Behaviour epigenetics – The connection between environment, stress and welfare

Stress-induced epigenetic effects driven by maternal lactation in dairy cattle: a comethylation network approach

Epigenetic marks do not follow the Mendelian laws of inheritance. The environment can alter the epigenotype of an individual when exposed to different external stressors. In lactating cows, the first stages of gestation overlap with the lactation peak, creating a negative energy balance that is difficult to overcome with diet. This negative energy balance could affect early embryo development that must compete with the mammary tissue for nutrients. We hypothesize that the methylation profiles of calves born to nonlactating heifers are different from those of calves born to lactating cows. We found 50,277 differentially methylated cytosines and 2,281 differentially methylated regions between these two groups of animals. A comethylation network was constructed to study the correlation between the phenotypes of the mothers and the epigenome of the calves, revealing 265 regions associated with the phenotypes. Our study revealed the presence of DMCs and DMRs in calves gestated by heifers and lactating cows, which were linked to the dam's lactation and the calves' ICAP and milk EBV. Gene-specific analysis highlighted associations with vasculature and organ morphogenesis and cell communication and signalling. These finding support the hypothesis that calves gestated by nonlactating mothers have a different methylation profile than those gestated by lactating cows.

The Omics Revolution in Understanding Chicken Reproduction: A Comprehensive Review

Omics approaches have significantly contributed to our understanding of several aspects of chicken reproduction. This review paper gives an overview of the use of omics technologies such as genomics, transcriptomics, proteomics, and metabolomics to elucidate the mechanisms of chicken reproduction. Genomics has transformed the study of chicken reproduction by allowing the examination of the full genetic makeup of chickens, resulting in the discovery of genes associated with reproductive features and disorders. Transcriptomics has provided insights into the gene expression patterns and regulatory mechanisms involved in reproductive processes, allowing for a better knowledge of developmental stages and hormone regulation. Furthermore, proteomics has made it easier to identify and quantify the proteins involved in reproductive physiology to better understand the molecular mechanisms driving fertility, embryonic development, and egg quality. Metabolomics has emerged as a useful technique for understanding the metabolic pathways and biomarkers linked to reproductive performance, providing vital insights for enhancing breeding tactics and reproductive health. The integration of omics data has resulted in the identification of critical molecular pathways and biomarkers linked with chicken reproductive features, providing the opportunity for targeted genetic selection and improved reproductive management approaches. Furthermore, omics technologies have helped to create biomarkers for fertility and embryonic viability, providing the poultry sector with tools for effective breeding and reproductive health management. Finally, omics technologies have greatly improved our understanding of chicken reproduction by revealing the molecular complexities that underpin reproductive processes.

Direct and cross-generational effects of reproduction on fitness and behavioral variability in male-biased environments

Population structure determines individuals’ interactions and trade-offs with evolutionary consequences. Male-biased populations increase intrasexual competition and intersexual harassment, reducing female resource acquisition, and thus, resources availability for the following generation. We analyzed direct and cross-generational effects of male harassment in two generations of damselflies (Odonata). We exposed adult females to treatments with different sex-ratio and density (balanced and male-biased) to modify the male harassment level. We analyzed female fecundity, fertility, and number of faecal deposits as an indirect measure of resources acquisition. We studied female flight performance after repeated exposures to males. We analyzed survivorship, development, exploration, thigmotaxis, and feeding latency of larvae produced by the experimental females. In both generations, we analyzed four metrics of behavior: mean value, interindividual differences in plasticity, intra-individual unpredictability, and repeatability. Mating duration increased in male-biased treatment, whereas female resources acquisition and fertility decreased. Females that mated longer showed higher fecundity when they were exposed to balanced treatment, but not if they were exposed to male-biased treatment. Females from the male-biased treatment showed interindividual differences in plasticity and no repeatability in flight performance. Offspring showed balanced sex-ratio and similar survivorship, development, and feeding latency independently of the parental treatment; however, females exposed to male-biased treatment produced offspring with higher differences in exploration plasticity and daughters less explorative and with higher unpredictable thigmotaxis. We propose prolonged copulation as courtship at balanced sex-ratio but a cost to females under male-biased sex-ratio. Cross-generational effects in behavioral variability may be a mechanism to cope with predicted future environments.

Effects of stress during commercial hatching on growth, egg production and feather pecking in laying hens

Every year, billions of egg layer chicks around the world are hatched under highly stressful, industrial circumstances. Here, it is investigated how the stressful procedure in the commercial hatchery, including incubation, hatching, processing, and transport affects the chicks with regards to traits relevant for the egg production industry. These traits were compared to those of a control group hatched in a small incubator and handled gently och quietly in a quiet room without any processing and transport. The chicks were weighed at hatch and at eight additional time points: 4 days, 1 week (w), 2 w, 3 w, 5 w, 8 w, 20 w and 25 w of age. Feather pecking was studied at 15 w of age and damages to the feathers and injuries on the comb and wattle were assessed at 25 w of age. From 19 w of age, eggs were collected on three days per week, counted and weighed. Chicks from a commercial hatchery had a lower hatch weight than control chicks (p<0.001). At 20 w of age, the weight of the commercial hatched chicks was still numerically lower, although this did not reach statistical significance. Commercially hatched chicks tended to show more feather pecking behaviour at 15 w of age compared to control chicks (p<0.1), although feather condition at 25 w of age showed the opposite pattern. Regarding production, commercially hatched chickens laid fewer (p<0.05) and smaller (p<0.05) eggs than chicks hatched and handled under calm circumstances. From this experiment, it is concluded that the stressful experience in the commercial hatchery has an overall negative effect on traits relevant for the industry.

Epigenetic inheritance and reproductive mode in plants and animals

Epigenetic inheritance is another piece of the puzzle of nongenetic inheritance, although the prevalence, sources, persistence, and phenotypic consequences of heritable epigenetic marks across taxa remain unclear. We systematically reviewed over 500 studies from the past 5 years to identify trends in the frequency of epigenetic inheritance due to differences in reproductive mode and germline development. Genetic, intrinsic (e.g., disease), and extrinsic (e.g., environmental) factors were identified as sources of epigenetic inheritance, with impacts on phenotype and adaptation depending on environmental predictability. Our review shows that multigenerational persistence of epigenomic patterns is common in both plants and animals, but also highlights many knowledge gaps that remain to be filled. We provide a framework to guide future studies towards understanding the generational persistence and eco-evolutionary significance of epigenomic patterns.

Short- and long-term consequences of stocking density during rearing on the immune system and welfare of laying hens

Already during early life, chickens need to cope with chronic stressors that can impair their health and welfare, with stocking density being one of the most influential factors. Nevertheless, there is a gap in research on the influence of stocking density on laying hens during rearing and in the subsequent laying period. This study therefore investigated how stocking density during rearing affects the immune system and welfare of pullets, and whether effects are persistent later in life. Pullets were reared at either low (13 birds/m²) or high (23 birds/m²) stocking densities but in identical group sizes from wk 7 to 17. Afterward, hens were kept at the same stocking density (2.4 birds/m²) until wk 28. Blood and tissue samples (spleen and cecal tonsils) were collected at the end of the rearing period and in the laying period. The parameters evaluated encompassed number and distribution of leukocytes and lymphocyte subsets in blood and lymphatic tissue, lymphocyte functionality, plasma corticosterone concentrations as well as behavior and physical appearance of hens. At the end of rearing, pullets kept under high stocking density had lower numbers of T lymphocytes, especially γδ T cells in blood, spleen, and cecal tonsils and displayed a higher heterophil to lymphocyte ratio. These effects are mostly persistent during the laying period, although stocking density was identical at this time. Furthermore, birds from the high stocking density group showed less active behavior, more pecking behavior and worse physical appearance throughout both examination periods. In conclusion, stocking density during rearing affects pullets' immune system and behavior not only in the rearing, but also subsequently in the laying period, indicating a strong correlation between health and welfare during rearing and the laying period.

Removal of roosters alters the domestic phenotype and microbial and genetic profile of hens

Hens are raised apart from roosters in modern poultry production, a substantial change from their natural social structure. We compared productivity, injuries, behavior, physiology, microbiome and transcriptome of hens housed with (R+) or without (R-) roosters to quantify the effects of this change in social structure. Hens were raised free-range from 70 to 280 days when 30 birds per treatment were assigned to battery cages until Day 315 (R+C vs. R-C), while 30 birds per treatment remained in free-range pens (R+F vs. R-F). Response to a novel environment and object, behavioral time budgets, cecum microbiome, blood composition and transcriptomic sequencing of thigh muscle and spleen were analyzed. Hens housed without roosters showed better survival, consumed less food, produced more eggs and had better feed conversion. R+F hens clustered around the rooster and were less mobile in the novel environment and object tests. R+F hens displayed the richest microbiome, and the presence of roosters resulted in differentially expressed genes related to muscle development, cellular processes, environmental information processing and immune function. Removing roosters from housed hens intensified desirable characteristics favored by domestication probably operating by deprivation of mating behavior and reduced fear, along with altered microbial and genetic function.

The Impact of Acute Loud Noise on the Behavior of Laboratory Birds

Husbandry procedures and facility settings, such as low-frequency fire alarms, can produce noises in a laboratory environment that cause stress to animals used in research. However, most of the data demonstrating harmful effects that have, consequently, led to adaptations to management, have largely come from laboratory rodents with little known of the impacts on avian behavior and physiology. Here we examined whether exposure to a routine laboratory noise, a low-frequency fire alarm test, induced behavioral changes in laboratory zebra finches (Taeniopygia guttata). Twenty-four breeding pairs of zebra finches were randomly selected and exposed to the low-frequency fire alarm (sounding for 10-20 s) or no noise (control) on separate test days. All birds were filmed before and after the alarm sounded and on a control day (without the alarm). The zebra finches decreased their general activity and increased stationary and social behaviors after exposure to the alarm. Brief exposure to a low-frequency alarm disrupted the birds' behavior for at least 15 min. The induction of this behavioral stress response suggests that low-frequency sound alarms in laboratory facilities have the potential to compromise the welfare of laboratory birds.

Transcriptome changes underlie alterations in behavioral traits in different types of chicken

In recent decades, artificial selection has contributed greatly to meeting the demands for animal meat, eggs, and milk. However, it has also resulted in changes in behavior, metabolic and digestive function, and alterations in tissue development, including the brain and skeleton. Our study aimed to profile the behavioral traits and transcriptome pattern of chickens (broilers, layers, and dual-purpose breeds) in response to artificial selection. Broilers spent less time gathered as a group in a novel arena (P < 0.01), suggesting reduced fearfulness in these birds. Broilers also showed a greater willingness to approach a model predator during a vigilance test but had a greater behavioral response when first exposed to the vocalization of the predator. Genes found to be upregulated and downregulated in previous work on chickens divergently selected for fear responses also showed consistent differences in expression between breeds in our study and indicated a reduction in fearfulness in broilers. Gene ACTB_G1 (actin) was differentially expressed between breeds and is a candidate gene involved with skeletal muscle growth and disease susceptibility in broilers. Furthermore, breed-specific alterations in the chicken domestic phenotype leading to differences in growth and egg production were associated with behavioral changes, which are probably underpinned by alterations in gene expression, gene ontology terms, and Kyoto Encyclopedia of Genes and Genomes pathways. The results highlight the change in behavior and gene expression of the broiler strain relative to the layer and a dual-purpose native breed.

On the Search for Grazing Personalities: From Individual to Collective Behaviors

While grazing lands can offer a diverse range of forages, individuals within herds prefer to graze some habitats and not others. They can have consistent differences in grazing patterns and occupy specific spatial domains, whilst developing tactics and strategies for foraging that are specific to their grazing personalities. In this review, we explore the development of our understanding of grazing personalities, as we move away from the search for an "optimal animal" toward designing behavior-customized herds with an arrangement of individual grazing personalities that enhance ecosystem services and productivity. We present a "grazing personality model" that accounts for the personality of individual animals and for collective behaviors of herds. We argue that grazing personalities of grazing ruminants and other large herbivores are in part genetically determined, and that they can act at the individual and collective level. The social and biophysical environments as well as the emotional state of animals regulate the expression of "grazing genes" that are observed phenotypically as distinct grazing personalities. The reproductive and sexual successes of individuals and herds filter for allele variants of grazing genes and in turn determines their relative frequency. While the selection of one grazing personality may be adequate for homogeneous pastoral systems, the design of herds with a range of grazing personalities that are matched to the habitat diversity may be a better approach to improving the distribution of grazing animals, enhancing ecosystem services, and maximizing productivity.

Inter-generational resemblance of methylation levels at circadian genes and associations with phenology in the barn swallow

Regulation of gene expression can occur via epigenetic effects as mediated by DNA methylation. The potential for epigenetic effects to be transmitted across generations, thus modulating phenotypic variation and affecting ecological and evolutionary processes, is increasingly appreciated. However, the study of variation in epigenomes and inter-generational transmission of epigenetic alterations in wild populations is at its very infancy. We studied sex- and age-related variation in DNA methylation and parent-offspring resemblance in methylation profiles in the barn swallows. We focused on a class of highly conserved 'clock' genes (clock, cry1, per2, per3, timeless) relevant in the timing of activities of major ecological importance. In addition, we considerably expanded previous analyses on the relationship between methylation at clock genes and breeding date, a key fitness trait in barn swallows. We found positive assortative mating for methylation at one clock locus. Methylation varied between the nestling and the adult stage, and according to sex. Individuals with relatively high methylation as nestlings also had high methylation levels when adults. Extensive parent-nestling resemblance in methylation levels was observed. Occurrence of extra-pair fertilizations allowed to disclose evidence hinting at a prevalence of paternal germline or sperm quality effects over common environment effects in generating father-offspring resemblance in methylation. Finally, we found an association between methylation at the clock poly-Q region, but not at other loci, and breeding date. We thus provided evidence for sex-dependent variation and the first account of parent-offspring resemblance in methylation in any wild vertebrate. We also showed that epigenetics may influence phenotypic plasticity of timing of life cycle events, thus having a major impact on fitness.

Transgenerational epigenetic inheritance in birds

While it has been shown that epigenetics accounts for a portion of the variability of complex traits linked to interactions with the environment, the real contribution of epigenetics to phenotypic variation remains to be assessed. In recent years, a growing number of studies have revealed that epigenetic modifications can be transmitted across generations in several animal species. Numerous studies have demonstrated inter- or multi-generational effects of changing environment in birds, but very few studies have been published showing epigenetic transgenerational inheritance in these species. In this review, we mention work conducted in parent-to-offspring transmission analyses in bird species, with a focus on the impact of early stressors on behaviour. We then present recent advances in transgenerational epigenetics in birds, which involve germline linked non-Mendelian inheritance, underline the advantages and drawbacks of working on birds in this field and comment on future directions of transgenerational studies in bird species.

DNA methylation profiles in red blood cells of adult hens correlate with their rearing conditions

Stressful conditions are common in the environment where production animals are reared. Stress in animals is usually determined by the levels of stress-related hormones. A big challenge, however, is in determining the history of exposure of an organism to stress, because the release of stress hormones can show an acute (and recent) but not a sustained exposure to stress. Epigenetic tools provide an alternative option to evaluate past exposure to long-term stress. Chickens provide a unique model to study stress effects in the epigenome of red blood cells (RBCs), a cell type of easy access and nucleated in birds. The present study investigated whether two different rearing conditions in chickens can be identified by looking at DNA methylation patterns in their RBCs later in life. These conditions were rearing in open aviaries versus in cages, which are likely to differ regarding the amount of stress they generate. Our comparison revealed 115 genomic windows with significant changes in RBC DNA methylation between experimental groups, which were located around 53 genes and within 22 intronic regions. Our results set the ground for future detection of long-term stress in live production animals by measuring DNA methylation in a cell type of easy accessibility.

Rare phenotypes in domestic animals: unique resources for multiple applications

Preservation of specific and inheritable phenotypes of current or potential future importance is one of the main purposes of conservation of animal genetic resources. In this review, we investigate the issues behind the characterisation, utilisation and conservation of rare phenotypes, considering their multiple paths of relevance, variable levels of complexity and mode of inheritance. Accurately assessing the rarity of a given phenotype, especially a complex one, is not a simple task, because it requires the phenotypic and genetic characterisation of a large number of animals and populations and remains dependent of the scale of the study. Once characterised, specific phenotypes may contribute to various purposes (adaptedness, production, biological model, aesthetics, etc.) with adequate introgression programmes, which justifies the consideration of (real or potential) existence of such characteristics in in situ or ex situ conservation strategies. Recent biotechnological developments (genomic and genetic engineering) will undoubtedly bring important changes to the way phenotypes are characterised, introgressed and managed.