Genetic and Targeted eQTL Mapping Reveals Strong Candidate Genes Modulating the Stress Response During Chicken Domestication

Practical application of a Bayesian network approach to poultry epigenetics and stress

Background

Relationships among genetic or epigenetic features can be explored by learning probabilistic networks and unravelling the dependencies among a set of given genetic/epigenetic features. Bayesian networks (BNs) consist of nodes that represent the variables and arcs that represent the probabilistic relationships between the variables. However, practical guidance on how to make choices among the wide array of possibilities in Bayesian network analysis is limited. Our study aimed to apply a BN approach, while clearly laying out our analysis choices as an example for future researchers, in order to provide further insights into the relationships among epigenetic features and a stressful condition in chickens (Gallus gallus).

Results

Chickens raised under control conditions (n = 22) and chickens exposed to a social isolation protocol (n = 24) were used to identify differentially methylated regions (DMRs). A total of 60 DMRs were selected by a threshold, after bioinformatic pre-processing and analysis. The treatment was included as a binary variable (control = 0; stress = 1). Thereafter, a BN approach was applied: initially, a pre-filtering test was used for identifying pairs of features that must not be included in the process of learning the structure of the network; then, the average probability values for each arc of being part of the network were calculated; and finally, the arcs that were part of the consensus network were selected. The structure of the BN consisted of 47 out of 61 features (60 DMRs and the stressful condition), displaying 43 functional relationships. The stress condition was connected to two DMRs, one of them playing a role in tight and adhesive intracellular junctions in organs such as ovary, intestine, and brain.

Conclusions

We clearly explain our steps in making each analysis choice, from discrete BN models to final generation of a consensus network from multiple model averaging searches. The epigenetic BN unravelled functional relationships among the DMRs, as well as epigenetic features in close association with the stressful condition the chickens were exposed to. The DMRs interacting with the stress condition could be further explored in future studies as possible biomarkers of stress in poultry species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-022-04800-0.

Effects of the domestic thyroid stimulating hormone receptor (TSHR) variant on the hypothalamic-pituitary-thyroid axis and behavior in chicken

Domestic chickens are less fearful, have a faster sexual development, grow bigger, and lay more eggs than their primary ancestor, the red junglefowl. Several candidate genetic variants selected during domestication have been identified, but only a few studies have directly linked them with distinct phenotypic traits. Notably, a variant of the thyroid stimulating hormone receptor (TSHR) gene has been under strong positive selection over the past millennium, but it's function and mechanisms of action are still largely unresolved. We therefore assessed the abundance of the domestic TSHR variant and possible genomic selection signatures in an extensive data set comprising multiple commercial and village chicken populations as well as wild-living extant members of the genus Gallus. Furthermore, by mean of extensive backcrossing we introgressed the wild-type TSHR variant from red junglefowl into domestic White Leghorn chickens and investigated gene expression, hormone levels, cold adaptation, and behavior in chickens possessing either the wild-type or domestic TSHR variant. While the domestic TSHR was the most common variant in all studied domestic populations and in one of two red junglefowl population, it was not detected in the other Gallus species. Functionally, the individuals with the domestic TSHR variant had a lower expression of the TSHR in the hypothalamus and marginally higher in the thyroid gland than wild-type TSHR individuals. Expression of TSHB and DIO2, two regulators of sexual maturity and reproduction in birds, was higher in the pituitary gland of the domestic-variant chickens. Furthermore, the domestic variant was associated with higher activity in the open field test. Our findings confirm that the spread of the domestic TSHR variant is limited to domesticated chickens, and to a lesser extent, their wild counterpart, the red junglefowl. Furthermore, we showed that effects of genetic variability in TSHR mirror key differences in gene expression and behavior previously described between the red junglefowl and domestic chicken.

Variants That Differentiate Wolf and Dog Populations Are Enriched in Regulatory Elements

Research on the genetics of domestication most often focuses on the protein-coding exons. However, exons cover only a minor part (1–2%) of the canine genome, whereas functional mutations may be located also in regions beyond the exome, in regulatory regions. Therefore, a large proportion of phenotypical differences between dogs and wolves may remain genetically unexplained. In this study, we identified variants that have high allelic frequency differences (i.e., highly differentiated variants) between wolves and dogs across the canine genome and investigated the potential functionality. We found that the enrichment of highly differentiated variants was substantially higher in promoters than in exons and that such variants were enriched also in enhancers. Several enriched pathways were identified including oxytocin signaling, carbohydrate digestion and absorption, cancer risk, and facial and body features, many of which reflect phenotypes of potential importance during domestication, including phenotypes of the domestication syndrome. The results highlight the importance of regulatory mutations during dog domestication and motivate the functional annotation of the noncoding part of the canine genome.

Why Do Hens Pile? Hypothesizing the Causes and Consequences

Piling is a behavior in laying hens whereby individuals aggregate in larger densities than would be normally expected. When piling behavior leads to mortalities it is known as smothering and its frequent but unpredictable occurrence is a major concern for many egg producers. There are generally considered to be three types of piling: panic, nest box and recurring piling. Whilst nest box and panic piling have apparent triggers, recurring piling does not, making it an enigmatic and ethologically intriguing behavior. The repetitive nature of recurring piling may result in a higher incidence of smothering and could have unconsidered, sub-lethal consequences. Here, we consider the possible causes of recurring piling from an ethological perspective and outline the potential welfare and production consequences. Drawing on a wide range of literature, we consider different timescales of causes from immediate triggers to ontogeny and domestication processes, and finally consider the evolution of collective behavior. By considering different timescales of influence, we built four hypotheses relevant to the causes of piling, which state that the behavior: (i) is caused by hens moving toward or away from an attractant/repellent; (ii) is socially influenced; (iii) is influenced by early life experiences and; (iv) can be described as a maladaptive collective behavior. We further propose that the following could be welfare consequences of piling behavior: Heat stress, physical injury (such as keel bone damage), and behavioral and physiological stress effects. Production consequences include direct and indirect mortality (smothering and knock-on effects of piling, respectively), potential negative impacts on egg quality and on worker welfare. In future studies the causes of piling and smothering should be considered according to the different timescales on which causes might occur. Here, both epidemiological and modeling approaches could support further study of piling behavior, where empirical studies can be challenging.

The Effects of Quantitative Trait Architecture on Detection Power in Short-Term Artificial Selection Experiments

Evolve and resequence (E&R) experiments, in which artificial selection is imposed on organisms in a controlled environment, are becoming an increasingly accessible tool for studying the genetic basis of adaptation. Previous work has assessed how different experimental design parameters affect the power to detect the quantitative trait loci (QTL) that underlie adaptive responses in such experiments, but so far there has been little exploration of how this power varies with the genetic architecture of the evolving traits. In this study, we use forward simulation to build a more realistic model of an E&R experiment in which a quantitative polygenic trait experiences a short, but strong, episode of truncation selection. We study the expected power for QTL detection in such an experiment and how this power is influenced by different aspects of trait architecture, including the number of QTL affecting the trait, their starting frequencies, effect sizes, clustering along a chromosome, dominance, and epistasis patterns. We show that all of these parameters can affect allele frequency dynamics at the QTL and linked loci in complex and often unintuitive ways, and thus influence our power to detect them. One consequence of this is that existing detection methods based on models of independent selective sweeps at individual QTL often have lower detection power than a simple measurement of allele frequency differences before and after selection. Our findings highlight the importance of taking trait architecture into account when designing and interpreting studies of molecular adaptation with temporal data. We provide a customizable modeling framework that will enable researchers to easily simulate E&R experiments with different trait architectures and parameters tuned to their specific study system, allowing for assessment of expected detection power and optimization of experimental design.

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.

Hypothalamic transcriptome of tame and aggressive silver foxes (Vulpes vulpes) identifies gene expression differences shared across brain regions

The underlying neurological events accompanying dog domestication remain elusive. To reconstruct the domestication process in an experimental setting, silver foxes (Vulpes vulpes) have been deliberately bred for tame vs aggressive behaviors for more than 50 generations at the Institute for Cytology and Genetics in Novosibirsk, Russia. The hypothalamus is an essential part of the hypothalamic-pituitary-adrenal axis and regulates the fight-or-flight response, and thus, we hypothesized that selective breeding for tameness/aggressiveness has shaped the hypothalamic transcriptomic profile. RNA-seq analysis identified 70 differentially expressed genes (DEGs). Seven of these genes, DKKL1, FBLN7, NPL, PRIMPOL, PTGRN, SHCBP1L and SKIV2L, showed the same direction expression differences in the hypothalamus, basal forebrain and prefrontal cortex. The genes differentially expressed across the three tissues are involved in cell division, differentiation, adhesion and carbohydrate processing, suggesting an association of these processes with selective breeding. Additionally, 159 transcripts from the hypothalamus demonstrated differences in the abundance of alternative spliced forms between the tame and aggressive foxes. Weighted gene coexpression network analyses also suggested that gene modules in hypothalamus were significantly associated with tame vs aggressive behavior. Pathways associated with these modules include signal transduction, interleukin signaling, cytokine-cytokine receptor interaction and peptide ligand-binding receptors (eg, G-protein coupled receptor [GPCR] ligand binding). Current studies show the selection for tameness vs aggressiveness in foxes is associated with unique hypothalamic gene profiles partly shared with other brain regions and highlight DEGs involved in biological processes such as development, differentiation and immunological responses. The role of these processes in fox and dog domestication remains to be determined.

Genetical Genomics of Tonic Immobility in the Chicken

Identifying the molecular mechanisms of animal behaviour is an enduring goal for researchers. Gaining insight into these mechanisms enables us to gain a greater understanding of behaviour and their genetic control. In this paper, we perform Quantitative Trait Loci (QTL) mapping of tonic immobility behaviour in an advanced intercross line between wild and domestic chickens. Genes located within the QTL interval were further investigated using global expression QTL (eQTL) mapping from hypothalamus tissue, as well as causality analysis. This identified five candidate genes, with the genes PRDX4 and ACOT9 emerging as the best supported candidates. In addition, we also investigated the connection between tonic immobility, meat pH and struggling behaviour, as the two candidate genes PRDX4 and ACOT9 have previously been implicated in controlling muscle pH at slaughter. We did not find any phenotypic correlations between tonic immobility, struggling behaviour and muscle pH in a smaller additional cohort, despite these behaviours being repeatable within-test.

Chicken domestication changes expression of stress-related genes in brain, pituitary and adrenals

Domesticated species have an attenuated behavioral and physiological stress response compared to their wild counterparts, but the genetic mechanisms underlying this change are not fully understood. We investigated gene expression of a panel of stress response-related genes in five tissues known for their involvement in the stress response: hippocampus, hypothalamus, pituitary, adrenal glands and liver of domesticated White Leghorn chickens and compared it with the wild ancestor of all domesticated breeds, the Red Junglefowl. Gene expression was measured both at baseline and after 45 min of restraint stress. Most of the changes in gene expression related to stress were similar to mammals, with an upregulation of genes such as FKBP5, C-FOS and EGR1 in hippocampus and hypothalamus and StAR, MC2R and TH in adrenal glands. We also found a decrease in the expression of CRHR1 in the pituitary of chickens after stress, which could be involved in negative feedback regulation of the stress response. Furthermore, we observed a downregulation of EGR1 and C-FOS in the pituitary following stress, which could be a potential link between stress and its effects on reproduction and growth in chickens. We also found changes in the expression of important genes between breeds such as GR in the hypothalamus, POMC and PC1 in the pituitary and CYP11A1 and HSD3B2 in the adrenal glands. These results suggest that the domesticated White Leghorn may have a higher capacity for negative feedback of the HPA axis, a lower capacity for synthesis of ACTH in the pituitary and a reduced synthesis rate of corticosterone in the adrenal glands compared to Red Junglefowl. All of these findings could explain the attenuated stress response in the domesticated birds.

A Hypothesis and Review of the Relationship between Selection for Improved Production Efficiency, Coping Behavior, and Domestication

Coping styles in response to stressors have been described both in humans and in other animal species. Because coping styles are directly related to individual fitness they are part of the life history strategy. Behavioral styles trade off with other life-history traits through the acquisition and allocation of resources. Domestication and subsequent artificial selection for production traits specifically focused on selection of individuals with energy sparing mechanisms for non-production traits. Domestication resulted in animals with low levels of aggression and activity, and a low hypothalamic-pituitary-adrenal (HPA) axis reactivity. In the present work, we propose that, vice versa, selection for improved production efficiency may to some extent continue to favor docile domesticated phenotypes. It is hypothesized that both domestication and selection for improved production efficiency may result in the selection of reactive style animals. Both domesticated and reactive style animals are characterized by low levels of aggression and activity, and increased serotonin neurotransmitter levels. However, whereas domestication quite consistently results in a decrease in the functional state of the HPA axis, the reactive coping style is often found to be dominated by a high HPA response. This may suggest that fearfulness and coping behavior are two independent underlying dimensions to the coping response. Although it is generally proposed that animal welfare improves with selection for calmer animals that are less fearful and reactive to novelty, animals bred to be less sensitive with fewer desires may be undesirable from an ethical point of view.