Genetical Genomics of Tonic Immobility in the Chicken

Pharmacological validation of an attention bias test for conventional broiler chickens

Fear and anxiety are considered concerns for animal welfare as they are associated with negative affective states. This study aimed to pharmacologically validate an attention bias test (ABT) for broiler chickens (Gallus gallus domesticus) as a cognitive bias test to determine anxiety. Two-hundred-and-four male Ross 708 broiler chickens were arbitrarily allocated to either the anxiogenic or control treatment at 25 days of age (n = 102/treatment). Birds from the anxiogenic group were administered with 2.5 mg of β-CCM (β-carboline-3-carboxylic acid-N-methylamide [FG 7142]) per kg of body weight through an intraperitoneal injection (0.1 ml/100 g of body weight). Birds from the control group were administered with 9 mg of a saline solution per kg of body weight. During ABT, birds were tested in groups of three (n = 34 groups of three birds/treatment) with commercial feed and mealworms as positive stimuli and a conspecific alarm call as a negative stimulus. Control birds were 45 s faster to begin feeding than anxiogenic birds. Birds from the control group vocalized 40 s later and stepped 57 s later than birds from the anxiogenic group. The occurrence of vigilance behaviors did not differ between treatments. This study was successful in pharmacologically validating an attention bias test for fast-growing broiler chickens, testing three birds simultaneously. Our findings showed that latencies to begin feeding, first vocalization, and first step were valid measures to quantify anxiety.

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.

Intermittent light program impacts on reproductive performance, health and welfare of breeding hens

The lighting regime significantly impacts poultry production, reproductive performance, health and welfare. This study aimed to test the effect of the intermittent light (IL) regime on reproductive organs and hormones, semen quality, and behavioral performance. Thus, 270 Rhode Island Red hens aged 20 weeks were distributed among three groups of six replicates and 15 birds each, housed in floor pens. The first group was used as a control (C) and was exposed to constant light for 16 h d- 1 , while birds in other groups were exposed to IL for 20 min h- 1 (T20) and 40 min h- 1 (T40) during the 16 h light period. The outcomes were that follicle number was higher for T20 compared to T40 but not the controls, while T40 is different from T20 but not the controls. The same is true for testosterone. The sperm concentration is lower for T40 compared to the controls, with no difference between T20 and the controls. Body temperature was not different among groups. Conversely, differences were not noticed for leg alterations; plumage conditions; and relative ovary, oviduct, and/or testes weight and hatchability. Thus, the IL T20 program should be further investigated as a lighting regimen for managing Rhode Island Red laying hens for stimulating follicle number and testosterone without negatively impacting the physiological response and health traits. From a practical point of view, the IL schedule of 20 min h- 1 during 20-36 weeks of age can be economically viable due to saving 66 % of the light cost.

Increased duration of laser environmental enrichment increased broiler physical activity and pen-wide movement without altering tibia measurements

Inactivity and leg disorders negatively impact broiler welfare. Enrichment designed to increase barn complexity may encourage physical exercise. The study aim was to implement a second-generation laser enrichment device, previously shown to increase broiler activity, for extended periods of time and to measure behavior and tibia quality. A total of 1,360 Ross 708 broilers in 40 pens of 34 were assigned to laser enrichment or control (no laser enrichment) for 49 d. Seventy focal birds were randomly selected on d 0 for individual behavior analysis. Laser-enriched birds were exposed to 6-min laser periods 4 times daily. A 3-min novel object test was performed on all pens and tonic immobility was induced on 1 bird/pen on wk 1 and 6. Focal bird time budget and walking distance and pen-wide laser-following behavior and movement were obtained during laser periods d 0 to 8 and 1 d/wk through wk 7. Right tibias were collected from focal birds on d 49 for dual energy x-ray absorptiometry and bone breaking analysis. Time spent active during laser periods was increased on d 3, 6, and 8 and wk 2 to 3 in laser-enriched vs. control focal birds (P = 0.04). Time at the feeder was increased in laser-enriched focal birds on d 0, 3 to 4, and 8 and wk 2 and 4 (P < 0.01). Distance walked during laser periods was increased in laser-enriched focal birds on d 1, 3 to 5, 8, and wk 2 compared to the control (P < 0.01). Pen-wide movement was increased on d 0, 2, 4 to 8, and wk 1 to 5 and 7 in laser-enriched vs. control birds (P < 0.01). More laser-enriched broilers were within 25 cm of the novel object at 1 min 30 s than the control (P = 0.03), and latency to approach the novel object was reduced in both treatments at wk 6 compared to wk 1 (P < 0.01). Tonic immobility duration was increased by 123 s on wk 6 compared to wk 1, regardless of treatment (P < 0.01). Daily laser enrichment for extended periods increased bird activity without inducing fearfulness or altering tibia measures.

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

Background

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

Methods

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

Results

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

Conclusions

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

Identification of candidate genes responsible for innate fear behavior in the chicken

Identifying the genes responsible for quantitative traits remains a major challenge. We previously found a major QTL on chromosome 4 affecting several innate fear behavioral traits obtained by an open-field test in an F2 population between White Leghorn and Nagoya breeds of chickens (Gallus gallus). Here, an integrated approach of transcriptome, haplotype frequency, and association analyses was used to identify candidate genes for the QTL in phenotypically extreme individuals selected from the same segregating F2 population as that used in the initial QTL analysis. QTL mapping for the first principal component, which summarizes the variances of all affected behavioral traits in the F2 population, revealed the behavioral QTL located at 14-35 Mb on chromosome 4 with 333 genes. After RNA-seq analysis using two pooled RNAs from extreme F2 individuals, real-time qPCR analysis in the two parental breeds and their F1 individuals greatly reduced the number of candidate genes in the QTL interval from 333 to 16 genes. Haplotype frequency analysis in the two extreme F2 groups further reduced the number of candidate genes from 16 to 11. After comparing gene expression in the two extreme groups, a conditional correlation analysis of diplotypes between gene expression and phenotype of extreme individuals revealed that NPY5R and LOC101749214 genes were strong candidate genes for innate fear behavior. This study illustrates how the integrated approach can identify candidate genes more rapidly than fine mapping of the initial QTL interval and provides new information for studying the genetic basis of innate fear behavior in chickens.

Genomic and gene expression associations to morphology of a sexual ornament in the chicken

How sexual selection affects the genome ultimately relies on the strength and type of selection, and the genetic architecture of the involved traits. While associating genotype with phenotype often utilizes standard trait morphology, trait representations in morphospace using geometric morphometric approaches receive less focus in this regard. Here, we identify genetic associations to a sexual ornament, the comb, in the chicken system (Gallus gallus). Our approach combined genome-wide genotype and gene expression data (>30k genes) with different aspects of comb morphology in an advanced intercross line (F8) generated by crossing a wild-type Red Junglefowl with a domestic breed of chicken (White Leghorn). In total, 10 quantitative trait loci were found associated to various aspects of comb shape and size, while 1,184 expression QTL were found associated to gene expression patterns, among which 98 had overlapping confidence intervals with those of quantitative trait loci. Our results highlight both known genomic regions confirming previous records of a large effect quantitative trait loci associated to comb size, and novel quantitative trait loci associated to comb shape. Genes were considered candidates affecting comb morphology if they were found within both confidence intervals of the underlying quantitative trait loci and eQTL. Overlaps between quantitative trait loci and genome-wide selective sweeps identified in a previous study revealed that only loci associated to comb size may be experiencing on-going selection under domestication.

Effects of Housing System on Anxiety, Chronic Stress, Fear, and Immune Function in Bovan Brown Laying Hens

The scientific community needs objective measures to appropriately assess animal welfare. The study objective was to assess the impact of housing system on novel physiological and behavioral measurements of animal welfare for laying hens, including secretory and plasma Immunoglobulin (IgA; immune function), feather corticosterone (chronic stress), and attention bias testing (ABT; anxiety), in addition to the well-validated tonic immobility test (TI; fearfulness). To test this, 184 Bovan brown hens were housed in 28 conventional cages (3 birds/cage) and 4 enriched pens (25 birds/pen). Feces, blood, and feathers were collected 4 times between week 22 and 43 to quantify secretory and plasma IgA and feather corticosterone concentrations. TI tests and ABT were performed once. Hens that were from cages tended to show longer TI, had increased feather corticosterone, and decreased secretory IgA at 22 weeks of age. The caged hens fed quicker, and more hens fed during the ABT compared to the penned hens. Hens that were in conventional cages showed somewhat poorer welfare outcomes than the hens in enriched pens, as indicated by increased chronic stress, decreased immune function at 22 weeks of age but no other ages, somewhat increased fear, but reduced anxiety. Overall, these novel markers show some appropriate contrast between housing treatments and may be useful in an animal welfare assessment context for laying hens. More research is needed to confirm these findings.

Myeloperoxidase expression in diencephalon is potentially associated with fear‐related behavior in chicks of laying hen

Preventing feather pecking (FP) in adult laying hens is important for the welfare of intensively poultry farming. Fear-related behavior in growing female layer chicks may predict FP in adult hens. In this study, in two representative laying breeds (White Leghorn [WL] and Rhode Island Red [RIR]) that have different FP frequencies, we identified a candidate gene associated with fear-related behavior in chicks and FP in adult hens. In the tonic immobility test and open-field test, the behavioral activity was lower in WL chicks than in RIR chicks (P < 0.01), suggesting that WL chicks were more fearful than RIR chicks. Based on previous studies, 51 genes that have been found to be differentially expressed in the brain between high- and low-FP populations were chosen, and their expression levels were screened in the chick diencephalon. This analysis revealed that myeloperoxidase (MPO) gene expression level was higher in WL chicks than that in RIR chicks (P < 0.05). Furthermore, STRING analysis predicted the gene network including MPO and MPO-related genes and revealed the association of these genes with fear-related behavior. These results suggest that MPO is potentially associated with fear-related behavior in growing female layer chicks and FP in adult hens.

Effect of Environmental Complexity and Stocking Density on Fear and Anxiety in Broiler Chickens

Barren housing and high stocking densities may contribute to negative affective states in broiler chickens, reducing their welfare. We investigated the effects of environmental complexity and stocking density on broilers' attention bias (measure of anxiety) and tonic immobility (measure of fear). In Experiment 1, individual birds were tested for attention bias (n = 60) and in Experiment 2, groups of three birds were tested (n = 144). Tonic immobility testing was performed on days 12 and 26 (n = 36) in Experiment 1, and on day 19 (n = 72) in Experiment 2. In Experiment 1, no differences were observed in the attention bias test. In Experiment 2, birds from high-complexity pens began feeding faster and more birds resumed feeding than from low-complexity pens following playback of an alarm call, suggesting that birds housed in the complex environment were less anxious. Furthermore, birds housed in high-density or high-complexity pens had shorter tonic immobility durations on day 12 compared to day 26 in Experiment 1. In Experiment 2, birds from high-density pens had shorter tonic immobility durations than birds housed in low-density pens, which is contrary to expectations. Our results suggest that birds at 3 weeks of age were less fearful under high stocking density conditions than low density conditions. In addition, results indicated that the complex environment improved welfare of broilers through reduced anxiety.

From the Farm to the Lab: How Chicken Embryos Contribute to the Field of Teratology

Congenital anomalies and its causes, particularly, by external factors are the aim of the field called teratology. The external factors studied by teratology are known as teratogens and can be biological or environmental factors for example, chemicals, medications, recreational drugs, environmental pollutants, physical agents (e.g., X-rays and maternal hyperthermia) and maternal metabolic conditions. Proving the teratogenicity of a factor is a difficult task requiring epidemiology studies as well as experimental teratology evidence from the use of animal models, one of which is the chicken embryo. This model in particular has the advantage of being able to follow development live and in vivo, with rapid development hatching around 21 days, is cheap and easy to manipulate and to observe development. All this allows the chicken embryo to be used in drug screening studies, teratogenic evaluation and studies of mechanisms of teratogenicity. The chicken embryo shares morphological, biochemical and genetic similarities with humans as well as mammalian species, making them ideal to ascertain the actions of teratogens, as well as screen drugs to test for their safety. Pre-clinical trials for new drugs are carried out in rodents and rabbits, however, chicken embryos have been used to screen new compounds or analogs of thalidomide as well as to investigate how some drugs can lead to congenital malformations. Indeed, the chicken embryo has proved valuable in understanding how many congenital anomalies, seen in humans, arise following teratogen exposure. The aim of this review is to highlight the role of the chicken embryo as an experimental model for studies in teratology, exploring its use in drug screening studies, phenotypic evaluation and studies of teratogenic mechanisms of action. Here, we discuss many known teratogens, that have been evaluated using the chicken embryo model including some medicines, such as, thalidomide, valproic acid; recreational drugs including alcohol; environmental influences, such as viruses, specifically ZIKV, which is a newly discovered human teratogen. In addition, we discuss how the chicken embryo has provided insight on the mechanisms of teratogenesis of many compounds and also how this impact on drug safety.

The methylation landscape and its role in domestication and gene regulation in the chicken

Domestication is one of the strongest examples of artificial selection and has produced some of the most extreme within-species phenotypic variation known. In the case of the chicken, it has been hypothesized that DNA methylation may play a mechanistic role in the domestication response. By inter-crossing wild-derived red junglefowl with domestic chickens, we mapped quantitative trait loci for hypothalamic methylation (methQTL), gene expression (eQTL) and behaviour. We find large, stable methylation differences, with 6,179 cis and 2,973 trans methQTL identified. Over 46% of the trans effects were genotypically controlled by five loci, mainly associated with increased methylation in the junglefowl genotype. In a third of eQTL, we find that there is a correlation between gene expression and methylation, while statistical causality analysis reveals multiple instances where methylation is driving gene expression, as well as the reverse. We also show that methylation is correlated with some aspects of behavioural variation in the inter-cross. In conclusion, our data suggest a role for methylation in the regulation of gene expression underlying the domesticated phenotype of the chicken.

Intra-Individual Behavioural Variability: A Trait under Genetic Control

When individuals are measured more than once in the same context they do not behave in exactly the same way each time. The degree of predictability differs between individuals, with some individuals showing low levels of variation around their behavioural mean while others show high levels of variation. This intra-individual variability in behaviour has received much less attention than between-individual variability in behaviour, and very little is known about the underlying mechanisms that affect this potentially large but understudied component of behavioural variation. In this study, we combine standardized behavioural tests in a chicken intercross to estimate intra-individual behavioural variability with a large-scale genomics analysis to identify genes affecting intra-individual behavioural variability in an avian population. We used a variety of different anxiety-related behavioural phenotypes for this purpose. Our study shows that intra-individual variability in behaviour has a direct genetic basis that is largely unique compared to the genetic architecture for the standard behavioural measures they are based on (at least in the detected quantitative trait locus). We identify six suggestive candidate genes that may underpin differences in intra-individual behavioural variability, with several of these candidates having previously been linked to behaviour and mental health. These findings demonstrate that intra-individual variability in behaviour appears to be a heritable trait in and of itself on which evolution can act.

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.

The genetic regulation of size variation in the transcriptome of the cerebrum in the chicken and its role in domestication and brain size evolution

Background

Large difference in cerebrum size exist between avian species and populations of the same species and is believed to reflect differences in processing power, i.e. in the speed and efficiency of processing information in this brain region. During domestication chickens developed a larger cerebrum compared to their wild progenitor, the Red jungle fowl. The underlying mechanisms that control cerebrum size and the extent to which genetic regulation is similar across brain regions is not well understood. In this study, we combine measurement of cerebrum size with genome-wide genetical genomics analysis to identify the genetic architecture of the cerebrum, as well as compare the regulation of gene expression in this brain region with gene expression in other regions of the brain (the hypothalamus) and somatic tissue (liver).

Results

We identify one candidate gene that putatively regulates cerebrum size (MTF2) as well as a large number of eQTL that regulate the transcriptome in cerebrum tissue, with the majority of these eQTL being trans-acting. The overall regulation of gene expression variation in the cerebrum was markedly different to the hypothalamus, with relatively few eQTL in common. In comparison, the cerebrum tissue shared more eQTL with a distant tissue (liver) than with a neighboring tissue (hypothalamus).

Conclusion

The candidate gene for cerebrum size (MTF2) has previously been linked to brain development making it a good candidate for further investigation as a regulator of inter-population variation in cerebrum size. The lack of shared eQTL between the two brain regions implies that genetic regulation of gene expression appears to be relatively independent between the two brain regions and suggest that coevolution between these two brain regions might be more functionally driven than developmental. These findings have relevance for current brain size evolution theories.

Tonic Immobility and Open Field Responses in Nagoya, White Leghorn, and White Plymouth Rock Chicks

Innate fear responses to tonic immobility (TI) and open field (OF) were evaluated in newly hatched chicks of three breeds with distinct breed origin and genetic relationships. The breeds studied were Nagoya (NAG), a native Japanese breed; White Leghorn (WL), a representative of layers; and White Plymouth Rock (WPR), a parental breed of common broilers. The TI test revealed that WL was the most sensitive to extensive fear evoked by the TI test among the three breeds, followed in order by WPR, and NAG. In contrast, the OF test revealed that NAG was the most sensitive to mild fear evoked by the OF test, followed in order by WPR, and WL. The different fear responses between NAG and WL were supported by minimal phenotypic correlations between TI and OF traits in each breed. These results demonstrated that NAG and WL breeds exhibit extreme and opposite responses to TI and OF fears.