A Comprehensive Systematic Review Coupled with an Interacting Network Analysis Identified Candidate Genes and Biological Pathways Related to Bovine Temperament

Comprehension of the genetic basis of temperament has been improved by recent advances in the identification of genes and genetic variants. However, due to the complexity of the temperament traits, the elucidation of the genetic architecture of temperament is incomplete. A systematic review was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement to analyze candidate genes related to bovine temperament, using bovine as the population, SNPs and genes as the exposure, and temperament test as the outcome, as principal search terms for population, exposure, and outcome (PEO) categories to define the scope of the search. The search results allowed the selection of 36 articles after removing duplicates and filtering by relevance. One hundred-two candidate genes associated with temperament traits were identified. The genes were further analyzed to construct an interaction network using the STRING database, resulting in 113 nodes and 346 interactions and the identification of 31 new candidate genes for temperament. Notably, the main genes identified were SST and members of the Kelch family. The candidate genes displayed interactions with pathways associated with different functions such as AMPA receptors, hormones, neuronal maintenance, protein signaling, neuronal regulation, serotonin synthesis, splicing, and ubiquitination activities. These new findings demonstrate the complexity of interconnected biological processes that regulate behavior and stress response in mammals. This insight now enables our targeted analysis of these newly identified temperament candidate genes in bovines.

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.

Commercial laying hens exhibit long-term consistent individual differences and behavioural syndromes in spatial traits

Past research has supported the importance of animal personalities for the productivity and welfare of farm animals. However, current assessments of personality traits are commonly conducted over short periods using standardized assays and may not reflect all important aspects of behaviours in commercial settings throughout the production period. This study aimed to evaluate consistent behavioural differences between 194 commercial laying hens within an aviary across most of the production period (eight months). We used five spatial behaviours related to various aspects of commercial hens' daily routine, including the sleeping, feeding, nesting, indoor movements and outdoor usage. All behaviours were repeatable over time and across contexts, with consistent differences between individuals explaining between 23% and 66% of the variation. These long-term consistencies revealed the potential applicability of the behaviours as personality traits of commercial hens. Moreover, we identified behavioural syndromes comprising all behaviours except the nesting-related behaviour, indicating two axes of spatial personalities that may be driven by different mechanisms. We discussed the significance of such individual differences in using personality traits to breed more resilient farm animals. Future research should evaluate associations of these behaviours with animal welfare and productivity to inform breeding efforts.

Increasing plant group productivity through latent genetic variation for cooperation

Historic yield advances in the major crops have, to a large extent, been achieved by selection for improved productivity of groups of plant individuals such as high-density stands. Research suggests that such improved group productivity depends on "cooperative" traits (e.g., erect leaves, short stems) that-while beneficial to the group-decrease individual fitness under competition. This poses a problem for some traditional breeding approaches, especially when selection occurs at the level of individuals, because "selfish" traits will be selected for and reduce yield in high-density monocultures. One approach, therefore, has been to select individuals based on ideotypes with traits expected to promote group productivity. However, this approach is limited to architectural and physiological traits whose effects on growth and competition are relatively easy to anticipate. Here, we developed a general and simple method for the discovery of alleles promoting cooperation in plant stands. Our method is based on the game-theoretical premise that alleles increasing cooperation benefit the monoculture group but are disadvantageous to the individual when facing noncooperative neighbors. Testing the approach using the model plant Arabidopsis thaliana, we found a major effect locus where the rarer allele was associated with increased cooperation and productivity in high-density stands. The allele likely affects a pleiotropic gene, since we find that it is also associated with reduced root competition but higher resistance against disease. Thus, even though cooperation is considered evolutionarily unstable except under special circumstances, conflicting selective forces acting on a pleiotropic gene might maintain latent genetic variation for cooperation in nature. Such variation, once identified in a crop, could rapidly be leveraged in modern breeding programs and provide efficient routes to increase yields.

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.

Human-Animal Interactions with Bos taurus Cattle and Their Impacts on On-Farm Safety: A Systematic Review

Cattle production necessitates potentially dangerous human-animal interactions. Cattle are physically strong, large animals that can inflict injuries on humans accidentally or through aggressive behaviour. This study provides a systematic review of literature relating to farm management practices (including humans involved, facilities, and the individual animal) associated with cattle temperament and human's on-farm safety. The Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) was used to frame the review. Population, Exposure, and Outcomes (PEO) components of the research question are defined as "Bovine" (population), "Handling" (exposure), and outcomes of "Behaviour", and "Safety". The review included 17 papers and identified six main themes: actions of humans; human demographics, attitude, and experience; facilities and the environment; the animal involved; under-reporting and poor records; and mitigation of dangerous interactions. Cattle-related incidents were found to be underreported, with contradictory advice to prevent injury. The introduction of standardised reporting and recording of incidents to clearly identify the behaviours and facilities which increase injuries could inform policy to reduce injuries. Global differences in management systems and animal types mean that it would be impractical to impose global methods of best practice to reduce the chance of injury. Thus, any recommendations should be regionally specific, easily accessible, and practicable.

Adrenergic Tone as an Intermediary in the Temperament Syndrome Associated With Flight Speed in Beef Cattle

The temperament of farm animals can influence their resilience to everyday variations within the managed production environment and has been under strong direct and indirect selection during the course of domestication. A prominent objective measure used for assessing temperament in beef cattle is the behavioral flight response to release from confinement in a crush or chute. This behavioral measure, termed flight speed (also known as escape velocity) is associated with physiological processes including body temperature, feeding behavior, growth rate, carcass composition, immune function, and health outcomes. This review examines the functional links between this suite of traits and adrenergic activity of the sympathetic nervous system and the adrenomedullary hormonal system. It is suggested that flight speed is the behavioral aspect of an underlying “flightiness” temperament syndrome, and that elevated adrenergic tone in animals with a high level of flightiness (i.e., flighty animals) tunes physiological activities toward a sustained “fight or flight” defense profile that reduces productivity and the capacity to flourish within the production environment. Nonetheless, despite a common influence of adrenergic tone on this suite of traits, variation in each trait is also influenced by other regulatory pathways and by the capacity of tissues to respond to a range of modulators in addition to adrenergic stimuli. It is suggested that tuning by adrenergic tone is an example of homeorhetic regulation that can help account for the persistent expression of behavioral and somatic traits associated with the flight speed temperament syndrome across the life of the animal. At a population level, temperament may modulate ecological fit within and across generations in the face of environmental variability and change. Associations of flight speed with the psychological affective state of the animal, and implications for welfare are also considered. The review will help advance understanding of the developmental biology and physiological regulation of temperament syndromes.

The effect of rearing conditions during the milk-fed period on milk yield, growth, and maze behaviour of dairy cows during their first lactation

The objective was to find whether cow growth, milk performance, and behaviour are affected by (1) rearing conditions until weaning after a milk-fed period of 84 d and (2) the sire lineage. Thirty-five Holstein heifers were assigned to one of three treatments: SM, n=13, pen with mother to 21st day, then group pen (they received a maximum of 6 kg of milk daily); SN, n=9, after 3 d with own mother in pen with nursing cow (they received a maximum of 6 kg of milk daily); H, n=13, in hutch from the 2nd to 56th day (6 kg of milk replacer daily), then loose housing pen to weaning (6 kg of milk replacer daily). After weaning at the 84th day, all heifers were kept in pens with the same ration as during calving. During lactation, live body weight (LBW) was measured each month and milk yield each day. Maze learning was evaluated in the fifth month of lactation. The data were analysed using a general linear model ANOVA. At the 30th day, the LBW tended to be the highest in SN (SM 528.2 ± 11.4 kg, SN 571.7 ± 15.3 kg, H 533.2 ± 12.3 kg). When lactation ended, the highest LBW was in SN and the lowest in H (SM 612.6 ± 12.2 kg, SN 623.1 ± 16.4 kg, H 569.8 ± 13.2 kg; P<0.05). The SN tended to have the highest production of milk (SM 7143.9 ± 241.5 kg, SN 7345.1 ± 319.0 kg, H 7146.7 ± 234 kg), and the H for FCM (SM 6290.3 ± 203.2 kg, SN 6307.6 ± 268.4 kg, H 6399.3 ± 197.1 kg) for 305 d lactation. Group SN crossed the maze fastest (SM 1141.4 ± 120.5 s, SN 810.3 ± 160.5 s, H 1120.8 ± 118.6 s). The vocalization number differed significantly (SM 32.3 ± 5.7, SN 20.8 ± 4.4, H 9.9 ± 2.6; P<0.01). The results indicated that the rearing method up to weaning may have an impact on dairy cows' performance and behaviour.

Novel genes involved in the genetic architecture of temperament in Brahman cattle

Cattle temperament is a complex and economically relevant trait. The objective of this study was to identify genomic regions and genes associated with cattle temperament. From a Brahman cattle population of 1,370 animals evaluated for temperament traits (Exit velocity-EV, Pen Score-PS, Temperament Score-TS), two groups of temperament-contrasting animals were identified based on their EV-average values ±1/2 standard deviation (SD). To be considered in the calm group, the EV of females ranged between 0.16–1.82 m/s (n = 50) and the EV of males ranged between 0.4–1.56 m/s (n = 48). Females were classified as temperamental if their EV ranged between 3.13–7.66 m/s (n = 46) and males were classified as temperamental if their EV ranged between 3.05–10.83 m/s (n = 45). Selected animals were genotyped using a total of 139,376 SNPs (GGP-HD-150K), evaluated for their association with EV. The Genome-Wide Association analysis (GWAS) identified fourteen SNPs: rs135340276, rs134895560, rs110190635, rs42949831, rs135982573, rs109393235, rs109531929, rs135087545, rs41839733, rs42486577, rs136661522, rs110882543, rs110864071, rs109722627, (P<8.1E-05), nine of them were located on intergenic regions, harboring seventeen genes, of which only ACER3, VRK2, FANCL and SLCO3A1 were considered candidate associated with bovine temperament due to their reported biological functions. Five SNPs were located at introns of the NRXN3, EXOC4, CACNG4 and SLC9A4 genes. The indicated candidate genes are implicated in a wide range of behavioural phenotypes and complex cognitive functions. The association of the fourteen SNPs on bovine temperament traits (EV, PS and TS) was evaluated; all these SNPs were significant for EV; only some were associated with PS and TS. Fourteen SNPs were associated with EV which allowed the identification of twenty-one candidate genes for Brahman temperament. From a functional point of view, the five intronic SNPs identified in this study, are candidates to address control of bovine temperament, further investigation will probe their role in expression of this trait.

Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB

Background

Distinct domestication events, adaptation to different climatic zones, and divergent selection in productive traits have shaped the genomic differences between taurine and indicine cattle. In this study, we assessed the impact of artificial selection and environmental adaptation by comparing whole-genome sequences from European taurine and Asian indicine breeds and from African cattle. Next, we studied the impact of divergent selection by exploiting predicted and experimental functional annotation of the bovine genome.

Results

We identified selective sweeps in beef cattle taurine and indicine populations, including a 430-kb selective sweep on indicine cattle chromosome 5 that is located between 47,670,001 and 48,100,000 bp and spans five genes, i.e. HELB, IRAK3, ENSBTAG00000026993, GRIP1 and part of HMGA2. Regions under selection in indicine cattle display significant enrichment for promoters and coding genes. At the nucleotide level, sites that show a strong divergence in allele frequency between European taurine and Asian indicine are enriched for the same functional categories. We identified nine single nucleotide polymorphisms (SNPs) in coding regions that are fixed for different alleles between subspecies, eight of which were located within the DNA helicase B (HELB) gene. By mining information from the 1000 Bull Genomes Project, we found that HELB carries mutations that are specific to indicine cattle but also found in taurine cattle, which are known to have been subject to indicine introgression from breeds, such as N’Dama, Anatolian Red, Marchigiana, Chianina, and Piedmontese. Based on in-house genome sequences, we proved that mutations in HELB segregate independently of the copy number variation HMGA2-CNV, which is located in the same region.

Conclusions

Major genomic sequence differences between Bos taurus and Bos indicus are enriched for promoter and coding regions. We identified a 430-kb selective sweep in Asian indicine cattle located on chromosome 5, which carries SNPs that are fixed in indicine populations and located in the coding sequences of the HELB gene. HELB is involved in the response to DNA damage including exposure to ultra-violet light and is associated with reproductive traits and yearling weight in tropical cattle. Thus, HELB likely contributed to the adaptation of tropical cattle to their harsh environment.

Predictors of beef calf temperament at weaning and its impact on temperament at breeding and reproductive performance

Two experiments were conducted to determine (i) factors influencing calf temperament at weaning, (ii) association between heifer-calf temperament at weaning and temperament at breeding and (iii) effect of heifer-calf temperament on pregnancy rate per artificial insemination (P/AI). In experiment 1, beef cows and their calves (n = 285) from three farms were used. Sire docility estimated progeny difference (EPD) score, birth type (normal or assisted), calf gender, calf behaviour (during 1st 4 weeks) and calf health status (until weaning) were recorded. Cows and calves were assigned a temperament score (0-calm; 1-excitable), and all cows were given a body condition score (BCS, 1-9; 1-emaciated; 9-obese) at weaning. Calf's illness (p < .05), low sire docility EPD score (p < .05), altered gait (p < .05), altered resting behaviour (p < .01), reduced/no play behaviour (p < .05) and cow excitable temperament (p < .001) increased calf excitable temperament at weaning. In experiment 2, replacement heifer-calves (n = 758) from 12 farms were assigned a temperament score at weaning and later at breeding. Blood from 40 calves at weaning and 31 heifers at initiation of synchronization (same animals) was collected by coccygeal venipuncture for determination of circulating cortisol and substance P concentrations. Heifers were assigned a BCS and reproductive tract score (RTS, 1-5; 1-immature, acyclic; 5-mature, cyclic), synchronized for fixed time AI, observed for oestrus and were artificially inseminated. Cortisol concentrations were increased in excitable heifer-calves compared to calm heifer-calves at weaning (p < .05), and substance P was increased in excitable compared to calm females both at weaning and breeding (p < .05). Low sire EPD docility score (p < .01), heifer-calf excitable temperament at weaning increased excitable temperament at breeding (p < .01). Controlling for BCS categories (p < .01), oestrous expression (p < .0001) and temperament at breeding by oestrous expression (p < .05), the calf's excitable temperament at weaning (p < .001) reduced P/AI (Calm, 62.7 (244/389) vs. Excitable, 53.4% (197/369); p < .01). In conclusion, selection of docile cows and sires with greater docility EPD score should be given consideration to reduce calf excitement. Temperament in beef female can be detected earlier in their life and could be used as a tool in the selection process and to improve their performances.

ANIMAL BEHAVIOR AND WELL-BEING SYMPOSIUM: Interaction between coping style/personality, stress, and welfare: Relevance for domestic farm animals

This paper will argue that understanding animal welfare and the individual vulnerability to stress-related disease requires a fundamental understanding of functional individual variation as it occurs in nature as well as the underlying neurobiology and neuroendocrinology. Ecological studies in feral populations of mice, fish, and birds start to recognize the functional significance of phenotypes that individually differ in their behavioral and neuroendocrine response to environmental challenge. Recent studies indicate that the individual variation within a species may buffer the species for strong fluctuations in the natural habitat. Similarly, evolutionary ancient behavioral trait characteristics have now been identified in a range of domestic farm animals including cattle, pigs, and horses. Individual variation in behavior can be summarized in a 3-dimensional model with coping style, emotionality, and sociality as independent dimensions. These dimensions can be considered trait characteristics that are stable over time and across situations within the individual. This conceptual model has several consequences. First, the coping style dimension is strongly associated with differential stress vulnerability. Social stress studies show that proactive individuals are resilient under stable environmental conditions but vulnerable when outcome expectancies are violated. Reactive individuals are, in fact, rather flexible and seem to adapt more easily to a changing environment. A second consequence relates to genetics and breeding. Genetic selection for one trait usually implies selection for other traits as well. It is discussed that a more balanced breeding program that takes into account biologically functional temperamental traits will lead to more robust domestic farm animals. Finally, the relationship between temperamental traits, animal production, fitness, and welfare is discussed.