Genetics of behavioural adaptation of livestock to farming conditions

Integration of selective sweeps across the sheep genome: understanding the relationship between production and adaptation traits

BACKGROUND

Livestock populations are under constant selective pressure for higher productivity levels for different selective purposes. This pressure results in the selection of animals with unique adaptive and production traits. The study of genomic regions associated with these unique characteristics has the potential to improve biological knowledge regarding the adaptive process and how it is connected to production levels and resilience, which is the ability of an animal to adapt to stress or an imbalance in homeostasis. Sheep is a species that has been subjected to several natural and artificial selective pressures during its history, resulting in a highly specialized species for production and adaptation to challenging environments. Here, the data from multiple studies that aim at mapping selective sweeps across the sheep genome associated with production and adaptation traits were integrated to identify confirmed selective sweeps (CSS).

RESULTS

In total, 37 studies were used to identify 518 CSS across the sheep genome, which were classified as production (147 prodCSS) and adaptation (219 adapCSS) CSS based on the frequency of each type of associated study. The genes within the CSS were associated with relevant biological processes for adaptation and production. For example, for adapCSS, the associated genes were related to the control of seasonality, circadian rhythm, and thermoregulation. On the other hand, genes associated with prodCSS were related to the control of feeding behaviour, reproduction, and cellular differentiation. In addition, genes harbouring both prodCSS and adapCSS showed an interesting association with lipid metabolism, suggesting a potential role of this process in the regulation of pleiotropic effects between these classes of traits.

CONCLUSIONS

The findings of this study contribute to a deeper understanding of the genetic link between productivity and adaptability in sheep breeds. This information may provide insights into the genetic mechanisms that underlie undesirable genetic correlations between these two groups of traits and pave the way for a better understanding of resilience as a positive ability to respond to environmental stressors, where the negative effects on production level are minimized.

Egg production in nests and nesting behaviour: genetic correlations with egg quality and BW for laying hens on the floor

In laying hen production, cage-free housing is growing rapidly to provide living conditions that meet hens' needs. Unlike cages, this housing requires nests for automatic collection of eggs, as eggs laid outside nests must be collected by hand. Selecting hens for nest-related traits, such as egg production in nests and nesting behaviour, could help meet the requirements of cage-free housing. However, genetic correlations between these traits and major traits of breeding programmes, such as egg quality or BW, are poorly known. In addition, the genetic determinism of major traits has rarely been studied under cage-free conditions. The objective of the present study was to estimate the heritability of egg quality and BW measured on the floor and their genetic correlations with nest-related traits. Egg production in nests was based on the laying rate in nests, laying rhythm (clutch number and mean oviposition time), and nest acceptance. Nesting behaviour was based on nest preference (mean distance between nests used for laying) and mean laying duration (time spent in the nest for laying). Nest-related traits were recorded from 24 to 64 weeks of age. BW and egg quality were measured at 50 and 55 weeks of age, respectively. Nest-related traits and identification of the eggs laid by each hen (for individual measurements of egg quality) were obtained using individual electronic nests used by hens raised in groups and on the floor. The phenotypes of 1 455 Rhode Island Red and 1 538 White Leghorn hens were analysed. Heritability coefficients and genetic correlations were estimated using a multi-trait animal model for each line. Heritability estimates for egg quality and BW were moderate to high for both lines (0.17-0.74). Overall, weak genetic correlations were estimated between nest-related traits and egg quality or BW for both lines. However, strong and antagonistic genetic correlations were estimated between eggshell strength and laying rate in the nests (-0.46 to -0.42) or laying rhythm (+0.46 to +0.68) for both lines. Several moderate-to-strong genetic correlations were found for White Leghorn between nest-related traits and egg weight, eggshell shape, albumen height, and BW. This study shows that nest-related traits can be used to select hens better adapted to cage-free housing without degrading overall egg quality and BW. It also shows that some traits, like the eggshell strength, must be carefully monitored if these new traits are included in breeding goals. These results must now be confirmed for other populations and larger datasets.

Avoidance-related behavioral and blood-based physiological responses of Nguni and Boran cattle subjected to routine handling activities post relocation

Introduction

This study aimed to investigate the avoidance-related behavioral and blood-based physiological responses of Nguni and Boran cattle during routine handling activities post-relocation, with a particular focus on the effect of breed, week, and waiting time.

Methods

A total of 20 animals, 10 from each breed, were subjected to handling activities at fortnight intervals post-relocation. The animals were observed for entry time (ES), chute score (CS), kicking score (KS), blood sampling time, cortisol, and glucose concentrations. The data were analyzed using ANOVA and regression analysis.

Results and Discussion

Results showed that breed had a significant effect on avoidance-related behavioral responses (ES: p = 0.0032; CS: p = 0.0071; and EX: p = 0.0320), with Nguni cattle displaying more active avoidance behaviors compared to Boran cattle. Additionally, breed differences were observed in physiological responses, with Nguni cattle exhibiting higher cortisol and glucose levels compared to Boran cattle. Waiting time in the race had a greater impact on chute score (CS: p = 0.0037) and cortisol release (p = 0.0375) in the two breeds. Regression analysis revealed that the amount of time spent in the handling facility prior to sampling and the duration of blood collection significantly increased from week 3 to 15. Steers that waited in the race for more than 10 min had higher cortisol levels (p = 0.0031). These findings suggest that breed-specific management practices may be necessary to reduce stress-related responses and improve animal welfare during routine handling activities post-relocation. Overall, this study highlights the importance of considering the effects of breed, week, and waiting time when evaluating the avoidance-related behavioral and blood-based physiological responses of cattle during routine handling activities. These factors play a significant role in understanding and addressing the stress and welfare concerns associated with handling procedures, particularly after relocation.

Differences among domestic chicken breeds in tonic immobility responses as a measure of fearfulness

Background

One priority for animal welfare is for animals to experience less fear, especially during human contact. For domestic animals, breeds that are less fearful may provide genetic resources to develop strains with improved welfare due to lower susceptibility to fear. Genetic predispositions inherited in these breeds might reflect the large diversity of chicken breeds. The goal of the present study was to systematically test a diverse group of chicken breeds to search for breeds that experience less fear.

Methods

Nineteen chicken breeds from commercial hybrid lines, native layer-type, meat-type and dual-purpose breeds, ornamental breeds as well as bantam breeds were tested in a standardized tonic immobility (TI) test. Chickens were manually restrained on their back, and the time to first head movement and first leg movement, the duration of TI, as well as the number of attempts needed to induce TI were measured.

Results

The TI response differed among chicken breeds (p ≤ 0.001) for naïve, mature hens. The median number of attempts required to induce TI ranged from 1 to 2 and did not differ significantly among breeds. Median durations were much more variable, with Lohmann Brown showing shortest durations (6 s, 12 s, 58 s for time to first head movement, first leg movement and total duration of TI, respectively). In contrast, medians reached the maximum of 600 s for all three measures in German Creepers. Repeated tests on the same individuals did not affect attempts needed to induce TI nor TI durations. Breeds clustered into two main groups, with layer-type native breeds and ornamental breeds having longer TI durations, and bantam, dual-purpose and meat-type native breeds having shorter TI durations.

Conclusions

Our findings provide evidence for substantial variation of fearfulness among breeds. This variation could be linked to the intended use during the breed's specific history. Knowledge and quantitative measurement of these behavioural responses provide the opportunity to improve welfare through selection and future breeding.

A Non-Invasive Millimetre-Wave Radar Sensor for Automated Behavioural Tracking in Precision Farming-Application to Sheep Husbandry

The automated quantification of the behaviour of freely moving animals is increasingly needed in applied ethology. State-of-the-art approaches often require tags to identify animals, high computational power for data collection and processing, and are sensitive to environmental conditions, which limits their large-scale utilization, for instance in genetic selection programs of animal breeding. Here we introduce a new automated tracking system based on millimetre-wave radars for real time robust and high precision monitoring of untagged animals. In contrast to conventional video tracking systems, radar tracking requires low processing power, is independent on light variations and has more accurate estimations of animal positions due to a lower misdetection rate. To validate our approach, we monitored the movements of 58 sheep in a standard indoor behavioural test used for assessing social motivation. We derived new estimators from the radar data that can be used to improve the behavioural phenotyping of the sheep. We then showed how radars can be used for movement tracking at larger spatial scales, in the field, by adjusting operating frequency and radiated electromagnetic power. Millimetre-wave radars thus hold considerable promises precision farming through high-throughput recording of the behaviour of untagged animals in different types of environments.

Ethological evaluation of pig welfare under different keeping technologies in Siberian conditions

The authors found that the system of keeping gestating sows on a breeding farm increases the risk of animal welfare related to technological problems and insufficient staff training (contamination, human fear, local infections, inflammation of joints). The negative impact of industrial technology on the welfare of gestating sows is manifested in the increased frequency of torso injuries and fear of humans. Limb problems in sows on a farm kept without walking are related to a low management level, as no such problems were observed in the industrial complex. The welfare of sows on small farms can be ensured by improving the technological level of production and the skills of maintenance personnel.

Feed intake and feeding behavior traits for gestating sows recorded using electronic sow feeders

Electronic sow feeding (ESF) systems are used to control feed delivery to individual sows that are group-housed. Feeding levels for gestating sows are typically restricted to prevent excessive body weight gain. Any alteration of intake from the allocated feeding curve or unusual feeding behavior could indicate potential health issues. The objective of this study was to use data recorded by ESF to establish and characterize novel feed intake and feeding behavior traits and to estimate their heritabilities. Raw data were available from two farms with in-house manufactured (Farm A) or commercial (Farm B) ESF. The traits derived included feed intake, time spent eating, and rate of feed consumption, averaged across or within specific time periods of gestation. Additional phenotypes included average daily number of feeding events (AFE), along with the cumulative numbers of days where sows spent longer than 30 min in the ESF (ABOVE30), missed their daily intake (MISSF), or consumed below 1 kg of feed (BELOW1). The appetite of sows was represented by averages of score (APPETITE), a binary value for allocation eaten or not (DA_bin), or the standard deviation of the difference between feed intake and allocation (SDA-I). Gilts took longer to eat than sows (15.5 ± 0.13 vs. 14.1 ± 0.11 min/d) despite a lower feed allocation (2.13 ± 0.00 vs. 2.36 ± 0.01 kg/d). The lowest heritability estimates (below 0.10) occurred for feed intake traits, due to the restriction in feed allocation, although heritabilities were slightly higher for Farm B, with restriction in the eating time. The low heritability for AFE (0.05 ± 0.02) may have reflected the lack of recording of nonfeeding visits, but repeatability was moderate (0.26 ± 0.03, Farm A). Time-related traits were moderately to highly heritable and repeatable, demonstrating genetic variation between individuals in their feeding behaviors. Heritabilities for BELOW1 (Farm A: 0.16 ± 0.04 and Farm B: 0.15 ± 0.09) and SDA-I (Farm A: 0.17 ± 0.04 and Farm B: 0.10 ± 0.08) were similar across farms. In contrast, MISSF was moderately heritable in Farm A (0.19 ± 0.04) but lowly heritable in Farm B (0.05 ± 0.07). Heritabilities for DA_bin were dissimilar between farms (Farm A: 0.02 ± 0.02 and Farm B: 0.23 ± 0.10) despite similar incidence. Individual phenotypes constructed from ESF data could be useful for genetic evaluation purposes, but equivalent capabilities to generate phenotypes were not available for both ESF systems.

Prospects for the Analysis and Reduction of Damaging Behaviour in Group-Housed Livestock, With Application to Pig Breeding

Innovations in the breeding and management of pigs are needed to improve the performance and welfare of animals raised in social groups, and in particular to minimise biting and damage to group mates. Depending on the context, social interactions between pigs can be frequent or infrequent, aggressive, or non-aggressive. Injuries or emotional distress may follow. The behaviours leading to damage to conspecifics include progeny savaging, tail, ear or vulva biting, and excessive aggression. In combination with changes in husbandry practices designed to improve living conditions, refined methods of genetic selection may be a solution reducing these behaviours. Knowledge gaps relating to lack of data and limits in statistical analyses have been identified. The originality of this paper lies in its proposal of several statistical methods for common use in analysing and predicting unwanted behaviours, and for genetic use in the breeding context. We focus on models of interaction reflecting the identity and behaviour of group mates which can be applied directly to damaging traits, social network analysis to define new and more integrative traits, and capture-recapture analysis to replace missing data by estimating the probability of behaviours. We provide the rationale for each method and suggest they should be combined for a more accurate estimation of the variation underlying damaging behaviours.

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.

Behavioral and Haemato-Biochemical Responses of Nguni and Boran Steers Post Relocation and Herd Regrouping in a Novel Environment

Behavioural and blood-based physiological responses of Nguni (NG) and Boran (BR) steers, following relocation to a new environment and herd regrouping were examined. Ten steers of each genotype aged 9 months and reared under similar conditions were studied over 16 weeks: 1 for acclimatization and baseline measurements in original groups, 15 for post regrouping measurements. Each sampling week, direct visual observations and durations of aggressive and affiliative interactions were recorded between 0500-1900h for 3 conservative days. Blood samples were drawn fortnightly by jugular venipuncture for plasma cortisol, glucose, creatine kinase (CK) and haematological analysis. In weeks 1-5, BR had higher instances of head-butting (P=0.0311), mounts (P=0.0142) and threats (P=0.0241) compared to NG (P<0.0001, P=0.0412 and P=0.0241, respectively). However, these significantly declined from weeks 7-15 in both genotypes. Grooming increased consistently over the weeks in both genotypes (P=0.0214). Head-butting correlated with cortisol (r=-0.116), CK (r=-0.295) and neutrophil-to-lymphocyte ratio (r=-0.144). Grooming correlated (r=0.137) with white-blood-cell-count. Herd regrouping temporarily disrupted social behaviour, with BR showing more aggression towards NG steers. Nevertheless, the two genotypes established some stability within five weeks of social mixing.

Cardiac and Skeletal Muscle Transcriptome Response to Heat Stress in Kenyan Chicken Ecotypes Adapted to Low and High Altitudes Reveal Differences in Thermal Tolerance and Stress Response

Heat stress (HS) negatively affects chicken performance. Agricultural expansion will happen in regions that experience high ambient temperatures, where fast-growing commercial chickens are vulnerable. Indigenous chickens of such regions, due to generations of exposure to environmental challenges, might have higher thermal tolerance. In this study, two indigenous chicken ecotypes, from the hot and humid Mombasa (lowland) and the colder Naivasha (highland) regions, were used to investigate the effects of acute (5 h, 35°C) and chronic (3 days of 35°C for 8 h/day) HS on the cardiac and skeletal muscle, through RNA sequencing. The rectal temperature gain and the number of differentially expressed genes (DEGs) [False Discovery Rate (FDR) < 0.05] were two times higher in the acute stage than in the chronic stage in both ecotypes, suggesting that cyclic exposure to HS can lead to adaptation. A tissue- and stage-specific difference in response to HS was observed, with peroxisome proliferator-activated-receptor (PPAR) signaling and mitogen-activate protein kinase (MAPK) signaling pathways, enriched in heart and skeletal muscle, respectively, and the p53 pathway enriched only in the acute stage in both tissues. The acute and chronic stage DEGs were integrated by a region-specific gene coexpression network (GCN), and genes with the highest number of connections (hub genes) were identified. The hub genes in the lowland network were CCNB2, Crb2, CHST9, SESN1, and NR4A3, while COMMD4, TTC32, H1F0, ACYP1, and RPS28 were the hub genes in the highland network. Pathway analysis of genes in the GCN showed that p53 and PPAR signaling pathways were enriched in both low and highland networks, while MAPK signaling and protein processing in endoplasmic reticulum were enriched only in the gene network of highland chickens. This shows that to dissipate the accumulated heat, to reduce heat induced apoptosis, and to promote DNA damage repair, the ecotypes activated or suppressed different genes, indicating the differences in thermal tolerance and HS response mechanisms between the ecotypes. This study provides information on the HS response of chickens, adapted to two different agro climatic environments, extending our understanding of the mechanisms of HS response and the effect of adaptation in counteracting HS.

Semen quality and diversity of morphological sperm abnormalities in bulls: breed and strain effects

At present great attention is paid to studying genetic regulation of farm animal adaptations to environmental conditions. This problem is very important due to a wide expansion of highly productive cattle breeds created in Europe and North America. However, until the present no investigation of changing semen quality in bulls of imported breeds during their adaptations to environmental conditions of Western Siberia has been conducted. The aim of this study was to investigate semen quality peculiarities and the diversity of morphological sperm abnormalities in bulls of imported and local breeds kept in the environmental conditions of the southern part of Western Siberia. We determined sperm concentration, sperm count, and rate of sperm with progressive motility and percentage of morphologically normal spermatozoa. The rate of sperm abnormalities according to Blome’s classifcation was determined too. It was found that the mean values of sperm concentration, sperm motility and percentage of morphologically normal spermatozoa in the bulls investigated were similar to those in bulls kept in European countries. Inter­breed differences in these parameters were not found. However, bulls of the Red Danish, Angler, and Simmental breeds had a higher percentage of misshapen sperm head and pyriform sperm head than bulls of the Black­White breed. An inter­strain difference in sperm motility in bulls of the Black­White breed was observed. It was found that bulls of Reflection Sovereign 198998 strain had lover sperm motility than bulls of Wis Burke Ideal 1013415 strain. No inter­strain differences in sperm production, percentage of morphologically normal spermatozoa and rate of main sperm abnormalities were found. Thus, it has been found that the environmental conditions of the southern part of Western Siberia do not seriously affect the sperm production, sperm motility or percentage of morphologically normal spermatozoa in bulls. However, the increased rate of misshapen and pyriform sperm heads in the bulls of the foreign breeds points to a need to study sperm DNA fragmentation.

Effects of parity and litter size on cortisol measures in commercially housed sows and their offspring

Breeding sows are regularly exposed to on-farm stressors throughout the duration of their production period. The impact of such stressors may differ for primi- and multiparous sows, as sows could learn to cope with stressors as they gain experience with them. If parity affects stress in sows, it may also impact their prenatal offspring through differential maternal stress. In addition to parity, litter size is another potential factor involved in stress of sows and piglets. Larger litters may be a source of discomfort for gestating sows, while it can result in intra-uterine growth restriction of piglets. In the current study, we aimed to assess whether parity and litter size affect cortisol measures in breeding sows and their offspring. To do this, we measured salivary cortisol concentrations of 16 primiparous and 16 multiparous sows at three time points: 1) while sows were group housed, 2) after sows were separated from the group prior to moving to the farrowing unit and 3) after handling procedures. In addition, hair cortisol concentration was determined for the sows during late gestation and for their low birth weight (n = 63) and normal birth weight (n = 43) offspring on day 3 after birth, to reflect in-utero cortisol exposure. It was expected that if sows adapt to on-farm stressors, the more experienced, multiparous sows would show decreased stress responses in comparison to primiparous sows. However, we found a comparable acute stress response of primi- and multiparous sows to separation from the group. Handling procedures did not influence sows' salivary cortisol concentrations. Sows' hair cortisol concentration was positively correlated with litter size. Future research is needed to assess whether this finding reflects increased stress in sows carrying larger litters. Parity or litter size did not have a direct effect on their offspring's hair cortisol concentration. Larger litters did have a higher occurrence of low birth weight piglets. For these piglets, females had higher neonatal hair cortisol concentrations than males. Overall, our results indicate that breeding sows do not adapt to all on-farm stressors. In addition, litter size may influence HPA axis activity in both sows and piglets.

Evaluating the temporal and situational consistency of personality traits in adult dairy cattle

Recent research suggests that personality, defined as consistent individual behavioral variation, in farm animals could be an important factor when considering their health, welfare, and productivity. However, behavioral tests are often performed individually and they might not reflect the behavioral differences manifested in every-day social environments. Furthermore, the contextual and longer-term temporal stability of personality traits have rarely been investigated in adult dairy cattle. In this study, we tested three groups of lactating Holstein cows (40 cows) using an individual arena test and a novel object test in groups to measure the contextual stability of behavior. Among the recorded individual test parameters, we used seven in the final analysis, which were determined by a systematic parameter reduction procedure. We found positive correlations between novel object contact duration in the group test and individual test parameters object contact duration (Rs = 0.361, P = 0.026) and movement duration (Rs = 0.336, P = 0.039). Both tests were repeated 6 months later to investigate their temporal stability whereby four individual test parameters were repeatable. There was no consistency in the group test results for 25 cows tested twice, possibly due to group composition changes. Furthermore, based on the seven individual test parameters, two personality traits (activity/exploration and boldness) were identified by principal component analysis. We found a positive association between the first and second tests for activity/exploration (Rs = 0.334, P = 0.058) and for boldness (Rs = 0.491, P = 0.004). Our results support the multidimensional nature of personality in adult dairy cattle and they indicate a link between behavior in individual and within-group situations. The lack of stability according to the group test results implies that group companions might have a stronger influence on individual behavior than expected. We suggest repeating the within-group behavioral measurements to study the relationship between the social environment and the manifestation of personality traits in every-day situations.

Systematic analysis of feeding behaviors and their effects on feed efficiency in Pekin ducks

Background

Feeding behavior study is important for animal husbandry and production. However, few studies were conducted on the feeding behavior and their relationship with feeding efficiency in Pekin ducks. In order to investigate the feeding behavior and their relationship with feed efficiency and other economic traits in Pekin ducks, we selected 358 male Pekin ducks and recorded feeding information between 3 to 6 wk of age using automatic electronic feeders, and compared the feeding behavior under different residual feed intake (RFI) levels.

Results

We observed that total feed time, daily feed intake and feed intake per meal had strong positive correlations with feed efficiency traits; moreover, strong correlation between feed intake per meal and body weight was found (R=0.32, 0.36). Daily feeding rate meal and meal duration had weak correlations with feed efficiency (R=0.14~0.15). The phenotypic correlation of between-meal pauses, with feed efficiency was not observed. When daily changes were analyzed, high RFI ducks had the highest feed consumption over all times, and obvious differences in daily visits were found among different RFI level animals during the middle period; these differences were magnified with age, but there was no difference in daily meal number. Moreover, our data indicate that high RFI birds mainly take their meals at the edge of the population enclosure, where they are more susceptible to environmental interference.

Conclusions

Overall, this study suggests that the general feeding behaviors can be accurately measured using automatic electronic feeders and certain feeding behaviors in Pekin ducks are associated with improved feed efficiency.

Electronic supplementary material

The online version of this article (10.1186/s40104-017-0212-2) contains supplementary material, which is available to authorized users.

Genomic Comparison of Indigenous African and Northern European Chickens Reveals Putative Mechanisms of Stress Tolerance Related to Environmental Selection Pressure

Global climate change is increasing the magnitude of environmental stressors, such as temperature, pathogens, and drought, that limit the survivability and sustainability of livestock production. Poultry production and its expansion is dependent upon robust animals that are able to cope with stressors in multiple environments. Understanding the genetic strategies that indigenous, noncommercial breeds have evolved to survive in their environment could help to elucidate molecular mechanisms underlying biological traits of environmental adaptation. We examined poultry from diverse breeds and climates of Africa and Northern Europe for selection signatures that have allowed them to adapt to their indigenous environments. Selection signatures were studied using a combination of population genomic methods that employed FST , integrated haplotype score (iHS), and runs of homozygosity (ROH) procedures. All the analyses indicated differences in environment as a driver of selective pressure in both groups of populations. The analyses revealed unique differences in the genomic regions under selection pressure from the environment for each population. The African chickens showed stronger selection toward stress signaling and angiogenesis, while the Northern European chickens showed more selection pressure toward processes related to energy homeostasis. The results suggest that chromosomes 2 and 27 are the most diverged between populations and the most selected upon within the African (chromosome 27) and Northern European (chromosome 2) birds. Examination of the divergent populations has provided new insight into genes under possible selection related to tolerance of a population's indigenous environment that may be baselines for examining the genomic contribution to tolerance adaptions.

Review: Deciphering animal robustness. A synthesis to facilitate its use in livestock breeding and management

As the environments in which livestock are reared become more variable, animal robustness becomes an increasingly valuable attribute. Consequently, there is increasing focus on managing and breeding for it. However, robustness is a difficult phenotype to properly characterise because it is a complex trait composed of multiple components, including dynamic elements such as the rates of response to, and recovery from, environmental perturbations. In this review, the following definition of robustness is used: the ability, in the face of environmental constraints, to carry on doing the various things that the animal needs to do to favour its future ability to reproduce. The different elements of this definition are discussed to provide a clearer understanding of the components of robustness. The implications for quantifying robustness are that there is no single measure of robustness but rather that it is the combination of multiple and interacting component mechanisms whose relative value is context dependent. This context encompasses both the prevailing environment and the prevailing selection pressure. One key issue for measuring robustness is to be clear on the use to which the robustness measurements will employed. If the purpose is to identify biomarkers that may be useful for molecular phenotyping or genotyping, the measurements should focus on the physiological mechanisms underlying robustness. However, if the purpose of measuring robustness is to quantify the extent to which animals can adapt to limiting conditions then the measurements should focus on the life functions, the trade-offs between them and the animal's capacity to increase resource acquisition. The time-related aspect of robustness also has important implications. Single time-point measurements are of limited value because they do not permit measurement of responses to (and recovery from) environmental perturbations. The exception being single measurements of the accumulated consequence of a good (or bad) adaptive capacity, such as productive longevity and lifetime efficiency. In contrast, repeated measurements over time have a high potential for quantification of the animal's ability to cope with environmental challenges. Thus, we should be able to quantify differences in adaptive capacity from the data that are increasingly becoming available with the deployment of automated monitoring technology on farm. The challenge for future management and breeding will be how to combine various proxy measures to obtain reliable estimates of robustness components in large populations. A key aspect for achieving this is to define phenotypes from consideration of their biological properties and not just from available measures.

Mutilating Procedures, Management Practices, and Housing Conditions That May Affect the Welfare of Farm Animals: Implications for Welfare Research

A number of mutilating procedures, such as dehorning in cattle and goats and beak trimming in laying hens, are common in farm animal husbandry systems in an attempt to prevent or solve problems, such as injuries from horns or feather pecking. These procedures and other practices, such as early maternal separation, overcrowding, and barren housing conditions, raise concerns about animal welfare. Efforts to ensure or improve animal welfare involve adapting the animal to its environment, i.e., by selective breeding (e.g., by selecting "robust" animals) adapting the environment to the animal (e.g., by developing social housing systems in which aggressive encounters are reduced to a minimum), or both. We propose adapting the environment to the animals by improving management practices and housing conditions, and by abandoning mutilating procedures. This approach requires the active involvement of all stakeholders: veterinarians and animal scientists, the industrial farming sector, the food processing and supply chain, and consumers of animal-derived products. Although scientific evidence about the welfare effects of current practices in farming such as mutilating procedures, management practices, and housing conditions is steadily growing, the gain in knowledge needs a boost through more scientific research. Considering the huge number of animals whose welfare is affected, all possible effort must be made to improve their welfare as quickly as possible in order to ban welfare-compromising procedures and practices as soon as possible.

Impact of selection for residual feed intake on production traits and behavior of mule ducks

A divergent selection experiment of Muscovy sires based on the residual feed intake (RFI) of their male mule progeny was initiated in 2009. Using electronic feeders, the aim of this study was to establish whether 3 generations of selection for RFI had an impact on feeding behavior traits and general behavior, and to examine its effect on liver and meat quality. Eighty mule ducks, issued from 8 Muscovy drakes per line with extreme RFI, were tested in a pen equipped with 4 electronic feeders. Feeding behaviors were recorded from 3 to 7 wk after hatching under ad libitum feeding conditions. Then animals were prepared for overfeeding with a 3-week period of restricted feeding, and overfed during 12 d before slaughter. The RFI was significantly lower in the low RFI line than in the high RFI line (−5.4 g/d, P = 0.0005) and daily feed intake was reduced both over the entire test period (−5 g/d, P = 0.049) and on a weekly basis (P = 0.006). Weekly and total feed conversion ratios were also significantly lower (−0.08, P = 0.03 and −0.06, P = 0.01, respectively). Low RFI ducks had more frequent meals, spent as much time eating as high RFI ducks, and their feeding rate was lower when analyzed at the wk level only. Additionally no significant correlation between feed efficiency and feeding behavior traits was evidenced, indicating only limited relationships between RFI and feeding patterns. Some differences in behavioral responses to stressors (open field test combined with a test measuring the response to human presence) suggested that a lower RFI is associated with less fearfulness. Selection for RFI had no effect on liver weight and quality and a slightly deleterious impact on meat quality (decreased drip loss and L*). Finally, low RFI animals had higher body weights after restricted feeding from wk 10 to wk 12 and after overfeeding than high RFI ducks. This suggests that selection for reduced RFI until 7 wk of age increases the feed efficiency up to slaughter.

Resilience in farm animals: biology, management, breeding and implications for animal welfare

A capacity for the animal to recover quickly from the impact of physical and social stressors and disease challenges is likely to improve evolutionary fitness of wild species and welfare and performance of farm animals. Salience and valence of stimuli sensed through neurosensors, chemosensors and immunosensors are perceived and integrated centrally to generate emotions and engage physiological, behavioural, immune, cognitive and morphological responses that defend against noxious challenges. These responses can be refined through experience to provide anticipatory and learned reactions at lower cost than innate less-specific reactions. Influences of behaviour type, coping style, and affective state and the relationships between immune responsiveness, disease resistance and resilience are reviewed. We define resilience as the capacity of animals to cope with short-term perturbations in their environment and return rapidly to their pre-challenge status. It is manifested in response to episodic, sporadic or situation-specific attributes of the environment and can be optimised via facultative learning by the individual. It is a comparative measure of differences between individuals in the outcomes that follow exposure to potentially adverse situations. In contrast, robustness is the capacity to maintain productivity in a wide range of environments without compromising reproduction, health and wellbeing. Robustness is manifested in response to persistent or cyclical attributes of the environment and is effected via activity of innate regulatory pathways. We suggest that for farm animals, husbandry practices that incorporate physical and social stressors and interactions with humans such as weaning, change of housing, and introduction to the milking parlour can be used to characterise resilience phenotypes. In these settings, resilience is likely to be more readily identified through the rate of return of variables to pre-challenge or normal status rather than through measuring the activity of diverse stress response and adaptation mechanisms. Our strategy for phenotyping resilience of sheep and cattle during weaning is described. Opportunities are examined to increase resilience through genetic selection and through improved management practices that provide emotional and cognitive enrichment and stress inoculation.

Genotype by environment interaction and breeding for robustness in livestock

The increasing size of the human population is projected to result in an increase in meat consumption. However, at the same time, the dominant position of meat as the center of meals is on the decline. Modern objections to the consumption of meat include public concerns with animal welfare in livestock production systems. Animal breeding practices have become part of the debate since it became recognized that animals in a population that have been selected for high production efficiency are more at risk for behavioral, physiological and immunological problems. As a solution, animal breeding practices need to include selection for robustness traits, which can be implemented through the use of reaction norms analysis, or though the direct inclusion of robustness traits in the breeding objective and in the selection index. This review gives an overview of genotype × environment interactions (the influence of the environment, reaction norms, phenotypic plasticity, canalization, and genetic homeostasis), reaction norms analysis in livestock production, options for selection for increased levels of production and against environmental sensitivity, and direct inclusion of robustness traits in the selection index. Ethical considerations of breeding for improved animal welfare are discussed. The discussion on animal breeding practices has been initiated and is very alive today. This positive trend is part of the sustainable food production movement that aims at feeding 9.15 billion people not just in the near future but also beyond.

Genetics of cattle temperament and its impact on livestock production and breeding – a review

Abstract. Cattle temperament, which describes individual behaviour differences with regard to a stressor or environmental challenge, is known for its impact on working safety, adaptability to new housing conditions, animal productivity and for evaluation of animal welfare. However, successful use of temperament in animal breeding and husbandry to improve keeping conditions in general or animal welfare in particular, requires the availability of informative and reproducible phenotypes and knowledge about the genetic modulation of these traits. However, the knowledge about genetic influences on cattle temperament is still limited. In this review, an outline is given for the interdependence between production systems and temperament as well as for the phenotyping of cattle temperament based on both behaviour tests and observations of behaviour under production conditions. In addition, the use of temperament as a selection criterion is discussed.

Genetic trends in maternal and neonatal behaviors and their association with perinatal survival in French Large White swine

Genetic trends in maternal abilities were studied in French Large White sows. Two lines representing old-type and modern-type pigs were obtained by inseminating modern sows with semen from boars born in 1977 or 1998. Successive generations were produced by inter-se mating. The maternal performance of sows from the second generation was compared in farrowing crates. Video analysis was performed for the 1st h after the onset of 43 and 36 farrowing events, and for the 6 first hours for 23 and 21 events, in old-type and modern-type sows, respectively. Genetic trends were estimated as twice the difference in estimates between the 2 lines. The contribution of behavior to the probability of stillbirth and piglet death in the first 2 days was estimated as the percentage of deviance reduction (DR) due to the addition of behavior traits as factors in the mortality model. Sow activity decreased strongly from the 1st to the 2nd h in both lines (P < 0.001). In the first 6 h, old-type sows sat (1st parity), stood (2nd parity) and rooted (both parities) for longer than modern-type sows, which were less active, especially in 2nd parity. In modern-type sows, stillbirth was associated positively with lying laterally in the first 6 h (4.6% DR) and negatively in the 1st h (9.1% DR). First-parity old-type sows were more attentive to piglets (P = 0.003) than modern-type sows which responded more to nose contacts at 2nd parity (P = 0.01). Maternal reactivity of modern-type sows was associated with a higher risk of piglet death (4.6% DR). Respiratory distress at birth tended to be higher in modern-type piglets than in old-type piglets (P < 0.10) and was associated with a higher risk of piglet death in both lines (2.7–3.1% DR). Mobility at birth was lower in modern-type than old-type piglets (P < 0.0001). Genetic trends show that sow and piglet behaviors at farrowing have changed. Our results indicate reduced welfare in parturient modern-type sows and their newborn piglets.

Identification of QTLs for behavioral reactivity to social separation and humans in sheep using the OvineSNP50 BeadChip

Background

Current trends in sheep farming practices rely on animals with a greater level of behavioral autonomy than before, a phenotype that actively contributes to the sustainability of animal production. Social reactivity and reactivity to humans are relevant behavioral traits in sheep, known for their strong gregariousness and weak tolerance to handling, which have previously been reported with moderate to high heritabilities. To identify loci underlying such behaviors, we performed a genome study in Romane lambs.

Results

The experiment was carried out on 934 male and female lambs allocated into 9 half-sib families (average of 103 lambs per family) and reared outside. After weaning, all the lambs were individually exposed to 4 standardized behavioral tests combining social isolation, exposure to humans or handling, confinement and novelty (i.e. arena test, corridor test, isolation box test, shearing test). A broad range of behaviors including vocalizations, locomotion, vigilance and flight distance, as well as the cortisol response to handling, were collected. All lambs were genotyped using the Illumina OvineSNP50 BeadChip. QTL detection was performed by linkage, association and joint linkage and association analyses using the QTLmap software. Five main QTL regions were identified on sheep chromosomes (Ovis Aries Region, OAR) 12, 16, 19, 21 and 23 among many other QTLs with small to moderate effects. The QTLs on OAR12, 16 and 21 showed significant associations with social reactivity. The QTLs on OAR19 and 23 were found to be associated with reactivity to humans. No overlapping QTLs were identified for the different traits measured in the behavioral tests, supporting the hypothesis that different genetic factors influence social reactivity and tolerance to humans.

Conclusion

The results of this study using ovine SNP data suggest that in domestic sheep the behavioral responses to social separation and exposure to humans are under polygenic influence. The most relevant QTLs reported in the present study contain interesting candidate genes previously described to be associated with various emotional and social behaviors in mammals.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-778) contains supplementary material, which is available to authorized users.

Injurious tail biting in pigs: how can it be controlled in existing systems without tail docking?

Tail biting is a serious animal welfare and economic problem in pig production. Tail docking, which reduces but does not eliminate tail biting, remains widespread. However, in the EU tail docking may not be used routinely, and some 'alternative' forms of pig production and certain countries do not allow tail docking at all. Against this background, using a novel approach focusing on research where tail injuries were quantified, we review the measures that can be used to control tail biting in pigs without tail docking. Using this strict criterion, there was good evidence that manipulable substrates and feeder space affect damaging tail biting. Only epidemiological evidence was available for effects of temperature and season, and the effect of stocking density was unclear. Studies suggest that group size has little effect, and the effects of nutrition, disease and breed require further investigation. The review identifies a number of knowledge gaps and promising avenues for future research into prevention and mitigation. We illustrate the diversity of hypotheses concerning how different proposed risk factors might increase tail biting through their effect on each other or on the proposed underlying processes of tail biting. A quantitative comparison of the efficacy of different methods of provision of manipulable materials, and a review of current practices in countries and assurance schemes where tail docking is banned, both suggest that daily provision of small quantities of destructible, manipulable natural materials can be of considerable benefit. Further comparative research is needed into materials, such as ropes, which are compatible with slatted floors. Also, materials which double as fuel for anaerobic digesters could be utilised. As well as optimising housing and management to reduce risk, it is important to detect and treat tail biting as soon as it occurs. Early warning signs before the first bloody tails appear, such as pigs holding their tails tucked under, could in future be automatically detected using precision livestock farming methods enabling earlier reaction and prevention of tail damage. However, there is a lack of scientific studies on how best to respond to outbreaks: the effectiveness of, for example, removing biters and/or bitten pigs, increasing enrichment, or applying substances to tails should be investigated. Finally, some breeding companies are exploring options for reducing the genetic propensity to tail bite. If these various approaches to reduce tail biting are implemented we propose that the need for tail docking will be reduced.

A note on the consistency of a behavioral play marker in piglets

Background

Play behavior has been proposed as a new potential indicator of animal welfare. Animals play only if they are in a relaxed state. Play may improve adaptability to challenging environments which may be of interest in the breeding objective. Little information is available on play behavior in livestock species. The aim of the present study is to investigate whether play behavior in post-weaned piglets can be induced instantly in the presence of additional space and whether play markers are body weight, sex, and litter dependent. It is investigated whether playfulness is elicited by the moment or if this measure is consistent over different days.

Methods

Thirty two piglets from four litters were released into a corridor and video recorded for eight min at 37, 41, 44 and 48 d of age. The first test was considered as an adjustment period and was not included in the analysis. In the second to the fourth test, joyful brusque movements (jumping, turning and running) were recorded with a camera and total number of movements (JOY#) and total time (JOYtime) were estimated individually. Animals were weighed at 41 d of age.

Results

Females had higher scores of JOY# and JOYtime than males but this was significant only for JOY# at 41 d of age (P < 0.05). The effect of age was highly significant both for JOY# and JOYtime (P < 0.01). Animals with a higher JOY# and JOYtime also expressed a higher JOY# and JOYtime in the other tests, but this was significant only between 44 and 48 d of age (P < 0.01). Body weight at 41 d of age was not significantly related to JOY# and JOYtime in any of the tests.

Conclusions

Locomotor play was induced instantly by the provision of increased space allowance. Litter origin had a significant effect on play behavior. In addition, locomotor play scores were consistent between two of the three tests.