A Growth QTL on Chicken Chromosome 1 Affects Emotionality and Sociality

Early and late cognitive and behavioral aspects associated with range use in free-range laying hens (Gallus gallus domesticus)

Individual differences in free-range chicken systems are important factors influencing how birds use the range (or not), even if individuals are reared in the same environmental conditions. Here, we investigated how various aspects of the birds' behavioral and cognitive tendencies, including their optimism/pessimism, cognitive flexibility, sociability, and exploration levels, are associated with range use and how they may change over time (before and after range access). To achieve this, 100 White Leghorn laying hen chicks underwent three distinct behavioral/cognitive tests-the cognitive bias test, the detour test, and the multivariate test-prior to gaining access to the range, between 9 and 39 days of age. After range access was allowed (from day 71), birds' range use was evaluated over 7 nonconsecutive days (from 74-91 days of age). Subsequently, a subset of birds, classified as high rangers (n = 15) and low rangers (n = 15) based on their range use, underwent retesting on the same three previous tests between 94 and 108 days of age. Our results unveiled a negative correlation trend between birds' evaluation of the ambiguous cue and their subsequent range use (rho = -0.19, p = 0.07). Furthermore, low rangers were faster to learn the detour task (χ2 = 7.34, df = 1, p = 0.006), coupled with increased sociability during the multivariate test (rho = -0.23, p = 0.02), contrasting with their high-ranging counterparts, who displayed more exploratory behaviors (F[1,27] = 3.64, p = 0.06). These behavioral patterns fluctuated over time (before and after range access); however, conclusively attributing these changes to birds' aging and development or the access to the range remains challenging. Overall, our results corroborate that behavioral and cognitive individual differences may be linked to range use and offer novel perspectives on the early behavioral and cognitive traits that may be linked to range use. These findings may serve as a foundation for adapting environments to meet individual needs and improve animal welfare in the future.

Quantitative trait loci mapping of innate fear behavior in day-old F2 chickens of Japanese Oh-Shamo and White Leghorn breeds using restriction site-associated DNA sequencing

Understanding the genetic mechanisms that underlie innate fear behavior is essential for improving the management and performance of the poultry industry. This study aimed to map QTL associated with innate fear responses in open field (OF) and tonic immobility (TI) tests, using an F2 chicken intercross population between 2 behaviorally distinct breeds: the aggressive Japanese Oh-Shamo (OSM) and the docile White Leghorn T-line (WL-T). Genome-wide QTL analysis for the OF and TI traits was conducted using 2,109 single nucleotide polymorphism (SNP) markers obtained through restriction site-associated DNA sequencing (RAD-seq). While several suggestive QTL were identified for TI and OF traits at genome-wide 20% significance threshold levels, the analysis revealed 2 significant QTL for 2 OF traits (total distance and maximum speed) at genome-wide 5% significance threshold levels. These significant QTL were located between 12.34 and 30.49 megabase (Mb) on chromosome 1 and between 40.02 and 63.38 Mb on chromosome 2, explaining 6.75 to 7.40% of the total variances. These findings provide valuable insights for the poultry industry, particularly in refining chicken management strategies and informing targeted breeding efforts.

Genetic Architecture of Innate Fear Behavior in Chickens

The genetic architecture of innate fear behavior in chickens is poorly understood. Here, we performed quantitative trait loci (QTL) analysis of innate responses to tonic immobility (TI) and open field (OF) fears in 242 newly hatched chicks of an F₂ population between the native Japanese Nagoya breed and the White Leghorn breed using 881 single nucleotide polymorphism markers obtained by restriction site-associated DNA sequencing. At genome-wide 5% significance levels, four QTL for TI traits were revealed on chromosomes 1-3 and 24. Two of these loci had sex-specific effects on the traits. For OF traits, three QTL were revealed on chromosomes 2, 4 and 7. The TI and OF QTL identified showed no overlaps in genomic regions and different modes of inheritance. The three TI QTL and one OF QTL exerted antagonistic effects on the traits. The results demonstrated that context-dependent QTL underlie the variations in innate TI and OF behaviors.

Newborn chicks show inherited variability in early social predispositions for hen-like stimuli

Predispositions of newborn vertebrates to preferentially attend to living beings and learn about them are pervasive. Their disturbance (e.g. in neonates at risk for autism), may compromise the proper development of a social brain. The genetic bases of such predispositions are unknown. We use the well-known visual preferences of newly-hatched chicks (Gallus gallus) for the head/neck region of the hen to investigate the presence of segregating variation in the predispositions to approach a stuffed hen vs. a scrambled version of it. We compared the spontaneous preferences of three breeds maintained genetically isolated for at least eighteen years while identically raised. Visually-naïve chicks of all breeds (Padovana, Polverara and Robusta maculata) showed the same initial preference for the predisposed stimulus, suggesting that the direction of the initial preference might be genetically fixed. A few minutes later though, striking differences emerged between breeds, which could indicate different strategies of dealing with affiliative objects: while the Polverara breed maintained a constant preference across the entire test, the Padovana and Robusta breeds progressively explored the alternative stimulus more. We hence documented the presence of inherited genetic variability in the expression of early social predispositions in interaction with environmental stimuli.

Domestication and tameness: brain gene expression in red junglefowl selected for less fear of humans suggests effects on reproduction and immunology

The domestication of animals has generated a set of phenotypic modifications, affecting behaviour, appearance, physiology and reproduction, which are consistent across a range of species. We hypothesized that some of these phenotypes could have evolved because of genetic correlation to tameness, an essential trait for successful domestication. Starting from an outbred population of red junglefowl, ancestor of all domestic chickens, we selected birds for either high or low fear of humans for five generations. Birds from the fifth selected generation (S₅) showed a divergent pattern of growth and reproduction, where low fear chickens grew larger and produced larger offspring. To examine underlying genetic mechanisms, we used microarrays to study gene expression in thalamus/hypothalamus, a brain region involved in fear and stress, in both the parental generation and the S₅. While parents of the selection lines did not show any differentially expressed genes, there were a total of 33 genes with adjusted p-values below 0.1 in S₅. These were mainly related to sperm-function, immunological functions, with only a few known to be relevant to behaviour. Hence, five generations of divergent selection for fear of humans produced changes in hypothalamic gene expression profiles related to pathways associated with male reproduction and to immunology. This may be linked to the effects seen on growth and size of offspring. These results support the hypothesis that domesticated phenotypes may evolve because of correlated effects related to reduced fear of humans.

Behavior genetics and the domestication of animals

Across species, a similar suite of traits tends to develop in response to domestication, including modifications in behavior. Reduced fear and increased stress tolerance were central in early domestication, and many domestication-related behaviors may have developed as traits correlated to reduced fear. Genetic mechanisms involved in domestication of behavior can be investigated by using top-down or bottom-up approaches, either starting from the behavior variation and searching for underlying genes or finding selected loci and then attempting to identify the associated phenotypes. Combinations of these approaches have proven powerful, and examples of results from such studies are presented and discussed. This includes loci associated with tameness in foxes and dogs, as well as loci correlated with reduced aggression and increased sociality in chickens. Finally, some examples are provided on epigenetic mechanisms in behavior, and it is suggested that selection of favorable epigenetic variants may have been an important mechanism in domestication.

The Effect of a Mutation in the Thyroid Stimulating Hormone Receptor (TSHR) on Development, Behaviour and TH Levels in Domesticated Chickens

The thyroid stimulating hormone receptor (TSHR) has been suggested to be a “domestication locus” in the chicken, due to a strong selective sweep over the gene found in domesticated chickens, differentiating them from their wild ancestor the Red Junglefowl (RJF). We investigated the effect of the mutation on development (incubation time), behaviour and thyroid hormone levels in intercross chickens homozygous for the mutation (d/d), wild type homozygotes (w/w) or heterozygotes (d/w). This allowed an assessment of the effect of genotype at this locus against a random mix of RJF and WL genotypes throughout the rest of the genome, controlling for family effects. The d/d genotype showed a longer incubation time, less fearful behaviours, lower number of aggressive behaviours and decreased levels of the thyroid hormone T4, in comparison to the w/w genotype. The difference between TSHR genotypes (d/d vs. w/w) in these respects mirrors the differences in development and behaviour between pure domesticated White Leghorns and pure RJF chickens. Higher individual T3 and T4 levels were associated with more aggression. Our study indicates that the TSHR mutation affects typical domestication traits, possibly through modifying plasma levels of thyroid hormones, and may therefore have been important during the evolution of the domestic chicken.

Genetic mapping of natural variation in schooling tendency in the threespine stickleback

Although there is a heritable basis for many animal behaviors, the genetic architecture of behavioral variation in natural populations remains mostly unknown, particularly in vertebrates. We sought to identify the genetic basis for social affiliation in two populations of threespine sticklebacks (Gasterosteus aculeatus) that differ in their propensity to school. Marine sticklebacks from Japan school strongly whereas benthic sticklebacks from a lake in Canada are more solitary. Here, we expanded on our previous efforts to identify quantitative trait loci (QTL) for differences in schooling tendency. We tested fish multiple times in two assays that test different aspects of schooling tendency: 1) the model school assay, which presents fish with a school of eight model sticklebacks; and 2) the choice assay, in which fish are given a choice between the model school and a stationary artificial plant. We found low-to-moderate levels of repeatability, ranging from 0.1 to 0.5, in schooling phenotypes. To identify the genomic regions that contribute to differences in schooling tendency, we used QTL mapping in two types of crosses: benthic × marine backcrosses and an F2 intercross. We found two QTL for time spent with the school in the model school assay, and one QTL for number of approaches to the school in the choice assay. These QTL were on three different linkage groups, not previously linked to behavioral differences in sticklebacks. Our results highlight the importance of using multiple crosses and robust behavioral assays to uncover the genetic basis of behavioral variation in natural populations.

A medium density genetic map and QTL for behavioral and production traits in Japanese quail

BACKGROUND

Behavioral traits such as sociability, emotional reactivity and aggressiveness are major factors in animal adaptation to breeding conditions. In order to investigate the genetic control of these traits as well as their relationships with production traits, a study was undertaken on a large second generation cross (F2) between two lines of Japanese Quail divergently selected on their social reinstatement behavior. All the birds were measured for several social behaviors (social reinstatement, response to social isolation, sexual motivation, aggression), behaviors measuring the emotional reactivity of the birds (reaction to an unknown object, tonic immobility reaction), and production traits (body weight and egg production).

RESULTS

We report the results of the first genome-wide QTL detection based on a medium density SNP panel obtained from whole genome sequencing of a pool of individuals from each divergent line. A genetic map was constructed using 2145 markers among which 1479 could be positioned on 28 different linkage groups. The sex-averaged linkage map spanned a total of 3057 cM with an average marker spacing of 2.1 cM. With the exception of a few regions, the marker order was the same in Japanese Quail and the chicken, which confirmed a well conserved synteny between the two species. The linkage analyses performed using QTLMAP software revealed a total of 45 QTLs related either to behavioral (23) or production (22) traits. The most numerous QTLs (15) concerned social motivation traits. Interestingly, our results pinpointed putative pleiotropic regions which controlled emotional reactivity and body-weight of birds (on CJA5 and CJA8) or their social motivation and the onset of egg laying (on CJA19).

CONCLUSION

This study identified several QTL regions for social and emotional behaviors in the Quail. Further research will be needed to refine the QTL and confirm or refute the role of candidate genes, which were suggested by bioinformatics analysis. It can be hoped that the identification of genes and polymorphisms related to behavioral traits in the quail will have further applications for other poultry species (especially the chicken) and will contribute to solving animal welfare issues in poultry production.

Adding ‘epi-’ to behaviour genetics: implications for animal domestication

In this review, it is argued that greatly improved understanding of domestication may be gained from extending the field of behaviour genetics to also include epigenetics. Domestication offers an interesting framework of rapid evolutionary changes caused by well-defined selection pressures. Behaviour is an important phenotype in this context, as it represents the primary means of response to environmental challenges. An overview is provided of the evidence for genetic involvement in behavioural control and the presently used methods for finding so-called behaviour genes. This shows that evolutionary changes in behaviour are to a large extent correlated to changes in patterns of gene expression, which brings epigenetics into the focus. This area is concerned with the mechanisms controlling the timing and extent of gene expression, and a lot of focus has been placed on methylation of cytosine in promoter regions, usually associated with genetic downregulation. The review considers the available evidence that environmental input, for example stress, can modify methylation and other epigenetic marks and subsequently affect behaviour. Furthermore, several studies are reviewed, demonstrating that acquired epigenetic modifications can be inherited and cause trans-generational behaviour changes. In conclusion, epigenetics may signify a new paradigm in this respect, as it shows that genomic modifications can be caused by environmental signals, and random mutations in DNA sequence are therefore not the only sources of heritable genetic variation.

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.

Effects of hatching time on behavior and weight development of chickens

The length of the embryonic period varies both among and within species and can affect the individual phenotype in many ways, both physiologically and behaviorally. In chickens, the hatch window may last 24–48 hours (up to 10% of the incubation time), and studies have shown that incubation length may affect post-hatch growth and physiology. However, little is known about effects on behavior. We therefore investigated how behavior variation correlates with hatching time in the early life of chickens. We also measured egg weight and egg weight loss in relation to hatching time, as well as post-hatch growth. For females, there was a negative correlation between hatch time and body weight from day 4 and throughout the experiment. For males, such a correlation was only observed when testing all hatched males up until day 10. The birds were exposed to a number of behavioral tests, and a principal components analysis was performed on the variables, resulting in four components. For the largest component, termed “Passivity”, a tendency of a difference was found between early and middle male hatchers. Furthermore, a significant difference between early and middle male hatchers was found in the second component, termed “Response to novelty”. In a spatial learning test, late hatchers tended to learn slower. The behavior of females was not significantly affected by hatching time in any of these tests. This study is among the first to demonstrate a link between time of hatching and early behavior in a precocial species like the chicken, and may help shedding light on the evolutionary trade-offs between incubation length and post-hatch traits. The results may also be relevant from a perspective of stress coping and therefore also for animal welfare and productivity in the chicken industry. The mechanisms linking hatching time with post-hatch phenotype remain to be investigated.

Evidence of phenotypic and genetic relationships between sociality, emotional reactivity and production traits in Japanese quail

The social behavior of animals, which is partially controlled by genetics, is one of the factors involved in their adaptation to large breeding groups. To understand better the relationships between different social behaviors, fear behaviors and production traits, we analyzed the phenotypic and genetic correlations of these traits in Japanese quail by a second generation crossing of two lines divergently selected for their social reinstatement behavior. Analyses of results for 900 individuals showed that the phenotypic correlations between behavioral traits were low with the exception of significant correlations between sexual behavior and aggressive pecks both at phenotypic (0.51) and genetic (0.90) levels. Significant positive genetic correlations were observed between emotional reactivity toward a novel object and sexual (0.89) or aggressive (0.63) behaviors. The other genetic correlations were observed mainly between behavioral and production traits. Thus, the level of emotional reactivity, estimated by the duration of tonic immobility, was positively correlated with weight at 17 and 65 days of age (0.76 and 0.79, respectively) and with delayed egg laying onset (0.74). In contrast, a higher level of social reinstatement behavior was associated with an earlier egg laying onset (-0.71). In addition, a strong sexual motivation was correlated with an earlier laying onset (-0.68) and a higher number of eggs laid (0.82). A low level of emotional reactivity toward a novel object and also a higher aggressive behavior were genetically correlated with a higher number of eggs laid (0.61 and 0.58, respectively). These results bring new insights into the complex determinism of social and emotional reactivity behaviors in birds and their relationships with production traits. Furthermore, they highlight the need to combine animal welfare and production traits in selection programs by taking into account traits of sociability and emotional reactivity.

Short copy number variations potentially associated with tonic immobility responses in newly hatched chicks

Introduction

Tonic immobility (TI) is fear-induced freezing that animals may undergo when confronted by a threat. It is principally observed in prey species as defence mechanisms. In our preliminary research, we detected large inter-individual variations in the frequency and duration of freezing behavior among newly hatched domestic chicks (Gallus gallus). In this study we aim to identify the copy number variations (CNVs) in the genome of chicks as genetic candidates that underlie the behavioral plasticity to fearful stimuli.

Methods

A total of 110 domestic chicks were used for an association study between TI responses and copy number polymorphisms. Array comparative genomic hybridization (aCGH) was conducted between chicks with high and low TI scores using an Agilent 4×180 custom microarray. We specifically focused on 3 genomic regions (>60 Mb) of chromosome 1 where previous quantitative trait loci (QTL) analysis showed significant F-values for fearful responses.

Results

ACGH successfully detected short CNVs within the regions overlapping 3 QTL peaks. Eleven of these identified loci were validated by real-time quantitative polymerase chain reaction (qPCR) as copy number polymorphisms. Although there wkas no significant p value in the correlation analysis between TI scores and the relative copy number within each breed, several CNV loci showed significant differences in the relative copy number between 2 breeds of chicken (White Leghorn and Nagoya) which had different quantitative characteristics of fear-induced responses.

Conclusion

Our data shows the potential CNVs that may be responsible for innate fear response in domestic chicks.

Differences in responses to repeated fear-relevant stimuli between Nagoya and White Leghorn chicks

Freezing responses to fearful stimuli are crucial for survival among all animal species within a prey-predator system. Generally, the degree of fearfulness correlates with intensity, duration, and frequency of freezing behaviours in response to fear-relevant stimuli. The present study examines innate fear responses to human handling in 144 newly hatched chicks through a tonic immobility (TI) test. Two fear responses-freezing duration and number of TI inductions-were examined. Individual variations in innate fear were investigated in chicks 1-2 days post-hatching when the restraint procedure was successively repeated 3 times within each day. Chicks showed sensitivity to fearful stimuli and considerable inter-individual variation in freezing duration and number of attempts required to induce TI. Moreover, differences were observed between breeds; White Leghorn chicks showed relatively low fear levels with gradual increases in TI duration, whereas Nagoya chicks showed extended TI duration and habituation to fearful stimuli. Our results suggest that TI reactions among newly hatched chicks are an innately determined behaviour specific to a breed or strain of chicken. Further, fearful responses among newborn chicks are not simple, but complex behaviours that involve multiple factors, such as breed-specific contextual fear learning and habituation/sensitisation processes.

Domestication-related variation in social preferences in chickens is affected by genotype on a growth QTL

A growth-related QTL on chicken chromosome 1 has previously been shown to influence domestication behaviour in chickens. In this study, we used Red Junglefowl (RJF) and White Leghorn (WL) as well as the intercross between them to investigate whether stress affects the way birds allocate their time between familiar and unfamiliar conspecifics in a social preference test ('social support seeking'), and how this is related to genotype at specific loci within the growth QTL. Red Junglefowl males spent more time with unfamiliar chickens before the stressful event compared to the other birds, whereas all birds except WL males tended to spend less time with unfamiliar ones after stress. A significant QTL locus was found to influence both social preference under undisturbed circumstances and social support seeking. The WL allele at this QTL was associated not only with a preference for unfamiliar individuals but also with a shift towards familiar ones in response to stress (social support seeking). A second, suggestive QTL also affected social support seeking, but in the opposite direction; the WL allele was associated with increased time spent with unfamiliar individuals. The region contains several possible candidate genes, and gene expression analysis of a number of them showed differential expression between RJF and WL of AVPR2 (receptor for vasotocin), and possibly AVPR1a (another vasotocin receptor) and NRCAM (involved in neural development) in the lower frontal lobes of the brains of RJF and WL animals. These three genes continue to be interesting candidates for the observed behavioural effects.

Genetics of behavioural adaptation of livestock to farming conditions

Behavioural adaptation of farm animals to environmental changes contributes to high levels of production under a wide range of farming conditions, from highly controlled indoor systems to harsh outdoor systems. The genetic variation in livestock behaviour is considerable. Animals and genotypes with a larger behavioural capacity for adaptation may cope more readily with varying farming conditions than those with a lower capacity for adaptation. This capacity should be exploited when the aim is to use a limited number of species extensively across the world. The genetics of behavioural traits is understood to some extent, but it is seldom accounted for in breeding programmes. This review summarizes the estimates of genetic parameters for behavioural traits in cattle, pigs, poultry and fish. On the basis of the major studies performed in the last two decades, we focus the review on traits of common interest in the four species. These concern the behavioural responses to both acute and chronic stressors in the physical environment (feed, temperature, etc.) and those in the social environment (other group members, progeny, humans). The genetic strategies used to improve the behavioural capacity for adaptation of animals differ between species. There is a greater emphasis on responses to acute environmental stress in fish and birds, and on responses to chronic social stress in mammals.