Estimation of genetic parameters for longevity traits in dairy cattle: a review with focus on the characteristics of analytical models

Multivariate analysis of milk metabolite measures shows potential for deriving new resilience phenotypes

In a context of growing interest in breeding more resilient animals, a noninvasive indicator of resilience would be very valuable. We hypothesized that the time-course of concentrations of several milk metabolites through a short-term underfeeding challenge could reflect the variation of resilience mechanisms to such a challenge. We submitted 138 one-year-old primiparous goats, selected for extreme functional longevity (i.e., productive longevity corrected for milk yield [60 low longevity line goats and 78 high longevity line goats]), to a 2-d underfeeding challenge during early lactation. We measured the concentration of 13 milk metabolites and the activity of 1 enzyme during prechallenge, challenge, and recovery periods. Functional principal component analysis summarized the trends of milk metabolite concentration over time efficiently without preliminary assumptions concerning the shapes of the curves. We first ran a supervised prediction of the longevity line of the goats based on the milk metabolite curves. The partial least square analysis could not predict the longevity line accurately. We thus decided to explore the large overall variability of milk metabolite curves with an unsupervised clustering. The large year × facility effect on the metabolite concentrations was precorrected for. This resulted in 3 clusters of goats defined by different metabolic responses to underfeeding. The cluster that showed higher β-hydroxybutyrate, cholesterol, and triacylglycerols increase during the underfeeding challenge was associated with poorer survival compared with the other 2 clusters. These results suggest that multivariate analysis of noninvasive milk measures show potential for deriving new resilience phenotypes.

Genetic analysis of longevity and their associations with fertility traits in Holstein cattle

The increase of longevity is intended to reduce involuntary culling rates, not extend the life span, and it reflects the ability of animals to successfully cope with the environment and disease during production. Sire model, animal model and repeatability animal models were used to estimate the (co) variance components of longevity and fertility traits. Six longevity and thirteen fertility traits were analysed, including herd life (HL), productive life (PL), number of days between first calving and the end of first lactation or culling (L1); number of days between first calving and the end of the second lactation or culling (L2); number of days between first calving and the end of the third lactation or culling (L3); number of days between first calving and the end of the fourth lactation or culling (L4); age at first service, age at first calving (AFC), the interval from first to last inseminations in heifer (IFLh), conception rate of first insemination in heifer, days open (DO), calving interval, gestation length, interval from calving to first insemination (ICF), interval from first to last inseminations in cow (IFLc), conception rate of first insemination in cow, calving ease (CE), birth weight, and calf survival. The estimated heritabilities (±SE) were 0.018 (±0.003), 0.015 (±0.003), 0.049 (±0.004), 0.025 (±0.003), 0.009 (±0.002) and 0.011 (±0.002) for HL, PL, L1, L2, L3 and L4, respectively. Strong correlations were appeared in HL and PL; the genetic and phenotypic correlation coefficients were 0.998 and 0.985, respectively. There were high genetic and phenotypic correlations which were observed in L1 and L2, L2 and L3, L3 and L4, respectively. All fertility traits of heifer showed medium to high heritability, while the cow showed low heritability. All heifer fertility traits had low genetic associations with longevity traits, ranging from -0.018 (L2 and IFLh) to 0.257 (L3 and AFC). Most of the fertility traits showed negative correlations with longevity traits in different parities, and we recommend DO, ICF, IFLc and CE as indirect indicators of longevity traits in dairy cows, but we also need to take into account the differences between parities.

Genomic and Phenotypic Udder Evaluation for Dairy Cattle Selection: A Review

The traditional point of view regarding dairy cattle selection has been challenged by recent genomic studies indicating that livestock productivity prediction can be redefined based on the evaluation of genomic and phenotypic data. Several studies that included different genomic-derived traits only indicated that interactions among them or even with conventional phenotypic evaluation criteria require further elucidation. Unfortunately, certain genomic and phenotypic-derived traits have been shown to be secondary factors influencing dairy production. Thus, these factors, as well as evaluation criteria, need to be defined. Owing to the variety of genomic and phenotypic udder-derived traits which may affect the modern dairy cow functionality and conformation, a definition of currently important traits in the broad sense is indicated. This is essential for cattle productivity and dairy sustainability. The main objective of the present review is to elucidate the possible relationships among genomic and phenotypic udder evaluation characteristics to define the most relevant traits related to selection for function and conformation in dairy cattle. This review aims to examine the potential impact of various udder-related evaluation criteria on dairy cattle productivity and explore how to mitigate the adverse effects of compromised udder conformation and functionality. Specifically, we will consider the implications for udder health, welfare, longevity, and production-derived traits. Subsequently, we will address several concerns covering the application of genomic and phenotypic evaluation criteria with emphasis on udder-related traits in dairy cattle selection as well as its evolution from origins to the present and future prospects.

Effect of Calving Difficulties and Calf Mortality on Functional Longevity in Polish Holstein-Friesian Cows

Simple Summary

Longevity, or the length of a cow’s productive life, is important in terms of profitability, animal welfare and environmental sustainability. In genetic evaluations, interest focuses on functional longevity, defined as a cow’s ability to avoid forced culling, an ability that increases the possibility of voluntary disposal based on economic criteria. Longevity is affected by several non-productive functional traits, among them those related to calving performance: calving ease (dystocia) and perinatal calf mortality (stillbirth). Parturition is a critical event in a cow’s life that has a number of different short- and long-term consequences. In the Polish Holstein-Friesian population, the incidence of dystocia and stillbirth is within the lower range of frequencies found in other dairy cattle populations. Our research showed that both traits affect functional longevity. Difficult calvings occur more frequently in heifers and increase the risk of involuntary culling more than in later parturitions. Additionally, a higher risk of culling is related to birth of a male calf. Moreover, the negative impact of calf mortality on longevity is also more pronounced in primiparous cows and in the case of delivery of male calves. Reducing the incidence of calving problems and perinatal mortality may improve the longevity of dairy cows.

Abstract

Longevity is one of the functional traits that considerably affect dairy herd profitability. A Weibull proportional hazards model was used to evaluate the impact of difficult calvings and calf stillbirths on cow functional longevity, defined as length of productive life corrected for milk production. The data for analysis comprised calving ease and calf mortality scores of 2,163,426 calvings, 34.4% of which came from primiparous cows. The percentage of male calves was 53.4%. Calving ease was scored as “without assistance” (34.44%), “with assistance” (62.03%), “difficult—hard pull” (3.39%), and “very difficult, including caesarean section” (0.14%). Calf mortality scores were “live born” (94.21%) and “stillborn or died within 24 h” (5.79%). The Weibull proportional hazards model included classes of calving ease or calf mortality scores × parity (1, ≥2) × sex of calf as time-dependent fixed effect. The model also included time-dependent fixed effects of year × season, parity × stage of lactation, annual change in herd size, fat yield and protein yield, time-independent fixed effect of age at first calving, and time dependent random herd × year × season. In first-parity cows, very difficult birth of a bull or heifer increased the relative risk of culling, respectively, 2.18 or 1.26 times as compared with calving without assistance. In later parities, the relative risk of culling related to very difficult calving was 2.0 times (for male calves) and 1.33 times (for female calves) higher than the relative risk of culling associated with calving without assistance. Calf mortality showed a negative impact on longevity in both heifers and cows. First-parity stillbirth increased the relative risk of culling depending on sex of calf by 18% in females and by 15% in males; in later parities the increase of the relative risk of culling was lower (by 7% for females, 9% for males). Difficult calvings and their consequences, especially in primiparous cows, may negatively influence dairy herd profitability by reducing the length of cows’ productive life.

Genetic Parameters and Genome-Wide Association Studies of Eight Longevity Traits Representing Either Full or Partial Lifespan in Chinese Holsteins

Due to the complexity of longevity trait in dairy cattle, two groups of trait definitions are widely used to measure longevity, either covering the full lifespan or representing only a part of it to achieve an early selection. Usually, only one group of longevity definition is used in breeding program for one population, and genetic studies on the comparisons of two groups of trait definitions are scarce. Based on the data of eight traits well representing the both groups of trait definitions, the current study investigated genetic parameters and genetic architectures of longevity in Holsteins. Heritabilities and correlations of eight longevity traits were estimated using single-trait and multi-trait animal models, with the data from 103,479 cows. Among the cows with phenotypes, 2,630 cows were genotyped with the 150K-SNP panel. A single-trait fixed and random Circuitous Probability Unification model was performed to detect candidate genes for eight longevity traits. Generally, all eight longevity traits had low heritabilities, ranging from 0.038 for total productive life and herd life to 0.090 for days from the first calving to the end of first lactation or culling. High genetic correlations were observed among the traits within the same definition group: from 0.946 to 0.997 for three traits reflecting full lifespan and from 0.666 to 0.997 for five traits reflecting partial productive life. Genetic correlations between two groups of traits ranged from 0.648 to 0.963, and increased gradually with the extension of lactations number regarding the partial productive life traits. A total of 55 SNPs located on 25 chromosomes were found genome-wide significantly associated with longevity, in which 12 SNPs were associated with more than one trait, even across traits of different definition groups. This is the first study to investigate the genetic architecture of longevity representing both full and the partial lifespan simultaneously, which will assist the selection of an appropriate trait definition for genetic improvement of longevity. Because of high genetic correlations with the full lifespan traits and higher heritability, the partial productive life trait measured as the days from the first calving to the end of the third lactation or culling could be a good alternative for early selection on longevity. The candidate genes identified by this study, such as RPRM, GRIA3, GTF2H5, CA5A, CACNA2D1, FGF10, and DNAJA3, could be used to pinpoint causative mutations for longevity and further benefit the genomic improvement of longevity in dairy cattle.

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.

Genomic selection strategies for breeding adaptation and production in dairy cattle under climate change

Livestock production both contributes to and is affected by global climate change, and substantial modifications will be required to increase its climate resilience. In this context, reliance on dominant commercial livestock breeds, featuring small effective population sizes, makes current production strategies vulnerable if their production is restricted to environments, which may be too costly to support under future climate scenarios. The adaptability of animal populations to future environments will therefore become important. To help evaluate the role of genetics in climate adaptation, we compared selection strategies in dairy cattle using breeding simulations, where genomic selection was used on two negatively correlated traits for production (assumed to be moderately heritable) and adaptation (assumed to have low heritability). Compared with within-population breeding, genomic introgression produced a more positive genetic change for both production and adaptation traits. Genomic introgression from highly adapted but low production value populations into highly productive but low adaptation populations was most successful when the adaptation trait was given a lower selection weight than the production trait. Genomic introgression from highly productive population to highly adapted population was most successful when the adaptation trait was given a higher selection weight than the production trait. Both these genomic introgression schemes had the lowest risk of inbreeding. Our results suggest that both adaptation and production can potentially be improved simultaneously by genomic introgression.

Estimation of genetic parameters for functional longevity in the South African Holstein cattle using a piecewise Weibull proportional hazards model

Non-genetic factors influencing functional longevity and the heritability of the trait were estimated in South African Holsteins using a piecewise Weibull proportional hazards model. Data consisted of records of 161,222 of daughters of 2,051 sires calving between 1995 and 2013. The reference model included fixed time-independent age at first calving and time-dependent interactions involving lactation number, region, season and age of calving, within-herd class of milk production, fat and protein content, class of annual variation in herd size and the random herd-year effect. Random sire and maternal grandsire effects were added to the model to estimate genetic parameters. The within-lactation Weibull baseline hazards were assumed to change at 0, 270, 380 days and at drying date. Within-herd milk production class had the largest contribution to the relative risk of culling. Relative culling risk increased with lower protein and fat per cent production classes and late age at first calving. Cows in large shrinking herds also had high relative risk of culling. The estimate of the sire genetic variance was 0.0472 ± 0.0017 giving a theoretical heritability estimate of 0.11 in the complete absence of censoring. Genetic trends indicated an overall decrease in functional longevity of 0.014 standard deviation from 1995 to 2007. There are opportunities for including the trait in the breeding objective for South African Holstein cattle.

Comparison of breeding values among cows with exceptional longevity and their contemporary herdmates in German Holsteins

Abstract. The present analysis compares the estimated breeding values (EBVs), relative breeding values (RBVs), and daughter yield deviations (YDs) of cows with exceptional longevity with their contemporary herdmates. In addition, the relative breeding values of their sires were compared among these two daughter groups; the RBVs of the sires were also compared with the proportion of their daughters with exceptional longevity. Data included 5037 sires born between 1963 and 1996 with a total of 61 988 daughter; of these sires, 486 had sired daughters that completed more than nine lactations (exceptional cows) and 4957 sires had sired the contemporary herdmates. Exceptional cows had on average significantly lower EBVs for milk yield, fat and protein yield, and significantly lower YDs for milk and protein yield in the first three lactations, significantly lower RBVs for milk production and type but significantly higher RBVs for somatic cell score and functional longevity. The sires of exceptional cows had significantly higher RBVs for somatic cell count (RZS), functional longevity (RZN), and fitness (RZFit) in comparison to the sires of contemporary herdmates. Correlations among the proportion of exceptional cows per sire and RZN, RZS as well as RZFit were positive, whereas milk production (RZM) showed a negative correlation. An increase in the number of cows with exceptional longevity may be possible through a relative total breeding value with high positive weights for RZN, RZS, and RZFit but negative weights for RZM and type (RZE).