Investigating gene expression differences in two chicken groups with variable propensity to feather pecking

Malfunctioned inflammatory response and serotonin metabolism at the microbiota-gut-brain axis drive feather pecking behavior in laying hens

Feather pecking (FP) is a multifactorial abnormal behavior in laying hens where they display harmful pecks in conspecifics. FP has been associated with the altered functioning of the microbiome-gut-brain axis affecting host emotions and social behavior. The altered levels of serotonin (5-HT), a key monoaminergic neurotransmitter at both terminals of the gut-brain axis, affect the development of abnormal behavior, such as FP in laying hens. However, the underlying mechanism involving reciprocal interactions along the microbiota-gut-brain axis, particularly about the metabolism of 5-HT, remains unclear in FP phenotypes. This study examined the microbiota diversity, intestinal microbial metabolites, inflammatory responses, and 5-HT metabolism in divergently selected high (HFP; n = 8) and low (LFP; n = 8) FP hens to investigate the possible interconnections between FP behavior and the examined parameters. The 16S rRNA analysis revealed that compared to LFP birds, the gut microbiota of HFP birds exhibited a decrease in the abundance of phylum Firmicutes and genera Lactobacillus, while an increase in the abundance of phylum Proteobacteria and genera Escherichia Shigella and Desulfovibrio. Furthermore, the intestinal differential metabolites associated with FP phenotypes were mainly enriched in the tryptophan metabolic pathway. HFP birds had higher tryptophan metabolites and possibly a more responsive immune system compared to the LFP birds. This was indirectly supported by altered TNF-α levels in the serum and expression of inflammatory factor in the gut and brain. Moreover, HFP birds had lower serum levels of tryptophan and 5-HT compared to LFP birds, which was consistent with the downregulation of 5-HT metabolism-related genes in the brain of HFP birds. The correlation analysis revealed that genera Lactobacillus and Desulfovibrio were associated with differences in intestinal metabolites, 5-HT metabolism, and inflammatory response between the LFP and HFP birds. In conclusion, differences in the cecal microbiota profile, immune response and 5-HT metabolism drive FP phenotypes, which could be associated with the gut abundance of genera Lactobacillus and Desulfovibrio.

The study of selection signature and its applications on identification of candidate genes using whole genome sequencing data in chicken - a review

Chicken is a major source of protein for the increasing human population and is useful for research purposes. There are almost 1,600 distinct regional breeds of chicken across the globe, among which a large body of genetic and phenotypic variations has been accumulated due to extensive natural and artificial selection. Moreover, natural selection is a crucial force for animal domestication. Several approaches have been adopted to detect selection signatures in different breeds of chicken using whole genome sequencing (WGS) data including integrated haplotype score (iHS), cross-populated extend haplotype homozygosity test (XP-EHH), fixation index (F_ST), cross-population composite likelihood ratio (XP-CLR), nucleotide diversity (Pi), and others. In addition, gene enrichment analyses are utilized to determine KEGG pathways and gene ontology (GO) terms related to traits of interest in chicken. Herein, we review different studies that have adopted diverse approaches to detect selection signatures in different breeds of chicken. This review systematically summarizes different findings on selection signatures and related candidate genes in chickens. Future studies could combine different selection signatures approaches to strengthen the quality of the results thereby providing more affirmative inference. This would further aid in deciphering the importance of selection in chicken conservation for the increasing human population.

Structural variation and eQTL analysis in two experimental populations of chickens divergently selected for feather-pecking behavior

Feather pecking (FP) is a damaging nonaggressive behavior in laying hens with a heritable component. Its occurrence has been linked to the immune system, the circadian clock, and foraging behavior. Furthermore, dysregulation of miRNA biogenesis, disturbance of the gamma-aminobutyric acid (GABAergic) system, as well as neurodevelopmental deficiencies are currently under debate as factors influencing the propensity for FP behavior. Past studies, which focused on the dissection of the genetic factors involved in FP, relied on single nucleotide polymorphisms (SNPs) and short insertions and deletions < 50 bp (InDels). These variant classes only represent a certain fraction of the genetic variation of an organism. Hence, we reanalyzed whole-genome sequencing data from two experimental populations, which have been divergently selected for FP behavior for over more than 15 generations, performed variant calling for structural variants (SVs) as well as tandem repeats (TRs), and jointly analyzed the data with SNPs and InDels. Genotype imputation and subsequent genome-wide association studies, in combination with expression quantitative trait loci analysis, led to the discovery of multiple variants influencing the GABAergic system. These include a significantly associated TR downstream of the GABA receptor subunit beta-3 (GABRB3) gene, two microRNAs targeting several GABA receptor genes, and dystrophin (DMD), a direct regulator of GABA receptor clustering. Furthermore, we found the transcription factor ETV1 to be associated with the differential expression of 23 genes, which points toward a role of ETV1, together with SMAD4 and KLF14, in the disturbed neurodevelopment of high-feather pecking chickens.

Effects of incubation lighting with green or white light on brown layers: Hatching performance, feather pecking and hypothalamic expressions of genes related with photoreception, serotonin and stress systems

The aim of this study was to evaluate the effect of 16L:8D photoperiod with green (GREEN) or white (WHITE) lights during incubation on hatching performance, blood melatonin, corticosterone, and serotonin levels, hypothalamic expressions of genes related to photoreception, serotonin, and stress systems in layers in relation with feather pecking behavior. Dark incubation (DARK) was the control. Eggs (n = 1,176) from Brown Nick breeders in 2 batches (n = 588/batch) were incubated in the experiment. A total of 396 female chicks and 261 hens were used at rearing and laying periods until 40 wk. Incubation lighting did not affect hatchability, day-old chick weight, and length, but resulted in a more synchronized hatch as compared with the DARK. The effect of incubation lighting on blood hormones was not significant except for reduced serotonin in the GREEN group at the end of the experiment. There was no effect of incubation lighting on gentle, severe, and aggressive pecking of birds during the early rearing period. From 16 wk, GREEN hens showed increased gentle pecking with increasing age. WHITE hens had the highest gentle pecking frequency at 16 wk while they performed less gentle but higher severe and aggressive pecks at 24 and 32 wk. At hatching, the hypothalamic expression of CRH, 5-HTR1A, and 5-HTR1B was higher for the WHITE group compared with both GREEN and DARK, however, 5-HTT expression was higher in GREEN than WHITE which was similar to DARK. Except for the highest VA opsin expression obtained for WHITE hens at 40 wk of age, there was no change in hypothalamic expression levels of rhodopsin, VA opsin, red, and green opsins at any age. Although blood hormone levels were not consistent, results provide preliminary evidence that incubation lighting modulates the pecking tendencies of laying hens, probably through the observed changes in hypothalamic expression of genes related to the serotonin system and stress. Significant correlations among the hypothalamic gene expression levels supplied further evidence for the associations among photoreception, serotonin, and stress systems.

A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes

Background

Various regions of the chicken genome have been under natural and artificial selection for thousands of years. The substantial diversity that exits among chickens from different geographic regions provides an excellent opportunity to investigate the genomic regions under selection which, in turn, will increase our knowledge about the mechanisms that underlie chicken diversity and adaptation. Several statistics have been developed to detect genomic regions that are under selection. In this study, we applied approaches based on differences in allele or haplotype frequencies (F_ST and hapFLK, respectively) between populations, differences in long stretches of consecutive homozygous sequences (ROH), and differences in allele frequencies within populations (composite likelihood ratio (CLR)) to identify inter- and intra-populations traces of selection in two Iranian indigenous chicken ecotypes, the Lari fighting chicken and the Khazak or creeper (short-leg) chicken.

Results

Using whole-genome resequencing data of 32 individuals from the two chicken ecotypes, approximately 11.9 million single nucleotide polymorphisms (SNPs) were detected and used in genomic analyses after quality processing. Examination of the distribution of ROH in the two populations indicated short to long ROH, ranging from 0.3 to 5.4 Mb. We found 90 genes that were detected by at least two of the four applied methods. Gene annotation of the detected putative regions under selection revealed candidate genes associated with growth (DCN, MEOX2 and CACNB1), reproduction (ESR1 and CALCR), disease resistance (S1PR1, ALPK1 and MHC-B), behavior pattern (AGMO, GNAO1 and PSEN1), and morphological traits (IHH and NHEJ1).

Conclusions

Our findings show that these two phenotypically different indigenous chicken populations have been under selection for reproduction, immune, behavioral, and morphology traits. The results illustrate that selection can play an important role in shaping signatures of differentiation across the genomic landscape of two chicken populations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00664-9.

Molecular Cloning and Functional Characterization of Three 5-HT Receptor Genes (HTR1B, HTR1E, and HTR1F) in Chickens

The serotonin (5-hydroxytryptamine, 5-HT) signaling system is involved in a variety of physiological functions, including the control of cognition, reward, learning, memory, and vasoconstriction in vertebrates. Contrary to the extensive studies in the mammalian system, little is known about the molecular characteristics of the avian serotonin signaling network. In this study, we cloned and characterized the full-length cDNA of three serotonin receptor genes (HTR1B, HTR1E and HTR1F) in chicken pituitaries. Synteny analyses indicated that HTR1B, HTR1E and HTR1F were highly conserved across vertebrates. Cell-based luciferase reporter assays showed that the three chicken HTRs were functional, capable of binding their natural ligands (5-HT) or selective agonists (CP94253, BRL54443, and LY344864) and inhibiting intracellular cAMP production in a dose-dependent manner. Moreover, activation of these receptors could stimulate the MAPK/ERK signaling cascade. Quantitative real-time PCR analyses revealed that HTR1B, HTR1E and HTR1F were primarily expressed in various brain regions and the pituitary. In cultured chicken pituitary cells, we found that LY344864 could significantly inhibit the secretion of PRL stimulated by vasoactive intestinal peptide (VIP) or forskolin, revealing that HTR1F might be involved in the release of prolactin in chicken. Our findings provide insights into the molecular mechanism and facilitate a better understanding of the serotonergic modulation via HTR1B, HTR1E and HTR1F in avian species.

Genome-wide association studies for mottled eggs in chickens using a high-density single-nucleotide polymorphism array

Mottled eggs in layer chickens are gaining increasing attention because of the economic impact on the egg industry caused by the reduced sale value of commodity eggs. However, the genetic architecture underlying mottled eggs is not well understood. The genetic architecture underlying the mottled egg trait was investigated using genome-wide association studies (GWAS) by high-density arrays, using a total of 407 pink eggs and 799 blue eggs from an F₂ resource population generated by crossing Dongxiang Blue-shelled and White Leghorn chickens. The mottled egg score in blue eggs was found to be higher than that in pink eggs. The single-nucleotide polymorphism heritability of mottled egg at laying day and storage for 7 days was 0.18 and 0.20, respectively. Bivariate GWAS provided 29 significant loci, mainly located on GGA2, GGA3, GGA8, GGA10, GGA15, GGA17, and GGA23, affecting mottled egg on laying day. Candidate genes RIMS2, SLC25A32, RIMBP2, VPS13B, and RGS3 were obtained for mottled eggshell by bivariate GWAS and gene annotation. Our findings provide new insights into the genetic architecture of mottled egg in hens, and demonstrate that a genomic selection method would be profitable for breeding out the mottled egg trait.

Analysis of the brain transcriptome in lines of laying hens divergently selected for feather pecking

Background

Feather pecking (FP) in laying hens reduces animal welfare and leads to economic losses for the layer industry. FP is considered a heritable condition that is influenced by dysregulation of neurotransmitter homeostasis, the gut microbiome, and the immune system. To identify genes and biological pathways responsible for FP behavior we compared the brain transcriptomes of 48 hens divergently selected for FP. In addition, we tested if high feather peckers (HFP) and low feather peckers (LFP) respond differently to light since light has been shown to trigger FP behavior.

Results

Of approximately 48 million reads/sample an average of 98.4% were mapped to the chicken genome (GRCg6a). We found 13,070 expressed genes in the analyzed brains of which 423 showed differential expression between HFP and LFP. Genes of uncertain function and non-coding RNAs were overrepresented among those transcripts. Functional analyses revealed the involvement of cholinergic signaling, postsynaptic activity, membrane channels, and the immune system. After the light stimulus, 28 genes were found to be differentially expressed. These included an interaction cluster of core components of the circadian clock. However, differences in the response to light between HFP and LFP were not detectable.

Conclusions

Genes involved in cholinergic signaling, channel activity, synaptic transmission, and immune response were found to be involved in FP behavior. We propose a model in which the gut microbiota modulates the immune system, which in turn affects cholinergic signaling. This might have an influence on monoamine signaling with possible involvement of GABA or glutamate signaling.

Review of Sensor Technologies in Animal Breeding: Phenotyping Behaviors of Laying Hens to Select Against Feather Pecking

Simple Summary

The European Cooperation in Science and Technology (COST) Action GroupHouseNet aims to provide synergy among scientists to prevent damaging behavior in group-housed pigs and laying hens. One goal of this network is to determine how genetic and genomic tools can be used to breed animals that are less likely to perform damaging behavior on their pen-mates. In this review, the focus is on feather-pecking behavior in laying hens. Reducing feather pecking in large groups of hens is a challenge, because it is difficult to identify and monitor individual birds. However, current developments in sensor technologies and animal breeding have the potential to identify individual animals, monitor individual behavior, and link this information back to the underlying genotype. We describe a combination of sensor technologies and “-omics” approaches that could be used to select against feather-pecking behavior in laying hens.

Abstract

Damaging behaviors, like feather pecking (FP), have large economic and welfare consequences in the commercial laying hen industry. Selective breeding can be used to obtain animals that are less likely to perform damaging behavior on their pen-mates. However, with the growing tendency to keep birds in large groups, identifying specific birds that are performing or receiving FP is difficult. With current developments in sensor technologies, it may now be possible to identify laying hens in large groups that show less FP behavior and select them for breeding. We propose using a combination of sensor technology and genomic methods to identify feather peckers and victims in groups. In this review, we will describe the use of “-omics” approaches to understand FP and give an overview of sensor technologies that can be used for animal monitoring, such as ultra-wideband, radio frequency identification, and computer vision. We will then discuss the identification of indicator traits from both sensor technologies and genomics approaches that can be used to select animals for breeding against damaging behavior.

Stress response, peripheral serotonin and natural antibodies in feather pecking genotypes and phenotypes and their relation with coping style

Feather pecking (FP), a serious welfare and economic issue in the egg production industry, has been related to coping style. Proactive and reactive coping styles differ in, among others, the stress response, serotonergic activity and immune activity. Yet, it is unknown whether genetic lines divergently selected on FP (i.e. FP genotypes) or individuals differing in FP (i.e. FP phenotypes) can be categorized into coping styles. Therefore, we determined peripheral serotonin (5-HT) levels, natural antibody (NAb) titers, behavioral and corticosterone (CORT) responses to manual restraint (MR) in FP genotypes (high FP (HFP), low FP (LFP) and unselected control (CON) line) and FP phenotypes (feather pecker, feather pecker-victim, victim and neutral). We further examined the consistency of and relationships between behavioral and physiological measures. FP genotypes differed in behavioral responses to MR, 5-HT levels and NAb titers, but not in CORT levels after MR. HFP birds had less active responses at adolescent age, but more active responses at adult age compared to LFP and CON birds. The CON line had higher 5-HT levels at adolescent age, while the HFP line had lower 5-HT levels than the other lines at adult age. Overall, the HFP line had lower IgM NAb titers, while the LFP line had lower IgG NAb titers compared to the other lines. FP phenotypes differed in behavioral responses to MR and 5-HT levels, but not in CORT levels after MR or NAb titers. Within the HFP line, feather peckers tended to have less active responses compared to neutrals at adolescent age, while victims had more active responses compared to the other phenotypes at adult age. Feather peckers had higher 5-HT levels than neutrals at adult age. Behavioral and CORT responses to MR were not consistent over time, suggesting that responses to MR might not reflect coping style in this study. Furthermore, proactive behavioral responses were correlated with reactive physiological measures and vice versa. Thus, it was not possible to categorize FP genotypes or FP phenotypes into specific coping styles.

Enhanced Expression of Serotonin Receptor 5-Hydroxytryptamine 2C is Associated with Increased Feather Damage in Dongxiang Blue-Shelled Layers

The gene encoding the serotonin receptor 5-hydroxytraptamine 2C (HTR2C) has been implicated in behavioral phenotypes in a number of species. In previous studies, a mutation in the chicken HTR2C gene was found to be associated with feather condition, thereby suggesting a relationship between the gene and receiving feather pecking activity. The present study analyzed the chicken HTR2C gene at both the genomic make-up and expression level in Dongxiang blue-shelled layer. A significant association between the single nucleotide polymorphism (SNP) rs13640917 (C/T) and feather condition was confirmed in the Chinese local layer. Enhanced HTR2C gene expression (151.1-fold) that was associated with high feather damage indicated that the right cerebrum might be the critical region for HTR2C to participate in the regulation of receiving feather pecking behavior.

A genome-wide association study in a large F2-cross of laying hens reveals novel genomic regions associated with feather pecking and aggressive pecking behavior

Background

Feather pecking and aggressive pecking in laying hens are serious economic and welfare issues. In spite of extensive research on feather pecking during the last decades, the motivation for this behavior is still not clear. A small to moderate heritability has frequently been reported for these traits. Recently, we identified several single-nucleotide polymorphisms (SNPs) associated with feather pecking by mapping selection signatures in two divergent feather pecking lines. Here, we performed a genome-wide association analysis (GWAS) for feather pecking and aggressive pecking behavior, then combined the results with those from the recent selection signature experiment, and linked them to those obtained from a differential gene expression study.

Methods

A large F2 cross of 960 F2 hens was generated using the divergent lines as founders. Hens were phenotyped for feather pecks delivered (FPD), aggressive pecks delivered (APD), and aggressive pecks received (APR). Individuals were genotyped with the Illumina 60K chicken Infinium iSelect chip. After data filtering, 29,376 SNPs remained for analyses. Single-marker GWAS was performed using a Poisson model. The results were combined with those from the selection signature experiment using Fisher’s combined probability test.

Results

Numerous significant SNPs were identified for all traits but with low false discovery rates. Nearly all significant SNPs were located in clusters that spanned a maximum of 3 Mb and included at least two significant SNPs. For FPD, four clusters were identified, which increased to 13 based on the meta-analysis (FPD_meta). Seven clusters were identified for APD and three for APR. Eight genes (of the 750 investigated genes located in the FPD_meta clusters) were significantly differentially-expressed in the brain of hens from both lines. One gene, SLC12A9, and the positional candidate gene for APD, GNG2, may be linked to the monomanine signaling pathway, which is involved in feather pecking and aggressive behavior.

Conclusions

Combining the results from the GWAS with those of the selection signature experiment substantially increased the statistical power. The behavioral traits were controlled by many genes with small effects and no single SNP had effects large enough to justify its use in marker-assisted selection.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-017-0287-4) contains supplementary material, which is available to authorized users.

Omnivores Going Astray: A Review and New Synthesis of Abnormal Behavior in Pigs and Laying Hens

Pigs and poultry are by far the most omnivorous of the domesticated farm animals and it is in their nature to be highly explorative. In the barren production environments, this motivation to explore can be expressed as abnormal oral manipulation directed toward pen mates. Tail biting (TB) in pigs and feather pecking (FP) in laying hens are examples of unwanted behaviors that are detrimental to the welfare of the animals. The aim of this review is to draw these two seemingly similar abnormalities together in a common framework, in order to seek underlying mechanisms and principles. Both TB and FP are affected by the physical and social environment, but not all individuals in a group express these behaviors and individual genetic and neurobiological characteristics play an important role. By synthesizing what is known about environmental and individual influences, we suggest a novel possible mechanism, common for pigs and poultry, involving the brain-gut-microbiota axis.

Genetic parameters and signatures of selection in two divergent laying hen lines selected for feather pecking behaviour

Background

Feather pecking (FP) in laying hens is a well-known and multi-factorial behaviour with a genetic background. In a selection experiment, two lines were developed for 11 generations for high (HFP) and low (LFP) feather pecking, respectively. Starting with the second generation of selection, there was a constant difference in mean number of FP bouts between both lines. We used the data from this experiment to perform a quantitative genetic analysis and to map selection signatures.

Methods

Pedigree and phenotypic data were available for the last six generations of both lines. Univariate quantitative genetic analyses were conducted using mixed linear and generalized mixed linear models assuming a Poisson distribution. Selection signatures were mapped using 33,228 single nucleotide polymorphisms (SNPs) genotyped on 41 HFP and 34 LFP individuals of generation 11. For each SNP, we estimated Wright’s fixation index (F_ST). We tested the null hypothesis that F_ST is driven purely by genetic drift against the alternative hypothesis that it is driven by genetic drift and selection.

Results

The mixed linear model failed to analyze the LFP data because of the large number of 0s in the observation vector. The Poisson model fitted the data well and revealed a small but continuous genetic trend in both lines. Most of the 17 genome-wide significant SNPs were located on chromosomes 3 and 4. Thirteen clusters with at least two significant SNPs within an interval of 3 Mb maximum were identified. Two clusters were mapped on chromosomes 3, 4, 8 and 19. Of the 17 genome-wide significant SNPs, 12 were located within the identified clusters. This indicates a non-random distribution of significant SNPs and points to the presence of selection sweeps.

Conclusions

Data on FP should be analysed using generalised linear mixed models assuming a Poisson distribution, especially if the number of FP bouts is small and the distribution is heavily peaked at 0. The F_ST-based approach was suitable to map selection signatures that need to be confirmed by linkage or association mapping.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0154-0) contains supplementary material, which is available to authorized users.

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.