Incorporating temperament traits in dairy cattle breeding programs: challenges and opportunities in the phenomics era

A systematic review with meta-analysis of heritability estimates for temperament-related traits in beef and dairy cattle populations

Temperament (docility) is a key breeding goal in the cattle industry due to its direct relationship with animal welfare, cattle handler's safety and animal productivity. Over the past six decades, numerous studies have reported heritability estimates for temperament-related traits in cattle populations ranging from low to high values. Therefore, the primary objective of this study was to perform a comprehensive systematic review with meta-analysis to obtain weighted estimates of heritability for temperament-related traits in worldwide cattle populations. After data editing and quality control, 106 studies were included in the systematic review, of which 29.2% and 70.8% reported estimates of heritability for temperament-related traits in dairy and beef cattle populations, respectively. Meta-analyses were performed for 95 heritability estimates using a random model approach. The weighted heritability estimates were as follow: (a) flight score at weaning = 0.23 (95% CI: 0.15-0.32); (b) flight speed at weaning = 0.30 (95% CI: 0.26-0.33); (c) joint analysis of flight speed and flight score at weaning = 0.27 (95% CI: 0.22-0.31); (d) flight speed at yearling = 0.26 (95% CI: 0.21-0.30); (e) joint analysis of flight speed at weaning and yearling = 0.27 (95% CI: 0.24-0.30); (f) movement score = 0.12 (95% CI: 0.08-0.15); (g) crush score at weaning = 0.21 (95% CI: 0.17-0.25); (h) pen score at weaning = 0.27 (95% CI: 0.19-0.34); (i) pen score at yearling = 0.20 (95% CI: 0.17-0.23); (j) joint analysis of pen score at weaning and yearling = 0.22 (95% CI: 0.18-0.26); (k) cow's aggressiveness at calving = 0.10 (95% CI: 0.01-0.19); (l) general temperament = 0.13 (95% CI: 0.06-0.19); (m) milking temperament = 0.16 (95% CI: 0.11-0.21); and (n) joint analysis of general and milking temperament = 0.14 (95% CI: 0.11-0.18). The heterogeneity index ranged from 0% to 77%, and the Q-test was significant (p < 0.05) for four single-trait meta-analyses. In conclusion, temperament is moderately heritable in beef cattle populations, and flight speed at weaning had the highest weighted heritability estimate. Moreover, between-study heterogeneity was low or moderate in beef cattle traits, suggesting reasonable standardization across studies. On the other hand, low-weighted heritability and high between-study heterogeneity were estimated for temperament-related traits in dairy cattle, suggesting that more studies are needed to better understand the genetic inheritance of temperament in dairy cattle populations.

Reproductive tract morphology and symmetry of farmed common eland (Tragelaphus oryx) bulls, and their relationship with secondary sexual traits and social rank

Common eland bulls are important game ranching animals in southern Africa, for tourism, breeding/live sales, trophy hunting, and game meat production. Interest has grown in their production potential, intensifying animal husbandry and breeding approaches. However, little scientific information is available regarding the intensive management of this species, including information regarding scientifically based selection criteria for breeding bulls. Often, simple phenotypic traits are utilised unless high-value game animals are being bred, with horn and body size often being the only traits considered for breeding bulls. This study provides basic information about the reproductive tract morphology, symmetry, and their relationships with secondary sexual traits, social rank, and temperament in common eland. Six eland males (2-2.5 years old; 203 ± 20 kg) were utilised for the study. Social rank, body weight and body condition score, temperament score, and horn size were determined before the animals were culled, and their reproductive tracts were collected for morphometric and histological evaluation. Results indicate relatively low asymmetry in bilateral reproductive tract components. Individual traits of eland bulls such as age, body weight, and social rank correlated the development of some testicular morphologies and thus may possibly be used in zoos, game ranching, and commercial production for the selection of breeding males, but not temperament and horn length, which should be carefully evaluated. Whilst this study provides baseline information from a limited sample size, further studies should incorporate the assessment of testicular hemodynamics, as well as the effects of factors such as season and androgen secretion patterns over a wider age range of common eland males and populations to provide further information for the management practices of breeding common eland bulls.

Defining valid breeding goals for animal breeds

BACKGROUND

The objective of any valid breeding program is to increase the suitability of a breed for its future purposes. The approach most often followed in animal breeding for optimizing breeding goals assumes that the sole desire of the owners is profit maximization. As this assumption is often violated, a generalized approach is needed that does not rely on this assumption.

RESULTS

The generalized approach is based on the niche concept. The niche of a breed is a set of environments in which a small population of the breed would have a positive population growth rate. Its growth rate depends on demand from prospective consumers and supply from producers. The approach involves defining the niche that is envisaged for the breed and identifying the trait optima that maximize the breed's adaptation to its envisaged niche within the set of permissible breeding goals. The set of permissible breeding goals is the set of all potential breeding goals that are compatible with animal welfare and could be reached within the planning horizon of the breeding program. In general, the breed's adaptation depends on the satisfaction of the producers with the animals and on the satisfaction of the consumers with the products produced by the animals. When consumers buy live animals, then the breed needs to adapt to both the environments provided by the producers, and the environments provided by the consumers. The profit function is replaced by a more general adaptedness function that measures the breed's adaptation to its envisaged niche.

CONCLUSIONS

The proposed approach coincides with the traditional approach if the producers have the sole desire to maximize their income, and if consumer preferences are well reflected by the product prices. If these assumptions are not met, then the traditional approach to breeding goal optimization is unlikely to result in a valid breeding goal. Using the example of companion breeds, this paper shows that the proposed approach has the potential to fill the gap.

Genomic Selection for Dairy Cattle Behaviour Considering Novel Traits in a Changing Technical Production Environment

Cow behaviour is a major factor influencing dairy herd profitability and is an indicator of animal welfare and disease. Behaviour is a complex network of behavioural patterns in response to environmental and social stimuli and human handling. Advances in agricultural technology have led to changes in dairy cow husbandry systems worldwide. Increasing herd sizes, less time availability to take care of the animals and modern technology such as automatic milking systems (AMSs) imply limited human-cow interactions. On the other hand, cow behaviour responses to the technical environment (cow-AMS interactions) simultaneously improve production efficiency and welfare and contribute to simplified "cow handling" and reduced labour time. Automatic milking systems generate objective behaviour traits linked to workability, milkability and health, which can be implemented into genomic selection tools. However, there is insufficient understanding of the genetic mechanisms influencing cow learning and social behaviour, in turn affecting herd management, productivity and welfare. Moreover, physiological and molecular biomarkers such as heart rate, neurotransmitters and hormones might be useful indicators and predictors of cow behaviour. This review gives an overview of published behaviour studies in dairy cows in the context of genetics and genomics and discusses possibilities for breeding approaches to achieve desired behaviour in a technical production environment.

Contemporary Knowledge on the Assessment of Temperament in Cattle and Its Impact on Production and Reproduction Including Some Immunological, Genetic and Metabolic Parameters

Temperament is associated with the well-being, health, production and reproduction of cattle. In order to increase the population of individuals with the desired temperament, its evaluation should be standardized and be made one of the obligatory elements of breeding and veterinary examination. A number of different tests are used for temperament assessment. In this article, the importance of temperament correlation with some metabolic, genetic, immunological, production and reproductive parameters have been shown, pointing at its influence on the economy and cattle handling. The most common methods for assessing the temperament of cattle are presented, including long-time scales of temperament assessment. At the same time, the relationship of the temperament of cattle with production efficiency, immunity and reproductive indicators has been shown, indicating that its correct assessment is an important aspect of the proper development of the herd and the associated economic growth.

Genomic-based genetic parameters for milkability traits derived from automatic milking systems in North American Holstein cattle

The number of dairy farms adopting automatic milking systems (AMS) has considerably increased around the world aiming to reduce labor costs, improve cow welfare, increase overall performance, and generate a large amount of daily data, including production, behavior, health, and milk quality records. In this context, this study aimed to (1) estimate genomic-based variance components for milkability traits derived from AMS in North American Holstein cattle based on random regression models; and (2) derive and estimate genetic parameters for novel behavioral indicators based on AMS-derived data. A total of 1,752,713 daily records collected using 36 milking robot stations and 70,958 test-day records from 4,118 genotyped Holstein cows were used in this study. A total of 57,600 SNP remained after quality control. The daily-measured traits evaluated were milk yield (MY, kg), somatic cell score (SCS, score unit), milk electrical conductivity (EC, mS), milking efficiency (ME, kg/min), average milk flow rate (FR, kg/min), maximum milk flow rate (FRM, kg/min), milking time (MT, min), milking failures (MFAIL), and milking refusals (MREF). Variance components and genetic parameters for MY, SCS, ME, FR, FRM, MT, and EC were estimated using the AIREMLF90 software under a random regression model fitting a third-order Legendre orthogonal polynomial. A threshold Bayesian model using the THRGIBBS1F90 software was used for genetically evaluating MFAIL and MREF. The daily heritability estimates across days in milk (DIM) ranged from 0.07 to 0.28 for MY, 0.02 to 0.08 for SCS, 0.38 to 0.49 for EC, 0.45 to 0.56 for ME, 0.43 to 0.52 for FR, 0.47 to 0.58 for FRM, and 0.22 to 0.28 for MT. The estimates of heritability (± SD) for MFAIL and MREF were 0.02 ± 0.01 and 0.09 ± 0.01, respectively. Slight differences in the genetic correlations were observed across DIM for each trait. Strong and positive genetic correlations were observed among ME, FR, and FRM, with estimates ranging from 0.94 to 0.99. Also, moderate to high and negative genetic correlations (ranging from -0.48 to -0.86) were observed between MT and other traits such as SCS, ME, FR, and FRM. The genetic correlation (± SD) between MFAIL and MREF was 0.25 ± 0.02, indicating that both traits are influenced by different sets of genes. High and negative genetic correlations were observed between MFAIL and FR (-0.58 ± 0.02) and MFAIL and FRM (-0.56 ± 0.02), indicating that cows with more MFAIL are those with lower FR. The use of random regression models is a useful alternative for genetically evaluating AMS-derived traits measured throughout the lactation. All the milkability traits evaluated in this study are heritable and have demonstrated selective potential, suggesting that their use in dairy cattle breeding programs can improve dairy production efficiency in AMS.

Unraveling the phenotypic and genomic background of behavioral plasticity and temperament in North American Angus cattle

BACKGROUND

Longitudinal records of temperament can be used for assessing behavioral plasticity, such as aptness to learn, memorize, or change behavioral responses based on affective state. In this study, we evaluated the phenotypic and genomic background of North American Angus cow temperament measured throughout their lifetime around the weaning season, including the development of a new indicator trait termed docility-based learning and behavioral plasticity. The analyses included 273,695 and 153,898 records for yearling (YT) and cow at weaning (CT) temperament, respectively, 723,248 animals in the pedigree, and 8784 genotyped animals. Both YT and CT were measured when the animal was loading into/exiting the chute. Moreover, CT was measured around the time in which the cow was separated from her calf. A random regression model fitting a first-order Legendre orthogonal polynomial was used to model the covariance structure of temperament and to assess the learning and behavioral plasticity (i.e., slope of the regression) of individual cows. This study provides, for the first time, a longitudinal perspective of the genetic and genomic mechanisms underlying temperament, learning, and behavioral plasticity in beef cattle.

RESULTS

CT measured across years is heritable (0.38-0.53). Positive and strong genetic correlations (0.91-1.00) were observed among all CT age-group pairs and between CT and YT (0.84). Over 90% of the candidate genes identified overlapped among CT age-groups and the estimated effect of genomic markers located within important candidate genes changed over time. A small but significant genetic component was observed for learning and behavioral plasticity (heritability = 0.02 ± 0.002). Various candidate genes were identified, revealing the polygenic nature of the traits evaluated. The pathways and candidate genes identified are associated with steroid and glucocorticoid hormones, development delay, cognitive development, and behavioral changes in cattle and other species.

CONCLUSIONS

Cow temperament is highly heritable and repeatable. The changes in temperament can be genetically improved by selecting animals with favorable learning and behavioral plasticity (i.e., habituation). Furthermore, the environment explains a large part of the variation in learning and behavioral plasticity, leading to opportunities to also improve the overall temperament by refining management practices. Moreover, behavioral plasticity offers opportunities to improve the long-term animal and handler welfare through habituation.

Invited review: integration of technologies and systems for precision animal agriculture-a case study on precision dairy farming

Precision livestock farming (PLF) offers a strategic solution to enhance the management capacity of large animal groups, while simultaneously improving profitability, efficiency, and minimizing environmental impacts associated with livestock production systems. Additionally, PLF contributes to optimizing the ability to manage and monitor animal welfare while providing solutions to global grand challenges posed by the growing demand for animal products and ensuring global food security. By enabling a return to the "per animal" approach by harnessing technological advancements, PLF enables cost-effective, individualized care for animals through enhanced monitoring and control capabilities within complex farming systems. Meeting the nutritional requirements of a global population exponentially approaching ten billion people will likely require the density of animal proteins for decades to come. The development and application of digital technologies are critical to facilitate the responsible and sustainable intensification of livestock production over the next several decades to maximize the potential benefits of PLF. Real-time continuous monitoring of each animal is expected to enable more precise and accurate tracking and management of health and well-being. Importantly, the digitalization of agriculture is expected to provide collateral benefits of ensuring auditability in value chains while assuaging concerns associated with labor shortages. Despite notable advances in PLF technology adoption, a number of critical concerns currently limit the viability of these state-of-the-art technologies. The potential benefits of PLF for livestock management systems which are enabled by autonomous continuous monitoring and environmental control can be rapidly enhanced through an Internet of Things approach to monitoring and (where appropriate) closed-loop management. In this paper, we analyze the multilayered network of sensors, actuators, communication, networking, and analytics currently used in PLF, focusing on dairy farming as an illustrative example. We explore the current state-of-the-art, identify key shortcomings, and propose potential solutions to bridge the gap between technology and animal agriculture. Additionally, we examine the potential implications of advancements in communication, robotics, and artificial intelligence on the health, security, and welfare of animals.

Water Buffalo Responsiveness during Milking: Implications for Production Outputs, Reproduction Fitness, and Animal Welfare

The overall objective of this study was to evaluate the effects that milking temperament (MT) of water buffaloes has on milking traits, welfare indicators, and reproductive outputs. The study was performed on 60 multiparous buffalo cows (6.7 ± 0.6 lactations) at the beginning of their lactation (100 days in milk, DIM). Each buffalo cow was scored by two independent observers using a temperament scoring system (1: extremely calm, 2: calm, 3: alert, 4: reactive, and 5: aggressive), and then grouped as 'calm' (scores 1, 2, and 3; n = 42) or 'nervous' (scores 4 and 5; n = 18). Additionally, the milk yield at 100 DIM (MY), milking speed (MS), calving interval (CI), age at first calving (AFC), body condition score (BCS), animal-based welfare parameters, and infrared thermography data (IRT) were evaluated. The MT significantly influenced the MY (p = 0.0082), with calmer cows outperforming their nervous counterparts. The MS was significantly influenced by the MT (p = 0.0015), with calmer animals having a higher milk ejection rate. The MT of the cows had no influence on the CI, AFC, or BCS. The evidence from this study suggests that the responsiveness of buffalo cows during milking affects their milk yield and milking speed, with no associations being found for reproduction efficiency indicators or animal-based welfare indicators.

Behavioural Traits in Bos taurus Cattle, Their Heritability, Potential Genetic Markers, and Associations with Production Traits

Simple Summary

Cattle have the potential to seriously injure humans and cause damage to property. The risk of cattle reacting in a dangerous manner can be reduced through genetic selection for cattle which have a better temperament. A literature search was undertaken which returned papers which met the criteria of “Bovine”, “Genetics” and “Behaviour” or terms therein. Behavioural traits were grouped and their heritability, genomic associations and correlations with production traits examined. It was found that heritability estimates were more accurate in studies with large populations (n > 1000). Gene associations with behavioural traits were found on all chromosomes except for chromosome 13, with associated SNPs reported on all chromosomes except 5, 13, 17, 18 and 23. Generally, it was found that correlations between behaviour and production traits were low or negligible, suggesting that genetic improvement can be undertaken without negatively affecting production. There was variation between the results of the studies examined, and this underlines that any genetic study is population specific. Thus, to assess the heritability, genetic associations with production and genomic areas of interest for behavioural traits, a large-scale study of the population of interest would be required.

Abstract

People who work with cattle are at severe risk of serious injury due to the size and strength of the cattle. This risk can be minimised by breeding less dangerous cattle, which have a more favourable reaction to humans. This study provides a systematic review of literature pertaining to cattle genetics relating to behaviour. The review protocol was developed using the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) framework, with Population, Exposure and Outcome components identified as Bovine, Genetics and Behaviour respectively. Forty-nine studies were identified in the sifting and assigned non-exclusively to groups of heritability (22), genomic associations (13) and production traits related to behaviour (24). Behavioural traits were clustered into the following groups: “temperament, disposition and/ or docility”, “aggression”, “chute score”, “flight speed”, “milking temperament”, “non-restrained methods” and “restrained methods”. Fourteen papers reported high accuracy (Standard Error ≤ 0.05) estimates of heritability, the majority (n = 12) of these studies measured over 1000 animals. The heritability estimates were found to vary between studies. Gene associations with behavioural traits were found on all chromosomes except for chromosome 13, with associated SNPs reported on all chromosomes except 5, 13, 17, 18 and 23. Generally, it was found that correlations between behaviour and production traits were low or negligible. These studies suggest that additive improvement of behavioural traits in cattle is possible and would not negatively impact performance. However, the variation between studies demonstrates that the genetic relationships are population specific. Thus, to assess the heritability, genetic associations with production and genomic areas of interest for behavioural traits, a large-scale study of the population of interest would be required.

Alternative Practices in Organic Dairy Production and Effects on Animal Behavior, Health, and Welfare

Simple Summary

The basis of livestock farming is preventing disease and improving animal welfare and well-being. Organic dairy farmers have very few options for the treatment of diseases and for the mitigation of pain in dairy calves and cows. Calving may be stressful for first-lactation cows because they must adapt to many different situations when they are milking. Alternative therapies to improve animal welfare must be researched in organic livestock production to verify that their use improves animal well-being. This review provides a brief background on organic production systems, illustrates current understanding of pain management for disbudding dairy calves, and discusses managing transition heifer behaviors and udder health to improve organic livestock well-being.

Abstract

The number of organic dairy farms has increased because of the increased growth of the organic market, higher organic milk price, and because some consumers prefer to purchase products from less intensive production systems. Best management practices are expected from organic dairy farms to ensure animal health and milk production. Organic dairy producers typically transition from conventional systems to avoid chemicals and pesticides, enhance economic viability, improve the environment, and increase soil fertility. Organic dairy producers respect and promote a natural environment for their animals, is also an important component of animal welfare. Organic producers have few options to mitigate pain in dairy calves. In the United States, therapies to mitigate pain for disbudded organic dairy calves are regulated by the US National Organic Program. Organic producers regularly use naturally derived alternatives for the treatment of health disorders of dairy calves, heifers, and cows. Alternative natural products may provide an option to mitigate pain in organic dairy calves. Despite the reluctance to implement pain alleviation methods, some organic farmers have expressed interest in or currently implement plant-based alternatives. Efficacy studies of alternative remedies for organic livestock are needed to verify that their use improves animal welfare. Non-effective practices represent a major challenge for organic dairy animal welfare. The relationship between humans and animals may be jeopardized during milking because first-lactation cows may exhibit adverse behaviors during the milking process, such as kicking and stomping. The periparturient period is particularly challenging for first-lactation cows. Adverse behaviors may jeopardize animal welfare and reduce safety for humans because stressed heifers may kick off the milking unit, kick at milkers, and display other unwanted behaviors in the milking parlor. This may reduce milking efficiency, overall production, and ultimately reduce the profitability of the dairy farm. Positive animal welfare is a challenging balancing act between the three overlapping ethic concerns. Identifying animal welfare deficits in organic livestock production is the first step in capitalizing on these opportunities to improve welfare.

Benchmarking animal handling outcomes on cow-calf operations and identifying associated factors

The assessment of animal handling is commonly included in cattle care programs. The guidelines set in the National Cattlemen’s Beef Association Beef Checkoff funded Beef Quality Assurance (BQA) program are often used for assessing handling on feedlot, stocker, and cow-calf operations. There is limited information about animal handling on cow-calf operations. Thus, the objectives of this study were to: (1) quantify handling outcomes on cow-calf operations and compare them to national BQA program thresholds, and (2) investigate factors associated with handling outcomes. Researchers visited 76 operations across the United States to observe the following outcomes, adapted from the BQA program, during the processing of cows or yearling heifers: Prod Use, Miscatch, Vocalization, Jump, Slip/Stumble, Fall and Run. One hundred cows or less (depending on herd size) were observed moving through a restraint system at each operation. Other information specific to the animal type, facilities, and management were also gathered to be explored as potential predictors of handling outcomes. Data were summarized using descriptive statistics on an operation basis and analyzed with multi-predictor ANOVA or Kruskal–Wallis tests to assess the relationship between outcomes and possible explanatory factors. Predictors included in the final analyses were: BQA certification (BQA), animal temperament (TEMP), region (REGION), chute style (CHUTE), and visual contact with humans (VISUAL). The 76 operations were sampled in 24 states (Central, n = 17; East, 30; West, 29), with herd sizes ranging from 10 animals to more than 5,000 animals. A total of 4,804 animals were observed. There were a substantial number of operations exceeding BQA thresholds for Prod Use (34.0%, 26), Miscatch (46.0%, 35), and Fall (31.6%, 24); the averages of these outcomes also exceeded the BQA thresholds (< 10%, 0%, and 2%, respectively). There was an association between Prod Use and several explanatory factors, including SIZE (P = 0.072), TEMP (P = 0.001), VISUAL (P = 0.027), and BQA (P = 0.104). Miscatch, Vocalization, and Fall all had single associated factors (REGION, P = 0.019; REGION, P = 0.002; VISUAL, P = 0.002, respectively). The VISUAL and TEMP factors had an association with the majority of outcomes. The findings suggest an opportunity for improving handling outcomes, which could be achieved through education and training support regarding the importance of animal handling on-farm. Future work should consider additional aspects of facilities and management that could impact cattle handling outcomes.

Function of m6A and its regulation of domesticated animals' complex traits

N6-methyladenosine (m6A) is the most functionally important epigenetic modification in RNA. The m6A modification widely exists in mRNA and noncoding RNA, influences the mRNA processing, and regulates the secondary structure and maturation of noncoding RNA. Studies showed the important regulatory roles of m6A modification in animal's complex traits, such as development, immunity, and reproduction-related traits. As an important intermediate stage from animal genome to phenotype, the function of m6A in the complex trait formation of domestic animals cannot be neglected. This review discusses recent research advances on m6A modification in well-studied organisms, such as human and model organisms, and introduces m6A detection technologies, small-molecule inhibitors of m6A-related enzymes, interaction between m6A and other biological progresses, and the regulation mechanisms of m6A in domesticated animals' complex traits.

Relationship between Temperament and Stage of Lactation, Productivity and Milk Composition of Dairy Cows

Simple Summary

Cattle temperament can be described as a response to changes in the environment and is crucial for successful herd management using innovative technologies. Despite the economic aspects of animal productivity and welfare, there is still a lack of objective evidence for a wider use of temperament in dairy cattle breeding programmes. The aim of this study was to evaluate the relationship between cow temperament and milk indices describing cow productivity, metabolic status and mastitis resistance. The coefficient of heritability of temperament was determined. Only a small part of the phenotypic changes in this indicator in the analysed population was associated with genetic factors; however, the correlation of cow temperament with milk lactose and somatic cells suggests that temperament could be used in sustainable breeding programmes, giving priority to animal welfare and health. A statistically significant decrease in temperament scores with increasing lactation periods was only found in primiparous cows. It is also argued that changes in milk production, milk composition and quality associated with mastitis and a cow’s metabolic status should be taken into account when assessing the cow’s temperament, as these factors can affect the welfare and behaviour of an animal, and therefore the expression and intensity of their reaction to their environment.

Abstract

The aim of this study was to assess the relationship between temperament and milk performance in cows at different stages of lactation, describing their productivity, metabolic status and resistance to mastitis. This study showed that with increasing lactation, cows’ temperament indicators decreased (p < 0.001) and they became calmer. The highest temperament score on a five-point scale was found in cows between 45 and 100 days of lactation. In the group of pregnant cows, we found more cows (p = 0.005) with a temperament score of 1–2 compared with non-pregnant cows A normal temperament was usually detected in cows with lactose levels in milk of 4.60% or more and when the somatic cell count (SCC) values in cow milk were <100,000/mL and 100,000–200,000/mL, with a milk fat-to-protein ratio of 1.2. A larger number of more sensitive and highly aggressive cows was detected at a low milk urea level. In contrast to a positive phenotypic correlation (p < 0.05), this study showed a negative genetic correlation between the temperament of cows and milk yield (p < 0.001). Positive genetic correlations between temperament scores and milk somatic cells (p < 0.001) and milk fat-to-protein ratio (p < 0.05) were found to indicate a lower genetic predisposition in cows with a calmer temperament to subclinical mastitis and ketosis. On the other hand, the heritability of temperament (h² = 0.044–0.100) showed that only a small part of the phenotypic changes in this indicator is associated with genetic factors.

Using imputed whole-genome sequence variants to uncover candidate mutations and genes affecting milking speed and temperament in Holstein cattle

Milking speed (MS) and temperament (MT) are 2 workability traits of great importance in dairy cattle production and breeding. This is mainly due to an increased intensification of the worldwide production systems and greater adoption of precision technologies with less human-cattle interaction. Both MS and MT are heritable traits and thus, genomic selection is a promising tool to expedite their genetic progress. However, the genetic architecture and biological mechanisms underlying the phenotypic expression of these traits remain underexplored. In this study, we investigated the association of >5.7 million imputed whole-genome sequence variants with MT and MS in 4,381 and 4,219 North American Holstein cattle, respectively. The statistical analyses were performed using a mixed linear model fitting a polygenic effect. We detected 40 and 35 significant SNPs independently associated with MT and MS, respectively, which were distributed across 26 chromosomes. Eight candidate genes (GRIN3A, KCNJ3, BOSTAUV1R417, BOSTAUV1R419, MAP2K5, KCTD3, GAP43, and LSAMP) were suggested to play an important role in MT as they are involved in biologically relevant pathways, such as glutamatergic synapse, vomeronasal receptor and oxytocin signaling. Within their coding and upstream sequences, we used an independent data set to further detect or validate significantly differentiated SNP between cattle breeds with known differences in MT. There were fewer candidate genes potentially implicated in MS, but immunity-related genes (e.g., BOLA-NC1 and LOC512672), also identified in other populations, were validated in this study. The significant SNP and novel candidate genes identified contribute to a better understanding of the biological mechanisms underlying both traits in dairy cattle. This information will also be useful for the optimization of prediction of genomic breeding values by giving greater weights to SNP located in the genomic regions identified.

Large-Scale Phenotyping of Livestock Welfare in Commercial Production Systems: A New Frontier in Animal Breeding

Genomic breeding programs have been paramount in improving the rates of genetic progress of productive efficiency traits in livestock. Such improvement has been accompanied by the intensification of production systems, use of a wider range of precision technologies in routine management practices, and high-throughput phenotyping. Simultaneously, a greater public awareness of animal welfare has influenced livestock producers to place more emphasis on welfare relative to production traits. Therefore, management practices and breeding technologies in livestock have been developed in recent years to enhance animal welfare. In particular, genomic selection can be used to improve livestock social behavior, resilience to disease and other stress factors, and ease habituation to production system changes. The main requirements for including novel behavioral and welfare traits in genomic breeding schemes are: (1) to identify traits that represent the biological mechanisms of the industry breeding goals; (2) the availability of individual phenotypic records measured on a large number of animals (ideally with genomic information); (3) the derived traits are heritable, biologically meaningful, repeatable, and (ideally) not highly correlated with other traits already included in the selection indexes; and (4) genomic information is available for a large number of individuals (or genetically close individuals) with phenotypic records. In this review, we (1) describe a potential route for development of novel welfare indicator traits (using ideal phenotypes) for both genetic and genomic selection schemes; (2) summarize key indicator variables of livestock behavior and welfare, including a detailed assessment of thermal stress in livestock; (3) describe the primary statistical and bioinformatic methods available for large-scale data analyses of animal welfare; and (4) identify major advancements, challenges, and opportunities to generate high-throughput and large-scale datasets to enable genetic and genomic selection for improved welfare in livestock. A wide variety of novel welfare indicator traits can be derived from information captured by modern technology such as sensors, automatic feeding systems, milking robots, activity monitors, video cameras, and indirect biomarkers at the cellular and physiological levels. The development of novel traits coupled with genomic selection schemes for improved welfare in livestock can be feasible and optimized based on recently developed (or developing) technologies. Efficient implementation of genetic and genomic selection for improved animal welfare also requires the integration of a multitude of scientific fields such as cell and molecular biology, neuroscience, immunology, stress physiology, computer science, engineering, quantitative genomics, and bioinformatics.