Chicken genomics: feather-pecking and victim pigmentation

Indian Red Jungle fowl reveals a genetic relationship with South East Asian Red Jungle fowl and Indian native chicken breeds as evidenced through whole mitochondrial genome sequences

Background: Native chickens are dispersed in a wide geographical range and have hereditary assets that are kept by farmers for various purposes. Mitochondrial DNA (mtDNA) is a widely utilized marker in molecular studies because of its quick advancement, matrilineal legacy, and simple molecular structure. Method and Results: We performed NGS sequencing to investigate mitochondrial genomes and to evaluate the hereditary connections, diversity, and measure of gene stream estimation in Indian native chicken breeds and Red Jungle fowl. The chicken breeds were genotyped using the D-loop region and 23 haplotypes were identified. When compared to Indian native breeds, more haplotypes were identified in the NADH dehydrogenase subunits, Cytochrome c oxidase, Cytochrome b, ATP synthase subunit 6, and Ribosomal RNA genes. The phylogenetic examination indicated that the analyzed chicken breeds were divided into six significant clades, namely A, B, C, D, E, and F, of which the F clade indicated the domestication of chicken breeds in India. Additionally, our work affirmed that the Indian Red Jungle Fowl is the origin for both reference Red Jungle Fowl as well as all Indian breeds, which is reflected in the dendrogram as well as network analysis based on the whole mtDNA and D-loop region. Indian Red Jungle Fowl is distributed as an outgroup, suggesting that this ancestry was reciprocally monophyletic. Conclusion: The mtDNA sequences of Indian native chickens provided novel insights into adaptation mechanisms and the significance of important mtDNA variations in understanding the maternal lineages of native birds.

Environmental and Socio-Cultural Factors Impacting the Unique Gene Pool Pattern of Mae Hong-Son Chicken

Understanding the genetic diversity of domestic chicken breeds under the impact of socio-cultural and ecological dynamics is vital for the conservation of natural resources. Mae Hong Son chicken is a local breed of North Thai domestic chicken widely distributed in Mae Hong Son Province, Thailand; however, its genetic characterization, origin, and diversity remain poorly understood. Here, we studied the socio-cultural, environmental, and genetic aspects of the Mae Hong Son chicken breed and investigated its diversity and allelic gene pool. We genotyped 28 microsatellite markers and analyzed mitochondrial D-loop sequencing data to evaluate genetic diversity and assessed spatial habitat suitability using maximum entropy modeling. Sequence diversity analysis revealed a total of 188 genotyped alleles, with overall nucleotide diversity of 0.014 ± 0.007, indicating that the Mae Hong Son chicken population is genetically highly diverse, with 35 (M1-M35) haplotypes clustered into haplogroups A, B, E, and F, mostly in the North ecotype. Allelic gene pool patterns showed a unique DNA fingerprint of the Mae Hong Son chicken, as compared to other breeds and red junglefowl. A genetic introgression of some parts of the gene pool of red junglefowl and other indigenous breeds was identified in the Mae Hong Son chicken, supporting the hypothesis of the origin of the Mae Hong Son chicken. During domestication in the past 200-300 years after the crossing of indigenous chickens and red junglefowl, the Mae Hong Son chicken has adapted to the highland environment and played a significant socio-cultural role in the Northern Thai community. The unique genetic fingerprint of the Mae Hong Son chicken, retaining a high level of genetic variability that includes a dynamic demographic and domestication history, as well as a range of ecological factors, might reshape the adaptation of this breed under selective pressure.

Phenotype alteration causes long-term changes to the social strategies of victimised birds

Phenotype alterations can occur naturally during the life span of the domestic fowl. These alterations increase the risk to become a target of aggression and may cause a severe impact on the welfare of affected birds. We analysed the behavioural consequences of sequential phenotype alterations and their long-term effects within stable social groups of adult birds differing in group size. Phenotypically homogeneous groups, with 100% or 0% marked individuals, and heterogeneous groups, with 70%, 50% or 30% marked birds, were housed at constant density in groups of 10, 20 or 40. We applied sequential phenotype alterations to homogeneous groups (by marking or unmarking birds) and compared their behavioural response to heterogeneous groups considered controls. Results show that aggression was greatly affected by phenotype alteration but, unexpectedly, group size did not play any relevant role modulating social responses. Aggression was directed towards the first altered birds and was significantly higher than in control groups. Long term effects were detected, as victimized individuals failed to engage in aggression at any time and adapted their behaviour to minimize aggressive encounters (e.g. high perch use). Therefore, we provide evidence of long-lasting submissive strategies in stable groups of adult domestic fowl, highlighting the relevance of phenotype alteration on the social dynamics of affected birds. Phenotype alterations could help explain much of the targeted aggression observed in producing flocks which severely affects animal welfare.

Discriminant Canonical Tool for Differential Biometric Characterization of Multivariety Endangered Hen Breeds

Simple Summary

Breed undefinition boosts the risk of irreversible breed loss due to its substitution by dominant breeds. Breed loss results detrimental for the fraction of the genetic pool which is linked to the value of livestock as perfectly adapted elements of domestic ecosystems among other desirable features. In turn, this ensures and maximizes population sustainability. The present study aimed to design a biometric characterization tool in autochthonous avian breeds and their varieties in Andalusia (south of Spain): Utrerana and Sureña breeds. For this, different quantitative and qualitative measurements were collected in 473 females and 135 roosters belonging to these breeds. Even though both genotypes belong to a common original trunk, discriminant canonical analysis (DCA) revealed clear differences between both breeds and within the varieties that they comprise. In particular, certain variables such as ocular ratio and phaneroptic characteristics, which may be intrinsically related to the capacity of the breeds to adapt to the environmental conditions in which they thrive, could allow breeders to develop breeding programs focused on the enhancement productive potential of individuals.

Abstract

This study aimed to develop a tool to perform the morphological characterization of Sureña and Utrerana breeds, two endangered autochthonous breeds ascribed to the Mediterranean trunk of Spanish autochthonous hens and their varieties (n = 608; 473 females and 135 males). Kruskal–Wallis H test reported sex dimorphism pieces of evidence (p < 0.05 at least). Multicollinearity analysis reported (variance inflation factor (VIF) >5 variables were discarded) white nails, ocular ratio, and back length (Wilks’ lambda values of 0.191, 0.357, and 0.429, respectively) to have the highest discriminant power in female morphological characterization. For males, ocular ratio and black/corneous and white beak colors (Wilks’ lambda values of 0.180, 0.210, and 0.349, respectively) displayed the greatest discriminant potential. The first two functions explained around 90% intergroup variability. A stepwise discriminant canonical analysis (DCA) was used to determine genotype clustering patterns. Interbreed and varieties proximity was evaluated through Mahalanobis distances. Despite the adaptability capacity to alternative production systems ascribed to both avian breeds, Sureña and Utrerana morphologically differ. Breed dimorphism may evidence differential adaptability mechanisms linked to their aptitude (dual purpose/egg production). The present tool may serve as a model for the first stages of breed protection to be applicable in other endangered avian breeds worldwide.

Genetic basis of chicken plumage color in artificial population of complex epistasis

Chicken plumage color, the genetic basis of which is often affected by epistasis, has long interested scientists. In the current study, a population of complex epistasis was constructed by crossing dominant White Leghorn chickens with recessive white feather chickens. Through a genome-wide association study, we identified single nucleotide polymorphisms and genes significantly associated with white and colored plumage in hens at different developmental stages. Interestingly, white plumage in adulthood was associated with the recessive white feather gene (TYR), whereas white feathers at birth stage were associated with the dominant white feather gene (PMEL), indicating age-related roles for these genes. TYR was shown to exert an epistatic effect on PMEL in adult hens. Additionally, TYR had an epistatic effect on barred plumage, while barred plumage had an epistatic effect on black plumage. TYR had no epistatic effect on the yellow plumage. We confirmed that the barred plumage gene is CDKN2A, as reported in previous studies. Golgb1 and REEP3, which play important roles in the Golgi network and affect the formation of feather pigments, are important candidate genes for yellow plumage. The candidate genes for black plumage are CAMKK1 and IFT22. Further research is warranted to elucidate the molecular mechanisms underlying these traits.

Associations between neck plumage and beak darkness, as well as comb size measurements and scores with ranging frequency of Sasso and Green-legged Partridge chickens

Despite the intensive genetic selection in modern poultry, variability of domestic fowl phenotypes has remained, especially in breeds adapted to local conditions. The relevance of this variability to the chicken outdoor ranging activities remains unknown. The aim of this study was to investigate if external features were associated with the ranging frequency of the 48 female chickens from each of the 2 breeds: Sasso and Green-legged Partridge. In each of 6 single-breed pens, 8 hens and 2 roosters were housed under conditions of EU requirements for organic meat chicken production, including free access to an outdoor range, from wk 5 to 10 of age. The birds were video-recorded during the experiment to obtain frequencies of individual birds' use of the ranges. Comb size (length and height) was measured using a digital ruler, while the sizes of the dark area of neck plumage and beak were processed and analyzed using ImageJ software. The same traits were scored using direct visual assessment by a trained observer on a scale of 1-3. In addition, the eye color of the bird was recorded. Statistical analysis was conducted independently for each breed using regression models, ANOVAs and Spearman correlations. Significant positive associations between neck plumage (P < 0.01), beak darkness (P = 0.03) measurements, comb length (P < 0.01) and comb height (P < 0.01) and frequency of range use were identified for Sasso. Sasso hens scored with darkest neck plumage (P = 0.03) and biggest comb size (P = 0.04) ranged the most, while their external features were significantly and positively correlated between each other, except beak darkness and comb length. No significant associations between ranging and external features were found in Green-legged Partridge birds, except that their comb height was significantly and positively correlated with neck plumage and beak darkness (r = 0.39 and 0.33, respectively). In some genetic strains, better understanding of the associations between chickens’ external features with ranging behavior could contribute to improve selection programs and bird welfare, assuring production of breeding stock suitable for outdoor conditions.

Pecking Behavior in Conventional Layer Hybrids and Dual-Purpose Hens Throughout the Laying Period

To avoid the killing of surplus male layer chickens, dual-purpose hybrids are suggested as an alternative approach. These strains may offer additional advantages compared to conventional laying hens, for instance, a lower tendency to develop injurious pecking behavior. The aim of this study was to assess the behavior, with focus on pecking behavior, of conventional layers (Lohmann Brown plus, LB+) and dual-purpose hens (Lohmann Dual, LD). About 1,845 hens per strain with intact beaks were housed in four stable compartments in aviary systems. Video-based scan sampling of general behaviors and continuous observations of pecking behavior were carried out between 25 and 69 weeks of life. With the exception of "dustbathing" and "scratching," hybrid × time during the laying period affected all of the observed general behaviors [F _{(2, 89)} = 3.92-10.81, P < 0.001-0.05]. With increasing age, the LB+ hens performed more general pecking, more locomotion and less comfort and sitting behavior. General pecking and comfort behavior did not change over time in the LD hens, whereas inactive behaviors increased with age. During continuous observations, a significant hybrid x period interaction was found for all forms of pecking behavior [F _{(2, 89)} = 4.55-14.80, P < 0.001-0.05]. The LB+ hens showed particularly more severe feather pecking (SFP), which increased with age. In contrast, SFP remained exceptionally low in the LD hens throughout production. Therefore, dual-purpose hybrids should be considered as an alternative to both avoid the killing of surplus male chickens and the development of SFP in laying hen production.

Current methods and techniques of beak trimming laying hens, welfare issues and alternative approaches

Beak trimming is used in the egg industry to prevent mortality from cannibalism and minimise injurious pecking, vent pecking, aggressive pecking at the head and all forms of feather pecking, although the practice does not completely reduce the damage. There are alternatives to beak trimming, but they have not been reliable in preventing injurious pecking. However, beak trimming should not be used without providing birds enriched indoor and outdoor environments. Even when birds are beak trimmed, providing enriched facilities is recommended. The two main methods of beak trimming are hot blade (HB) and infrared beak treatment (IRBT). HB trimming removes the beak tips and cauterises the beak stump. The IRBT method uses heat from an infrared lamp to treat the outer beak and the underlying tissue. Initially, the tips of the beak remain intact and then soften and wear as the bird uses its beak. In contrast, the HB method results in an open wound that takes 3 weeks to heal. Two major welfare issues arise from beak trimming. The first is loss of sensory input because of removal of or heat treatment of sensory receptors in the beak. The second issue is the potential for acute and chronic pain from severing or heat treatment of nerves. HB trimming initially results in acute pain but there is limited evidence for beak sensitivity in IRBT birds. The development of neuromas in the beak have been implicated as a cause of chronic pain after HB trimming. When birds are HB trimmed (one-half of upper beak; one-third of lower) in the first 10 days of life, neuromas will develop, but they will resolve, compared with birds trimmed at older ages. However, neuromas will not resolve in 10-day old birds if more than one-half of the beak is HB trimmed. While HB trimming is performed according to accreditation standards by removal of one-half the upper beak and one-third of the lower beak is considered excessive, it prevents beak regrowth and the need to subject birds to re-trimming and a second bout of acute pain from the beak wound. Current levels of IRBT to treat half of the beak using the vendors quality-assurance protocol have been implemented worldwide to ensure that neuroma formation is prevented; however, if severe levels of IRBT are used, acute pain and subsequent neuromas may persist. The main impact of beak trimming is how the bird uses its beak when it eats, drinks and pecks at other birds and the environment. Reduced feed intake after HB trimming indicates pain associated with pecking or difficulty in eating. HB-trimmed birds initially show an increase in listlessness and guarding behaviours and increased inactivity, which indicates pain. IRBT and HB-trimmed birds have fewer aggressive pecks at the head, and there is a reduction in severe feather pecking and better feather scores, which results in a large reduction in mortality. Depending on the severity of IRBT and HB trimming, the advantage of using IRBT is improved welfare.

Breeding history and candidate genes responsible for black skin of Xichuan black-bone chicken

Background

Domesticated chickens have a wide variety of phenotypes, in contrast with their wild progenitors. Unlike other chicken breeds, Xichuan black-bone chickens have blue-shelled eggs, and black meat, beaks, skin, bones, and legs. The breeding history and the economically important traits of this breed have not yet been explored at the genomic level. We therefore used whole genome resequencing to analyze the breeding history of the Xichuan black-bone chickens and to identify genes responsible for its unique phenotype.

Results

Principal component and population structure analysis showed that Xichuan black-bone chicken is in a distinct clade apart from eight other breeds. Linkage disequilibrium analysis showed that the selection intensity of Xichuan black-bone chickens is higher than for other chicken breeds. The estimated time of divergence between the Xichuan black-bone chickens and other breeds is 2.89 ka years ago. Fst analysis identified a selective sweep that contains genes related to melanogenesis. This region is probably associated with the black skin of the Xichuan black-bone chickens and may be the product of long-term artificial selection. A combined analysis of genomic and transcriptomic data suggests that the candidate gene related to the black-bone trait, EDN3, might interact with the upstream ncRNA LOC101747896 to generate black skin color during melanogenesis.

Conclusions

These findings help explain the unique genetic and phenotypic characteristics of Xichuan black-bone chickens, and provide basic research data for studying melanin deposition in animals.

The Dual-Purpose Hen as a Chance: Avoiding Injurious Pecking in Modern Laying Hen Husbandry

Simple Summary

Dual purpose chickens are one solution to the killing of male day-old chickens from the layer strains. However, modern laying hen husbandry faces further challenges, for instance, the frequent occurrence of injurious pecking. This behavior is seen as a sign of stress in the offending birds, it causes pain and damage in the victims, and thus impairs the health and welfare of the whole flock. In this study, the behavior of conventional laying hens and dual-purpose hens was evaluated comparatively by assessing the status of their feathers and skin over time. All hens were housed and managed under semi-commercial conditions. Severe feather loss and skin lesions due to injurious pecking only occurred in the conventional layer flocks. Therefore, keeping dual-purpose hens may also be an alternative approach to overcome damaging behaviors in laying hen husbandry.

Abstract

Dual-purpose strains, with hens housed for egg laying and roosters kept for meat production are one alternative to the killing of male day-old chickens. However, dual-purpose hens seem to have additional advantages compared to conventional layers, for instance, a lower tendency to develop behavioral disorders, such as feather pecking and cannibalism. In the present study, three batches of about 1850 conventional layers (Lohmann Brown plus, LB+) and 1850 dual-purpose hens (Lohmann Dual, LD) each, all of them with untrimmed beaks, were observed during production (20–71 (56) weeks of life) in a semi-commercial aviary system. The aim was to investigate whether the hybrid and batch affected the occurrence of injurious pecking, and to identify a detailed time course of the damage caused by this behavior. Therefore, the hens’ plumage and skin condition were assessed as an indicator by means of a visual scoring method. The LB+ hens had higher production performances and higher mortality rates compared to the LD hens. Plumage loss in the LB+ flocks started at 23 to 25 weeks of age, and deteriorated continuously. The LD hens showed only moderate feather loss on the head/neck region, which started at 34 to 41 weeks and remained almost constant until the end of the observations. Compared to feather loss, injuries occurred in the LB+ hens with a delay of several weeks, with a maximum of 8% to 12% of hens affected. In contrast, skin injuries were observed only sporadically in single LD hens. In all batches, hybrid had an effect on the occurrence of feather loss (p < 0.05). Within the LB+ strain, the proportions of hens affected by plumage loss and injuries differed among batches (p < 0.05), whereas this was not the case in the LD flocks. Thus, severe feather pecking and cannibalism seemed to occur in the conventional layer hybrids but not in the dual-purpose hens, though both genetic strains were raised and managed under the same semi-commercial conditions. Therefore, keeping dual-purpose hens should also be considered as an alternative approach to avoid injurious pecking in laying hen husbandry.

Molecular-genetic bases of plumage coloring in chicken

The color of plumage in birds is an important feature, often determining descent to a particular species or breed. It serves as a key factor in the interaction of birds with each other due to their well-developed visual perception of the surrounding world. In poultry including chickens, the color of the plumage can be treated as a genetic marker, useful for identifying breeds, populations and breeding groups with their specific traits. The origin of diverse color plumage is the result of two interrelated physical processes, chemical and optical, due to which pigment and structural colors in the color are formed. The pigment melanin, which is presented in two forms, eumelanin and pheomelanin, is widely spread in birds. The basis for the formation of melanin is the aromatic amino acid tyrosine. The process of melano-genesis involves many loci, part of the complex expression of plumage color genes. In birds, the solid black color locus encodes the melanocortin 1 receptor (MC1R), mutations in which lead to a change in receptor activation and form different variants of the E locus. Using the GWAS analysis, possible genes affecting the formation of color in chickens were detected. The biosynthesis and types of melanin are affected by the activity of the enzyme tyrosine, and mutations in the tyrosinase gene (TYR) cause albinism in different species. The formation mechanism of brown, silver, gold, lavender and a number of other shades is determined by the influence on the work of the MC1R genes and TYR specific modifier genes. Thus, locus I currently associated with the PMEL17 gene inhibits the expression of eumelanin, and the MLPH gene affects tyrosinase function. Research on the mechanisms of formation of the secondary coloring of plumage in chickens is being actively conducted nowadays. The formation of a marble feather pattern is associated with the mutation of the endothelin B2 receptor (EDNRB2), in the coding part of the gene of which a polymorphism is found associated with the mo locus. The molecular base that causes the feather banding (locus B and autosomal recessive banding) is identified. Today, only some genes that determine the color of the plumage of chickens are studied and described. Different genes can produce similar plumage patterns, and different phenotypes can be determined by the polymorphism of a single gene. Using molecular methods, you can more accurately identify these differences. This overview shows the nature of melanin coloration in birds using the example of chickens of various breeds and also attempts to systematize knowledge about the molecular-genetic mechanisms of the appearance of various types of coloration.

Feather colour affects the aggressive behaviour of chickens with the same genotype on the dominant white (I) locus

Aggression in chickens is a serious economic and animal welfare issue in poultry farming. Pigmentation traits have been documented to be associated with animal behaviour. Chicken pecking behaviour has been found to be related to feather colour, with premelanosome protein 17 (PMEL17) being one of the candidate genes. In the present study, we performed a genotypic and phenotypic association analysis between chicken plumage colour (red and white) and aggressive behaviour in an F1 hybrid group generated by crossing the autosomal dominant white-feathered breed White Leghorn (WL) and the red-feathered breed Rhode Island Red (RIR). In genetic theory, all the progeny should have white feathers because WL is homozygous autosomal dominant for white feathers. However, we found a few red-feathered female chickens. We compared the aggressiveness between the red and white females to determine whether the feather colour alone affected the behaviour, given that the genetic background should be the same except for feather colour. The aggressiveness was recorded 5 days after sexual maturity at 26 weeks. Generally, white plumage hens showed significantly higher aggressiveness compared to the red ones in chasing, attacking, pecking, and threatening behaviour traits. We assessed three candidate feather colour genes—PMEL17, solute carrier family 45 member 2 (SLC45A2), and SRY-box 10 (SOX10)—to determine the genetic basis for the red and white feather colour in our hybrid population; there was no association between the three loci and feather colour. The distinct behavioural findings observed herein provide clues to the mechanisms underlying the association between phenotype and behaviour in chickens. We suggest that mixing red and white chickens together might reduce the occurrence of aggressive behaviours.

An Investigation of Associations Between Management and Feather Damage in Canadian Laying Hens Housed in Furnished Cages

Feather pecking is a continuous welfare challenge in the housing of egg-laying hens. Canada is currently making the transition from conventional cages to alternative housing systems. However, feather damage (FD) among laying hens due to feather pecking remains a welfare concern. An explorative approach was taken to assess bird, housing, and management associations with FD in Canadian laying hens housed in alternative systems. A questionnaire focused on housing and management practices was administered to 122 laying farms across Canada in autumn of 2017 (response rate of 52.5%), yielding information on a subset of 26 flocks housed in furnished cages. Additionally, a three-point feather cover scoring system was developed to estimate the prevalence of FD. Farmers assessed FD by sampling 50 birds per flock. Linear regression modeling was applied to explain FD as a function of 6 variables (out of an available 54). Of the 6 modeled variables, "increased age", "brown feather colour", "midnight feeding", and "no scratch area" were associated with higher levels of FD at farm level (R² = 0.77). The results indicated that FD resulting from feather pecking is a multifactorial problem, and supported existing evidence that FD increases as birds age. These results also suggested that "feather colour", "midnight feeding", and "access to (or lack of) a scratch area or additional substrate" play a role in FD prevalence in furnished cages.

Effects of commercial hatchery processing on short- and long-term stress responses in laying hens

In commercial egg production, chicks are exposed to a potentially stressful procedure during their first day of life. Here, we investigated how this procedure affects the chickens in a short- as well as long-term perspective by conducting two behaviour tests and measuring corticosterone (CORT) and sex hormone levels at different time points. These results were compared with a group of control chickens from the same hatchery and incubator that did not go through the commercial hatchery routine. Chickens were continuously weighed, egg production data was collected and feather scoring was performed. We found that chicks have a significant increase in CORT during the hatchery process, which implies they are exposed to stress. During first weeks of life, these chicks were more fearful, had a higher CORT reactivity during restraint and weighed more than control chicks. Later in life, hatchery treated chickens had more feather damages and injuries on combs and wattles, a faster onset of egg laying and higher levels of estradiol. We conclude that processing at the commercial hatchery was a stressful event with short- and long-term effects on behaviour and stress reactivity, and potentially also positive effects on production. The results are relevant for a large number of individuals, since the chicken is by far the globally most common farm animal.

Whole-Genome Resequencing of Red Junglefowl and Indigenous Village Chicken Reveal New Insights on the Genome Dynamics of the Species

The red junglefowl Gallus gallus is the main progenitor of domestic chicken, the commonest livestock species, outnumbering humans by an approximate ratio of six to one. The genetic control for production traits have been well studied in commercial chicken, but the selection pressures underlying unique adaptation and production to local environments remain largely unknown in indigenous village chicken. Likewise, the genome regions under positive selection in the wild red junglefowl remain untapped. Here, using the pool heterozygosity approach, we analyzed indigenous village chicken populations from Ethiopia, Saudi Arabia, and Sri Lanka, alongside six red junglefowl, for signatures of positive selection across the autosomes. Two red junglefowl candidate selected regions were shared with all domestic chicken populations. Four candidates sweep regions, unique to and shared among all indigenous domestic chicken, were detected. Only one region includes annotated genes (TSHR and GTF2A1). Candidate regions that were unique to each domestic chicken population with functions relating to adaptation to temperature gradient, production, reproduction and immunity were identified. Our results provide new insights on the consequence of the selection pressures that followed domestication on the genome landscape of the domestic village chicken.

Feralisation targets different genomic loci to domestication in the chicken

Feralisation occurs when a domestic population recolonizes the wild, escaping its previous restricted environment, and has been considered as the reverse of domestication. We have previously shown that Kauai Island's feral chickens are a highly variable and admixed population. Here we map selective sweeps in feral Kauai chickens using whole-genome sequencing. The detected sweeps were mostly unique to feralisation and distinct to those selected for during domestication. To ascribe potential phenotypic functions to these genes we utilize a laboratory-controlled equivalent to the Kauai population-an advanced intercross between Red Junglefowl and domestic layer birds that has been used previously for both QTL and expression QTL studies. Certain sweep genes exhibit significant correlations with comb mass, maternal brooding behaviour and fecundity. Our analyses indicate that adaptations to feral and domestic environments involve different genomic regions and feral chickens show some evidence of adaptation at genes associated with sexual selection and reproduction.

PMEL Amyloid Fibril Formation: The Bright Steps of Pigmentation

In pigment cells, melanin synthesis takes place in specialized organelles, called melanosomes. The biogenesis and maturation of melanosomes is initiated by an unpigmented step that takes place prior to the initiation of melanin synthesis and leads to the formation of luminal fibrils deriving from the pigment cell-specific pre-melanosomal protein (PMEL). In the lumen of melanosomes, PMEL fibrils optimize sequestration and condensation of the pigment melanin. Interestingly, PMEL fibrils have been described to adopt a typical amyloid-like structure. In contrast to pathological amyloids often associated with neurodegenerative diseases, PMEL fibrils represent an emergent category of physiological amyloids due to their beneficial cellular functions. The formation of PMEL fibrils within melanosomes is tightly regulated by diverse mechanisms, such as PMEL traffic, cleavage and sorting. These mechanisms revealed increasing analogies between the formation of physiological PMEL fibrils and pathological amyloid fibrils. In this review we summarize the known mechanisms of PMEL fibrillation and discuss how the recent understanding of physiological PMEL amyloid formation may help to shed light on processes involved in pathological amyloid formation.

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.

Bird Integumentary Melanins: Biosynthesis, Forms, Function and Evolution

Melanins are the ubiquitous pigments distributed in nature. They are one of the main pigments responsible for colors in living cells. Birds are among the most diverse animals regarding melanin-based coloration, especially in the plumage, although they also pigment bare parts of the integument. This review is devoted to the main characteristics of bird melanins, including updated views of the formation and nature of melanin granules, whose interest has been raised in the last years for inferring the color of extinct birds and non-avian theropod dinosaurs using resistant fossil feathers. The molecular structure of the two main types of melanin, eumelanin and pheomelanin, and the environmental and genetic factors that regulate avian melanogenesis are also presented, establishing the main relationship between them. Finally, the special functions of melanin in bird feathers are also discussed, emphasizing the aspects more closely related to these animals, such as honest signaling, and the factors that may drive the evolution of pheomelanin and pheomelanin-based color traits, an issue for which birds have been pioneer study models.

Domestic animals as models for biomedical research

Domestic animals are unique models for biomedical research due to their long history (thousands of years) of strong phenotypic selection. This process has enriched for novel mutations that have contributed to phenotype evolution in domestic animals. The characterization of such mutations provides insights in gene function and biological mechanisms. This review summarizes genetic dissection of about 50 genetic variants affecting pigmentation, behaviour, metabolic regulation, and the pattern of locomotion. The variants are controlled by mutations in about 30 different genes, and for 10 of these our group was the first to report an association between the gene and a phenotype. Almost half of the reported mutations occur in non-coding sequences, suggesting that this is the most common type of polymorphism underlying phenotypic variation since this is a biased list where the proportion of coding mutations are inflated as they are easier to find. The review documents that structural changes (duplications, deletions, and inversions) have contributed significantly to the evolution of phenotypic diversity in domestic animals. Finally, we describe five examples of evolution of alleles, which means that alleles have evolved by the accumulation of several consecutive mutations affecting the function of the same gene.

The Genetic Architecture of Domestication in Animals

Domestication has been essential to the progress of human civilization, and the process itself has fascinated biologists for hundreds of years. Domestication has led to a series of remarkable changes in a variety of plants and animals, in what is termed the “domestication phenotype.” In domesticated animals, this general phenotype typically consists of similar changes in tameness, behavior, size/morphology, color, brain composition, and adrenal gland size. This domestication phenotype is seen in a range of different animals. However, the genetic basis of these associated changes is still puzzling. The genes for these different traits tend to be grouped together in clusters in the genome, though it is still not clear whether these clusters represent pleiotropic effects, or are in fact linked clusters. This review focuses on what is currently known about the genetic architecture of domesticated animal species, if genes of large effect (often referred to as major genes) are prevalent in driving the domestication phenotype, and whether pleiotropy can explain the loci underpinning these diverse traits being colocated.

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.

Behavior genetics and the domestication of animals

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

Individual Consistency of Feather Pecking Behavior in Laying Hens: Once a Feather Pecker Always a Feather Pecker?

The pecking behavior [severe feather, gentle feather, and aggressive pecks (AP)] of individual White Shaver non-cage laying hens (n = 300) was examined at 21, 24, 27, 32, and 37 weeks. Hens were housed in 30 groups of 10 hens each and on 3 cm litter with access to a feeder, perch, and two nest boxes. The number of severe feather pecks given (SFPG) and received (SFPR) was used to categorize hens as feather peckers (P), victims (V), neutrals (N), or feather pecker-victims (PV) at each age. Hens categorized as PV exhibited pecking behaviors similar to P and received pecks similar to V. SFP given were correlated with APs given, but not with gentle feather pecks (GFP) given throughout the study. State-transition plot maps illustrated that 22.5% of P remained P, while 44% of PV remained PV throughout the duration of the study. Lifetime behavioral categories identified hens as a consistent feather pecker (5%), consistent neutral (3.9%), consistent victim (7.9%), consistent feather pecker-victim (29.4%), or inconsistent (53.8%) in their behavioral patterns throughout their life. Consistent feather peckers performed more SFP than hens of other categories, and consistent neutral hens received fewer GFP than consistent feather PV. No differences in corticosterone or whole blood serotonin levels were observed among the categories. Approximately, half of the population was classified as a feather pecker at least once during the study, while the remainder was never categorized as a feather pecker. Therefore, even if the development and cause of feather pecking may be multifactorial, once the behavior has been developed, some hens may persist in feather pecking. However, as some hens were observed to never receive or perform SFP, emphasis should be made to select for these hens in future breeding practices.

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

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

Plumage condition in laying hens: genetic parameters for direct and indirect effects in two purebred layer lines

BACKGROUND

Feather pecking is a major welfare issue in laying hen industry that leads to mortality. Due to a ban on conventional cages in the EU and on beak trimming in some countries of the EU, feather pecking will become an even bigger problem. Its severity depends both on the victim receiving pecking and on its group mates inflicting pecking (indirect effects), which together determine plumage condition of the victim. Plumage condition may depend, therefore, on both the direct genetic effect of an individual itself and on the indirect genetic effects of its group mates. Here, we present estimated genetic parameters for direct and indirect effects on plumage condition of different body regions in two purebred layer lines, and estimates of genetic correlations between body regions.

METHODS

Feather condition scores (FCS) were recorded at 40 weeks of age for neck, back, rump and belly and these four scores were added-up into a total FCS. A classical animal model and a direct-indirect effects model were used to estimate genetic parameters for FCS. In addition, a bivariate model with mortality (0/1) was used to account for mortality before recording FCS. Due to mortality during the first 23 weeks of laying, 5363 (for W1) and 5089 (for WB) FCS records were available.

RESULTS

Total heritable variance for FCS ranged from 1.5% to 9.8% and from 9.8% to 53.6% when estimated respectively with the classical animal and the direct-indirect effects model. The direct-indirect effects model had a significantly higher likelihood. In both lines, 70% to 94% of the estimated total heritable variation in FCS was due to indirect effects. Using bivariate analysis of FCS and mortality did not affect estimates of genetic parameters. Genetic correlations were high between adjacent regions for FCS on neck, back, and rump but moderate to low for belly with other regions.

CONCLUSION

Our results show that 70% to 94% of the heritable variation in FCS relates to indirect effects, indicating that methods of genetic selection that include indirect genetic effects offer perspectives to improve plumage condition in laying hens. This, in turn could reduce a major welfare problem.

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

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

Social environmental effects on gene regulation

Social environmental conditions, particularly the experience of social adversity, have long been connected with health and mortality in humans and other social mammals. Efforts to identify the physiological basis for these effects have historically focused on their neurological, endocrinological, and immunological consequences. Recently, this search has been extended to understanding the role of gene regulation in sensing, mediating, and determining susceptibility to social environmental variation. Studies in laboratory rodents, captive primates, and human populations have revealed correlations between social conditions and the regulation of a large number of genes, some of which are likely causal. Gene expression responses to the social environment are, in turn, mediated by a set of underlying regulatory mechanisms, of which epigenetic marks are the best studied to date. Importantly, a number of genes involved in the response to the social environment are also associated with susceptibility to other external stressors, as well as certain diseases. Hence, gene regulatory studies are a promising avenue for understanding, and potentially developing strategies to address, the effects of social adversity on health.

PMEL: a pigment cell-specific model for functional amyloid formation

PMEL is a pigment cell-specific protein responsible for the formation of fibrillar sheets within the pigment organelle, the melanosome. The fibrillar sheets serve as a template upon which melanins polymerize as they are synthesized. The PMEL fibrils are required for optimal pigment cell function, as animals that either lack PMEL expression or express mutant PMEL variants show varying degrees of hypopigmentation and pigment cell inviability. The PMEL fibrils have biophysical properties of amyloid, a protein fold that is frequently associated with neurodegenerative and other diseases. However, PMEL is one of a growing number of non-pathogenic amyloid proteins that contribute to the function of the cell and/or organism that produces them. Understanding how PMEL generates amyloid in a non-pathogenic manner might provide insights into how to avoid toxicity due to pathological amyloid formation. In this review, we summarize and reconcile data concerning the fate of PMEL from its site of synthesis in the endoplasmic reticulum to newly formed melanosomes and the role of distinct PMEL subdomains in trafficking and amyloid fibril formation. We then discuss how its progression through the secretory pathway into the endosomal system might allow for the regulated and non-toxic conversion of PMEL into an ordered amyloid polymer.

Genetics of behavioural adaptation of livestock to farming conditions

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

Many quantitative trait loci for feather growth in an F(2) broiler × layer cross collocate with body weight loci

1. A genome-wide scan of 467 F(2) progeny of a broiler x layer cross was conducted to identify quantitative trait loci (QTL) affecting the rate of growth of the tail, wing and back feathers, and the width of the breast feather tract, at three weeks of age. 2. Correlations between the traits ranged from 0·36 to 0·61. Males had longer tail and wing feathers and shorter back feathers than females. Breast feather tract width was greater in females than males. 3. QTL effects were generally additive and accounted for 11 to 45% of sex average feather lengths of the breeds, and 100% of the breast feather tract width. Positive and negative alleles were inherited from both lines, whereas the layer allele was larger than the broiler allele after adjusting for body weight. 4. A total of 4 genome-significant and 4 suggestive QTL were detected. At three or 6 weeks of age, 5 of the QTL were located in similar regions as QTL for body weight. 5. Analysis of a model with body weight at three weeks as a covariate identified 5 genome significant and 6 suggestive QTL, of which only two were coincident with body weight QTL. One QTL for feather length at 148 cM on GGA1 was identified at a similar location in the unadjusted analysis. 6. The results suggest that the rate of feather growth is largely controlled by body weight QTL, and that QTL specific for feather growth also exist.

Identification of chromosomal locations associated with tail biting and being a victim of tail-biting behaviour in the domestic pig (Sus scrofa domesticus)

The objective of this study was to identify loci associated with tail biting or being a victim of tail biting in Norwegian crossbred pigs using a genome-wide association study with PLINK case-control analysis. DNA was extracted from hair or blood samples collected from 98 trios of crossbred pigs located across Norway. Each trio came from the same pen and consisted of one pig observed to initiate tail biting, one pig which was the victim of tail biting and a control pig which was not involved in either behaviour. DNA was genotyped using the Illumina PorcineSNP60 BeadChip whole-genome single-nucleotide polymorphism (SNP) assay. After quality assurance filtering, 53,952 SNPs remained comprising 74 animals (37 pairs) for the tail biter versus control comparison and 53,419 SNPs remained comprising 80 animals (40 pairs) for the victim of tail biting versus control comparison. An association with being a tail biter was observed on Sus scrofa chromosome 16 (SSC16; p = 1.6 × 10(-5)) and an unassigned chromosome (p = 3.9 × 10(-5)). An association with being the victim of tail biting was observed on Sus scrofa chromosomes 1 (SSC1; p = 4.7 × 10(-5)), 9 (SSC9; p = 3.9 × 10(-5)), 18 (SSC18; p = 7 × 10(-5) for 9,602,511 bp, p = 3.4 × 10(-5) for 9,653,881 bp and p = 5.3 × 10(-5) for 29,577,783 bp) and an unassigned chromosome (p = 6.1 × 10(-5)). An r(2) = 0.96 and a D' = 1 between the two SNPs at 9 Mb on SSC18 indicated extremely high linkage disequilibrium, suggesting that these two markers represent a single locus. These results provide evidence of a moderate genetic association between the propensity to participate in tail-biting behaviour and the likelihood of becoming a victim of this behaviour.

Deciphering the genetic basis of animal domestication

Genomic technologies for livestock and companion animal species have revolutionized the study of animal domestication, allowing an increasingly detailed description of the genetic changes accompanying domestication and breed development. This review describes important recent results derived from the application of population and quantitative genetic approaches to the study of genetic changes in the major domesticated species. These include findings of regions of the genome that show between-breed differentiation, evidence of selective sweeps within individual genomes and signatures of demographic events. Particular attention is focused on the study of the genetics of behavioural traits and the implications for domestication. Despite the operation of severe bottlenecks, high levels of inbreeding and intensive selection during the history of domestication, most domestic animal species are genetically diverse. Possible explanations for this phenomenon are discussed. The major insights from the surveyed studies are highlighted and directions for future study are suggested.

Hen welfare in different housing systems

Egg production systems have become subject to heightened levels of scrutiny. Multiple factors such as disease, skeletal and foot health, pest and parasite load, behavior, stress, affective states, nutrition, and genetics influence the level of welfare hens experience. Although the need to evaluate the influence of these factors on welfare is recognized, research is still in the early stages. We compared conventional cages, furnished cages, noncage systems, and outdoor systems. Specific attributes of each system are shown to affect welfare, and systems that have similar attributes are affected similarly. For instance, environments in which hens are exposed to litter and soil, such as noncage and outdoor systems, provide a greater opportunity for disease and parasites. The more complex the environment, the more difficult it is to clean, and the larger the group size, the more easily disease and parasites are able to spread. Environments such as conventional cages, which limit movement, can lead to osteoporosis, but environments that have increased complexity, such as noncage systems, expose hens to an increased incidence of bone fractures. More space allows for hens to perform a greater repertoire of behaviors, although some deleterious behaviors such as cannibalism and piling, which results in smothering, can occur in large groups. Less is understood about the stress that each system imposes on the hen, but it appears that each system has its unique challenges. Selective breeding for desired traits such as improved bone strength and decreased feather pecking and cannibalism may help to improve welfare. It appears that no single housing system is ideal from a hen welfare perspective. Although environmental complexity increases behavioral opportunities, it also introduces difficulties in terms of disease and pest control. In addition, environmental complexity can create opportunities for the hens to express behaviors that may be detrimental to their welfare. As a result, any attempt to evaluate the sustainability of a switch to an alternative housing system requires careful consideration of the merits and shortcomings of each housing system.

Variability of the melanocortin 1 receptor (MC1R) gene explains the segregation of the bronze locus in turkey (Meleagris gallopavo)

By sequencing the full coding region of the turkey melanocortin 1 receptor (MC1R) gene, we have found 4 mutations (c.96G > A, c.364A > T, c.450C > T, and c.887C > T) that are organized in 5 different haplotypes (MC1R*1 to MC1R*5). These haplotypes correlate perfectly with the 3 alleles of the bronze locus (i.e., B, b(+), and b(1)). We suggest that the dominant black phenotype, associated with the B allele, results from the constitutive activation of the receptor, an effect that might be mediated by the missense mutation c.364A > T (p.Ile122Phe). Moreover, we propose that the recessive black-winged bronze phenotype (linked to b(1)) might be produced by 2 deleterious mutations of MC1R (c.96G > A and c.887C > T). This is an unexpected finding because in mammals, MC1R deleterious polymorphisms are usually related with either red or lighter fur colors.

Genotype at the PMEL17 locus affects social and explorative behaviour in chickens

1. We studied behaviour and brain gene expression in homozygous PMEL17 genotypes, using chickens originating from an advanced White Leghorn x red junglefowl intercross. The behavioural studies consisted of three social and one explorative behaviour test. There were significant differences between the genotypes in both social and explorative behaviour. 2. Gene expression studies showed no PMEL17 expression in brain, so the genotype differences must depend on extra-neural gene expression or expression during embryonic development. However, linkage or spurious family effects (genetic drift) can not be excluded. 3. The study strongly suggests a correlated effect between plumage colour and behaviour, and we conclude that PMEL17 may have a pleiotropic effect on social and explorative behaviour in chickens.

Genotype on the pigmentation regulating PMEL17 gene affects behavior in chickens raised without physical contact with conspecifics

Chickens homozygous for the Dominant white or wild-type allele of PMEL17 were subjected to a broad phenotyping in order to detect consistent differences between genotypes. To exclude feather pecking, the chickens were individually housed without physical contact, from the day of hatching, and tested for social, aggressive, fear and exploratory behaviors, and corticosterone and testosterone levels were assessed. In a principal component analysis, 53.2% of the behavior variation was explained by two factors. Factor one was an activity and social factor, and there was a significant effect of genotype on the factor scores. On factor two, related to aggressive behavior, there were significant effects of genotype, sex and their interaction. There were no genotype effects on hormone levels or any other measured non-behavioral phenotypes. Hence, differences in behavior between PMEL17 genotypes remained when negative social experiences were excluded, indicating a direct pleiotropic effect of the gene on behavior.

Domestication, selection, behaviour and welfare of animals — genetic mechanisms for rapid responses

Increased production has been the major goal of animal breeding for many decades, and the correlated side-effects have grown to become a major issue in animal welfare. In this paper, the main genetic mechanisms in which such side-effects may occur are reviewed with examples from our own research in chickens. Pleiotropy, linkage and regulatory pathways are the most important means by which a number of traits may be affected simultaneously by the same selection pressure. Pleiotropy can be exemplified by the gene PMEL17 which causes a lack of black pigmentation in chickens and, simultaneously, predisposes them to become the victims of feather pecking. Linkage is a probable reason why a limited region on chicken chromosome 1 affects many different traits, such as growth, reproduction and fear-related behaviour. Gene regulation is affected by stress, and may cause modifications in behaviour and phenotype which are transferred from parents to offspring by means of epigenetic modifications. Insights into phenomena, such as these, may increase our understanding not only of how artificial selection works, but also evolution at large.