was 10.22, 12.88 and 14.65%, respectively. It was revealed from the results of logistic regression analysis that the male animals had greater risk (1.41-1.61 times) of mortality during S1, S2 and S3 as compared to female animals. However, calves born during rainy season had higher risk (1.36 to 1.44 times) of mortality than calves born during winter season. Among died animals, the simultaneous infection of respiratory and digestive diseases had leading contribution (26.84%-30.19%) to deaths while alone of them contributed to 18%-20% only. On evaluation of six threshold animal models, model 1 was found to be most appropriate model and the Bayesian estimates (95% highest posterior density confidence intervals) of direct additive heritability for S1, S2 and S3 under model 1 were 0.15 ± 0.07 (0.04-0.23), 0.23 ± 0.12, (0.02-0.44) and 0.26 ± 0.06 (0.08-0.41), respectively. It was concluded that the inclusion of survival traits in existing selection criteria may be helpful to increase calf survival and ultimately economic gain in the dairy herd.

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.

Genetic and phenotypic parameters for litter size, survival rate, gestation length, and litter weight traits in American mink

The economic efficiency of mink production is greatly influenced by reproductive performance. Therefore, the objective of this study was to estimate phenotypic and genetic parameters for reproduction traits including total number of kits born (TB), number of live kits at birth (LB), number of live kits at weaning (LW), survival rate at birth (SB), survival rate at weaning (SW), gestation length (GL), average kit weight per litter at birth (AWB), average kit weight per litter at week 3 (AW3), and average kit weight per litter at weaning (AWW) in American mink. Data included records of 3,046 litters collected by the Canadian Centre for Fur Animal Research at Dalhousie Faculty of Agriculture between 2002 and 2016. Significance (P < 0.05) of fixed effects (year, number of matings, color type, age of dam, origin of dam, sex ratio, and number of live kits) and random effects of permanent environment were determined using univariate repeatability models. A significant effect of permanent environment was only found for survival rate traits (P < 0.05). Subsequently, genetic and phenotypic parameters for all traits were estimated by fitting a set of bivariate models using ASREML 4.0. Heritabilities (± SE) were estimated to be 0.07 ± 0.03 for TB, 0.07 ± 0.02 for LB, 0.09 ± 0.04 for LW, 0.13 ± 0.03 for SB, 0.10 ± 0.02 for SW, 0.29 ± 0.03 for GL, 0.28 ± 0.05 for AWB, 0.19 ± 0.04 for AW3, and 0.10 ± 0.04 for AWW. Moderate positive genetic correlation was observed between AWB with SB (0.66 ± 0.10) and SW (0.61 ± 0.13). Furthermore, genetic correlations of LB with SW and AWB were 0.55 ± 0.16 and 0.53 ± 0.18, respectively. On the other hand, negative and moderate genetic correlations were observed between GL and survival rates at birth (-0.43 ± 0.14) and at weaning (-0.37 ± 0.15). These results indicated that selection for higher litter weights at birth can effectively improve survival rate and number of live kits in mink farms. It was suggested to incorporate litter weight traits as a selection criterion to increase maternal ability in mink breeding programs. Unfavorable genetic trends were observed for the studied traits indicating that phenotypic selection with low selection intensity had not been an efficient method to improve them over the last 10 yr. It was recommended to use genetic or genomic evaluation methods for mink selection.

Crossbreed genetic performance study in the eventing horse competition

Eventing is an equestrian discipline combining dressage, show jumping and cross-country exercises. The Spanish Sport Horse (SSH) was used in this study as an example to develop a method to ascertain the influence of parental breeds on particular performances by linking their parental genetic contribution with the individual phenotype value computing the optimal breed contribution for each trait evaluated in eventing. Data included 1220 eventing records from 210 SSH animals. The genetic contribution of six main founder populations were computed for each SSH: the Spanish Purebreed (SPB), Arab Horse (A), Thoroughbred (TB), Selle Français (SF), German breeds (G) and North(-west) European (N) breeds. For this analysis we used BLUP (best linear unbiased predictor) animal models for five defined traits and for the total score. The genetic contribution as linear and quadratic adjustment and the interaction between genetic contributions were included as covariates in the genetic model to separate the possible combining ability from the breeding values. The optimal breed genetic contribution for each trait was maximised by using a simplex method. The best combination for conformation was 51% SPB and 49% N, for cross-country aptitude 23% SPB and 77% N, for dressage 48% SF and 52% N, and for show jumping 64% A and 36% N. For cross-country the best performance was predicted using 100% N genetic contribution and for the total score of 24% SF and 76% N. The combination of two breeds (group of breeds) seemed to be the best option for most of the traits. Although the results should be interpreted with caution, the importance of this paper is that it can be considered as a starting point of the analysis. The methodology applied here performed nicely in searching for the best contribution of several breeds to find the best combination for particular interests and could, therefore, be useful for other species/populations.

Estimation of genetic parameters for reproductive traits in alpacas

One of the main deficiencies affecting animal breeding programs in Peruvian alpacas is the low reproductive performance leading to low number of animals available to select from, decreasing strongly the selection intensity. Some reproductive traits could be improved by artificial selection, but very few information about genetic parameters exists for these traits in this specie. The aim of this study was to estimate genetic parameters for six reproductive traits in alpacas both in Suri (SU) and Huacaya (HU) ecotypes, as well as their genetic relationship with fiber and morphological traits. Dataset belonging to Pacomarca experimental farm collected between 2000 and 2014 was used. Number of records for age at first service (AFS), age at first calving (AFC), copulation time (CT), pregnancy diagnosis (PD), gestation length (GL), and calving interval (CI) were, respectively, 1704, 854, 19,770, 5874, 4290 and 934. Pedigree consisted of 7742 animals. Regarding reproductive traits, model of analysis included additive and residual random effects for all traits, and also permanent environmental effect for CT, PD, GL and CI traits, with color and year of recording as fixed effects for all the reproductive traits and also age at mating and sex of calf for GL trait. Estimated heritabilities, respectively for HU and SU were 0.19 and 0.09 for AFS, 0.45 and 0.59 for AFC, 0.04 and 0.05 for CT, 0.07 and 0.05 for PD, 0.12 and 0.20 for GL, and 0.14 and 0.09 for CI. Genetic correlations between them ranged from -0.96 to 0.70. No important genetic correlations were found between reproductive traits and fiber or morphological traits in HU. However, some moderate favorable genetic correlations were found between reproductive and either fiber and morphological traits in SU. According to estimated genetic correlations, some reproductive traits might be included as additional selection criteria in HU.

Estimates of direct and indirect effects for early juvenile survival in captive populations maintained for conservation purposes: the case of Cuvier's gazelle

Together with the avoidance of any negative impact of inbreeding, preservation of genetic variability for life-history traits that could undergo future selective pressure is a major issue in endangered species management programmes. However, most of these programmes ignore that, apart from the direct action of genes on such traits, parents, as contributors of offspring environment, can influence offspring performance through indirect parental effects (when parental genotype and phenotype exerts environmental influences on offspring phenotype independently of additive genetic effects). Using quantitative genetic models, we estimated the additive genetic variance for juvenile survival in a population of the endangered Cuvier's gazelle kept in captivity since 1975. The dataset analyzed included performance recording for 700 calves and a total pedigree of 740 individuals. Results indicated that in this population juvenile survival harbors significant additive genetic variance. The estimates of heritability obtained were in general moderate (0.115-0.457) and not affected by the inclusion of inbreeding in the models. Maternal genetic contribution to juvenile survival seems to be of major importance in this gazelle's population as well. Indirect genetic and indirect environmental effects assigned to mothers (i.e., maternal genetic and maternal permanent environmental effects) roughly explain a quarter of the total variance estimated for the trait analyzed. These findings have major evolutionary consequences for the species as show that offspring phenotypes can evolve strictly through changes in the environment provided by mothers. They are also relevant for the captive breeding programme of the species. To take into account, the contribution that mothers have on offspring phenotype through indirect genetic effects when designing pairing strategies might serve to identify those females with better ability to recruit, and, additionally, to predict reliable responses to selection in the captive population.

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.

Genetic architecture of rainbow trout survival from egg to adult

Survival from birth to a reproductive adult is a challenge that only robust individuals resistant to a variety of mortality factors will overcome. To assess whether survival traits share genetic architecture throughout the life cycle, we estimated genetic correlations for survival within fingerling stage, and across egg, fingerling and grow-out stages in farmed rainbow trout. Genetic parameters of survival at three life cycle stages were estimated for 249 166 individuals originating from ten year classes of a pedigreed population. Despite being an important fitness component, survival traits harboured significant but modest amount of genetic variation (h2=0.07-0.27). Weak associations between survival during egg-fry and fingerling periods, between early and late fingerling periods (rG=0.30) and generally low genetic correlations between fingerling and grow-out survival (mean rG=0.06) suggested that life-stage specific survival traits are best regarded as separate traits. However, in the sub-set of data with detailed time of death records, positive genetic correlations between early and late fingerling survival (rG=0.89) showed that during certain years the best genotypes in the early period were also among the best in the late period. That survival across fingerling period can be genetically the same, trait was indicated also by only slightly higher heritability (h2=0.15) estimated with the survival analysis of time to death during fingerling period compared to the analysis treating fingerling survival as a binary character (h2=0.11). The results imply that (1) inherited resistance against unknown mortality factors exists, but (2) ranking of genotypes changes across life stages.

Survival of the currently fittest: genetics of rainbow trout survival across time and space

As a fitness trait, survival is assumed to exhibit low heritability due to strong selection eroding genetic variation and/or spatio-temporal variation in mortality agents reducing genetic and increasing residual variation. The latter phenomenon in particular may contribute to low heritability in multigeneration data, even if certain cohorts exhibit significant genetic variation. Analysis of survival data from 10 year classes of rainbow trout reared at three test stations showed that treating survival as a single trait across all generations resulted in low heritability (h2 = 0.08-0.17). However, when heritabilities were estimated from homogeneous generation and test station-specific cohorts, a wide range of heritability values was revealed (h2 = 0.04-0.71). Of 64 genetic correlations between different cohorts, 20 were positive, but 16 were significantly negative, confirming that genetic architecture of survival is not stable across generations and environments. These results reveal the existence of hidden genetic variation for survival and demonstrate that treating survival as one trait over several generations may not reveal its true genetic architecture. Negative genetic correlations between cohorts indicate that overall survival has limited potential to predict general resistance, and care should be taken when using it as selection criterion.

Genetic relationships among calving ease, calving interval, birth weight, and weaning weight in the Asturiana de los Valles beef cattle breed1

The aim of this paper was to estimate direct and maternal genetic parameters for calving ease (CE), birth weight (BrW), weaning weight (WW), and calving interval (CI) to assess the possibility of including this information in beef cattle improvement programs. Field data, including a total of 59,813 animals (1,390 sires and 1,147 maternal grand sires) from the Asturiana de los Valles beef cattle breed, were analyzed with a multivariate linear model. Estimates of heritability for direct genetic effects (CED, CID, BrWD, and WWD) were 0.191 +/- 0.019, 0.121 +/- 0.013, 0.390 +/- 0.030, and 0.453 +/- 0.035, respectively, whereas those for maternal genetic effects (CEM, BrWM, and WWM) were 0.140 +/- 0.015, 0.208 +/- 0.020, and 0.138 +/- 0.022, respectively. Genetic correlations between direct or maternal genetic effects across traits were, in general, positive and moderate to low. However, genetic correlation for the pair CED-BrWD was positive and high (0.604 +/- 0.064). Genetic correlations between the direct and maternal genetic effects within a trait were negative and moderate (-0.219 +/- 0.097 for CE, -0.337 +/- 0.080 for BrW, and -0.440 +/- 0.102 for WW). Genetic correlations for CED-BrWM and CED-WWM were -0.121 +/- 0.090 and -0.097 +/- 0.113, respectively. The genetic correlation for CEM-CID was unfavorable (0.485 +/- 0.078), and those for CEM-BrWD (-0.094 +/- 0.079) and CEM-WWD (-0.125 +/- 0.082) were low and negative. The genetic correlation between CID and WWM was favorable (-0.148 +/- 0.106). Overall, the data presented here support the hypothesis that maternal effects for CE and BrW are not the same and that the genetic relationships between CI and maternal effects for WW in beef cattle follow a similar pattern to that reported between CI and milk yield in dairy cattle. Moreover, the need to include direct and maternal breeding values in beef cattle selection programs is suggested.

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.

Genetic and environmental factors influencing mortality up to weaning of Bruna dels Pirineus beef calves in mountain areas. A survival analysis1

Survival analysis techniques were used to analyze survival up to weaning of beef calves in the Pyrenean mountains areas of Catalonia, Spain. The Kaplan-Meier curve showed that the survival experience was not constant throughout the lactation period, as the mortality rate was more pronounced during the first month of life. The proportional hazards model analysis showed that several factors influenced the instantaneous mortality rate, with the herd-year effect having the strongest influence. Calves born in the first part of the breeding season, from September to February, had the lowest mortality risk (P < 0.001), showing that mortality risk increases as births accumulate. Calves from cows younger than 1,300 d of productive life had a higher risk of mortality (P < 0.05). Unassisted calvings presented the smallest risk of mortality, and mortality risk increased up to five times as birth became more difficult (P < 0.001). This risk also tended to increase slightly when calf birth weight was small (P < 0.10); for bigger calves, no increase of risk was detected, probably because calving difficulty was included in the model. These results suggest the need for improving the environment in the second part of the breeding period and paying more attention to births from younger cows. The survival curve fitted a parametric piecewise exponential function very well, with cut points at 16 and 32 d. The lower risk corresponded to the period of 33 to 180 d, the risk for the periods 17 to 32 d and 1 to 16 d being multiplied by 7 and 26, respectively. Confirming the robustness of the Cox model, the relative risks estimated for the different factors under this piecewise exponential model or a Weibull time-dependent model were similar to those reported above, as well as to those estimated under a frailty model, including the sire as a random effect. The modal estimates of sire variance under different baseline functions were close to 0.3, although the standard errors were very large. At weaning, the heritability estimate in the binary scale reached a value of only 0.037 because the survival at weaning was very high (96.9%) in this population. Nevertheless, in populations with a higher mortality, the inclusion of survival to weaning in the breeding objective might be justified. Overall, these results show that survival analysis is a powerful tool to analyze the mortality curve until weaning of beef calves.