Global diversity and genetic contributions of chicken populations from African, Asian and European regions

Landscape genomics reveals regions associated with adaptive phenotypic and genetic variation in Ethiopian indigenous chickens

Climate change is a threat to sustainable livestock production and livelihoods in the tropics. It has adverse impacts on feed and water availability, disease prevalence, production, environmental temperature, and biodiversity. Unravelling the drivers of local adaptation and understanding the underlying genetic variation in random mating indigenous livestock populations informs the design of genetic improvement programmes that aim to increase productivity and resilience. In the present study, we combined environmental, genomic, and phenotypic information of Ethiopian indigenous chickens to investigate their environmental adaptability. Through a hybrid sampling strategy, we captured wide biological and ecological variabilities across the country. Our environmental dataset comprised mean values of 34 climatic, vegetation and soil variables collected over a thirty-year period for 260 geolocations. Our biological dataset included whole genome sequences and quantitative measurements (on eight traits) from 513 individuals, representing 26 chicken populations spread along 4 elevational gradients (6-7 populations per gradient). We performed signatures of selection analyses ([Formula: see text] and XP-EHH) to detect footprints of natural selection, and redundancy analyses (RDA) to determine genotype-environment and genotype-phenotype-associations. RDA identified 1909 outlier SNPs linked with six environmental predictors, which have the highest contributions as ecological drivers of adaptive phenotypic variation. The same method detected 2430 outlier SNPs that are associated with five traits. A large overlap has been observed between signatures of selection identified by[Formula: see text]and XP-EHH showing that both methods target similar selective sweep regions. Average genetic differences measured by [Formula: see text] are low between gradients, but XP-EHH signals are the strongest between agroecologies. Genes in the calcium signalling pathway, those associated with the hypoxia-inducible factor (HIF) transcription factors, and sports performance (GALNTL6) are under selection in high-altitude populations. Our study underscores the relevance of landscape genomics as a powerful interdisciplinary approach to dissect adaptive phenotypic and genetic variation in random mating indigenous livestock populations.

Raising laying hens: housing complexity and genetic strain affect startle reflex amplitude and behavioural response to fear-inducing stimuli

Individual variation in fearfulness can be modified during ontogeny, and high levels of fear can affect animal welfare. We asked whether early-life environmental complexity and genetic strain affect fear behaviour in young laying hens (pullets). Four replicates of brown (B) and white (W) genetic strains (breeds) of layers were each raised in four environmental treatments (housing): conventional cages (Conv) and different rearing aviaries with increasing space and complexity (Low < Mid < High). We used a startle reflex test (weeks 4 and 14) to measure startle amplitude and autonomic response (i.e. comb temperature). A combination of novel arena (NA) and novel object (NO) tests was used (week 14) to assess NA exploration and alertness, latency to approach the centre and initial NO avoidance and investigation. Housing × strain affected startle amplitude (B-Conv, B-High < B-Low, B-Mid; B > W; no housing effect in W) but not autonomic response. Fear behaviour was affected by housing (NA exploration, investigation: Conv < Low, Mid, High; NO avoidance: Conv, High < Low, Mid), strain (NA alertness: B > W, NO avoidance: W > B) and their interaction (NA centre approach: B-Conv < all other groups). We present evidence for strain-specific fear responses depending on early experience.

High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources

Italy counts a large number of local chicken populations, some without a recognized genetic structure, such as Val Platani (VPL) and Cornuta (COS), which represent noteworthy local genetic resources. In this study, the genotype data of 34 COS and 42 VPL, obtained with the Affymetrix Axiom600KChicken Genotyping Array, were used with the aim to investigate the genetic diversity, the runs of homozygosity (ROH) pattern, as well as the population structure and relationship within the framework of other local Italian and commercial chickens. The genetic diversity indices, estimated using different approaches, displayed moderate levels of genetic diversity in both populations. The identified ROH hotspots harbored genes related to immune response and adaptation to local hot temperatures. The results on genetic relationship and population structure reported a clear clustering of the populations according to their geographic origin. The COS formed a nonoverlapping genomic cluster and clearly separated from the other populations, but showed evident proximity to the Siciliana breed (SIC). The VPL highlighted intermediate relationships between the COS-SIC group and the rest of the sample, but closer to the other Italian local chickens. Moreover, VPL showed a complex genomic structure, highlighting the presence of 2 subpopulations that match with the different source of the samples. The results obtained from the survey on genetic differentiation underline the hypothesis that Cornuta is a population with a defined genetic structure. The substructure that characterizes the Val Platani chicken is probably the consequence of the combined effects of genetic drift, small population size, reproductive isolation, and inbreeding. These findings contribute to the understanding of genetic diversity and population structure, and represent a starting point for designing programs to monitor and safeguard these local genetic resources, in order to define a possible official recognition program as breeds.

Genome-wide mapping of signatures of selection using a high-density array identified candidate genes for growth traits and local adaptation in chickens

BACKGROUND

Availability of single nucleotide polymorphism (SNP) genotyping arrays and progress in statistical analyses have allowed the identification of genomic regions and genes under selection in chicken. In this study, SNP data from the 600 K Affymetrix chicken array were used to detect signatures of selection in 23 local Italian chicken populations. The populations were categorized into four groups for comparative analysis based on live weight (heavy vs light) and geographical area (Northern vs Southern Italy). Putative signatures of selection were investigated by combining three extended haplotype homozygosity (EHH) statistical approaches to quantify excess of haplotype homozygosity within (iHS) and between (Rsb and XP-EHH) groups. Presence of runs of homozygosity (ROH) islands was also analysed for each group.

RESULTS

After editing, 541 animals and 313,508 SNPs were available for statistical analyses. In total, 15 candidate genomic regions that are potentially under selection were detected among the four groups: eight within a group by iHS and seven by combining the results of Rsb and XP-EHH, which revealed divergent selection between the groups. The largest overlap between genomic regions identified to be under selection by the three approaches was on chicken chromosome 8. Twenty-one genomic regions were identified with the ROH approach but none of these overlapped with regions identified with the three EHH-derived statistics. Some of the identified regions under selection contained candidate genes with biological functions related to environmental stress, immune responses, and disease resistance, which indicate local adaptation of these chicken populations.

CONCLUSIONS

Compared to commercial lines, local populations are predominantly reared as backyard chickens, and thus, may have developed stronger resistance to environmental challenges. Our results indicate that selection can play an important role in shaping signatures of selection in local chicken populations and can be a starting point to identify gene mutations that could have a useful role with respect to climate change.

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.

Contrafreeloading and foraging-related behavior in hens differing in laying performance and phylogenetic origin

Different breeds of domestic and junglefowl differ in foraging strategies indicating that domestication resulted in modified energy saving behavioral strategies. In the present study we investigated foraging strategies and foraging-related behavior in 4 lines of laying hens differing in phylogenetic origin and laying performance to analyze a possible relationship between foraging and the level of egg production. High performing brown and white pure bred lines were compared with their low performing brown and white counterparts. To control possible effects on behavior other than genetic effects, all hens were reared and kept in an identical environment. A total of 72 hens from each line were kept in 6 compartments with 12 hens per compartment, respectively. Observations were done for 3 times during one laying period. Foraging strategy was tested by a contrafreeloading (CFL) paradigm. CFL describes a behavior in which animals prefer food that requires effort to obtain, although at the same time food is freely available. The hens were offered a commercial standard diet in one trough and a mixture of wood shavings and commercial standard diet in another trough. The behavior of hens was video recorded and the activity level of individual hens in the litter area was recorded by an antenna-transponder system. The high performing layers showed less CFL and foraging-related behavior compared with their low performing counterparts in both the white and brown layers. Despite differences in CFL, all hens showed a preference for the commercial standard diet compared to the mixture of wood-shavings. Our results show an association between foraging strategy and level of egg production. This suggests that a high level of egg production is accompanied by behaviors enabling the hens to satisfy their higher energy demand more efficiently. Saving energy by reduced activity probably allows them to reallocate energy into reproduction, that is, laying performance.

Commercial layer hybrids kept under organic conditions: a comparison of range use, welfare and egg production in two layer strains

Outdoor range areas provide laying hens with improved opportunities to perform natural behaviors and increase the available space per bird, however, birds are also exposed to potentially stressful factors including weather and predators. Ability to cope with challenging environments varies between different strains and must be considered to ensure good welfare. The aim of this study was to determine how suitable 2 hybrids, the Dekalb White (DW) and the Bovans Brown (BB), are for organic production with special emphasis on ranging behavior. A total of 1,200 hens were housed according to organic regulations across 12 flocks of 100 birds. Range and shelter use, effect of weather, vegetation cover, egg production and quality, and mortality were assessed in addition to a range of clinical welfare indicators. Initially a greater proportion of DW hens accessed the range. However, after approximately 2 mo, a greater proportion of BB were using the range and venturing further from the house. DW hens were more likely to use the shelters than BB hens (P < 0.001). Vegetation was also worn away to a greater extent in the BB ranges. Weather affected the proportion of hens that went outside, the distance ranged from the popholes, and shelter use. BB hens were found to have better plumage condition (P < 0.001), fewer footpad lesions (P < 0.001), fewer comb wounds (P < 0.001), and lower mortality rates (P = 0.013). Both hybrids experienced keel bone fractures, though DW hens had more at the cranial portion (P < 0.001) and BB at the caudal portion (P < 0.001). DW hens had an earlier onset of lay and higher egg production than BB hens (P < 0.001), though BB hens laid heavier eggs (P < 0.001) with thicker shells (P = 0.001). Overall, BB hens seemed to perform superiorly or equivalently to the DW hens for all variables apart from egg production. These results demonstrate the importance of considering the strain of bird selected for organic production systems in order for the birds to reap the potential benefits that are offered by outdoor access.

Avian leukosis virus (ALV) is highly prevalent in fancy-chicken flocks in Saxony

The current prevalence of avian leukosis virus (ALV) in fancy chickens in Germany is unknown. Therefore, 537 cloacal swabs from 50 purebred fancy-chicken flocks in Saxony were tested for the presence of the ALV p27 protein using a commercial antigen-capture ELISA. The detection rate was 28.7% at the individual-animal level and 56.0% at the flock level. Phylogenetic analysis of PCR products obtained from 22 different flocks revealed the highest similarity to ALV subtype K. When classifying breeds by their origin, ALV detection rates differed significantly. Evaluation of questionnaire data revealed no significant differences between ALV-positive and negative flocks regarding mortality.

Mathematical modeling of egg production curve in a multivariety endangered hen breed

This study aimed to compare the egg laying performance of the four varieties (white, franciscan, black, and partridge) of a Spanish endangered Utrerana hen breed. A flock of 60 Utrerana hens (15 hen/variety) were individually housed to enable daily egg traceability. Compartmental, Gamma, linear hyperbolic, logistic curvilinear, McNally, Narushin-Takma, and quadratic logarithmic nonlinear regression functions were fitted. Goodness-of-fit (coefficient of determination (R²)) and flexibility criteria (mean squared error (MSE), Akaike information criteria (AIC), corrected Akaike information criteria (AICc), Bayesian information criteria (BIC)) were evaluated to identify the best-fitting function to model for egg production curve. Best-fitting values were reported by the six-parameter Narushin-Takma model for white (R² = 0.828), franciscan (R² = 0.888), and black (R² = 0.899) varieties. By contrast, quadratic logarithmic was reported to be the best-fitting model for partridge Utrerana hen egg production curve (R² = 0.917). The characterization of the laying cycle of endangered avian breeds varieties permits tailoring productive strategies which may ensure animal welfare at the same that they boost economic potentialities, enabling the productive model to better simultaneously fulfill animal needs and human demands. As a result, breed diversity may act as the motor element to improve economic profitability, but in turn may also ensure the conservation of the local genetic resources from which desirable products, such as the egg, are obtained.

Population Structure and Genetic Diversity of Seven Chinese Indigenous Chicken Populations in Guizhou Province

To investigate the population structure and genetic diversity of indigenous chicken breeds in Guizhou, a total of 150 individual samples were collected from 12 breeds, including seven local chicken breeds in Guizhou Province, three Chinese native breeds found in other provinces, and two commercial breeds. The genotype datasets were obtained using a 50K single nucleotide polymorphism array method, and then a series of population analyses were performed. The obtained population parameters and linkage disequilibrium decay indicated a higher degree of genetic diversity in Guizhou chickens than in commercial breeds. Two Guizhou local breeds, Wumeng black-bone and Weining, were clustered with a breed from a neighboring province, Xinwen black-bone, which exhibited similar ancestral composition patterns. A newly found breed, Wumeng crested, had high genetic diversity and displayed genetic differences from other Guizhou breeds. These findings provide insight into the establishment of efficient conservation and utilization programs for Guizhou chicken breeds.

Comparison of major histocompatibility complex-B variability in Sri Lankan indigenous chickens with five global chicken populations using MHC-B SNP panel

In the present study, we investigated the major histocompatibility complex (MHC)-B haplotypes diversity of Sri Lankan indigenous chickens from three different geographical sites consisting of highly mixed populations using 90 SNPs in the MHC-B region. A total of 48 haplotypes were identified. Those included 37 novel haplotypes and 11 previously identified 'standard' haplotypes. The MHC-linked marker, LEI0258, had 23 alleles showing less diversity than defined by MHC-B SNP haplotypes. Among those identified haplotypes, five standard haplotypes-BSNP-O02, BSNP-M01, BSNP-A04, BSNP-K03, BSNP-T04-were most commonly observed, suggesting past introgression of imported breeds. Comparison of the MHC-B haplotypes of Sri Lankan and four other global populations with previously defined haplotypes indicated the sharing of 23 standard haplotypes with common origins. Novel haplotypes are population-specific and not shared among the geographical boundaries. Backyard indigenous chickens are unselected, highly crossbred, and generally thrive under dynamic environmental conditions. Hence free-range production systems may be responsible for maintaining high diversity in the MHC-B region with novel haplotypes.

Researching on the fine structure and admixture of the worldwide chicken population reveal connections between populations and important events in breeding history

Here, we have evaluated the general genomic structure and diversity and studied the divergence resulting from selection and historical admixture events for a collection of worldwide chicken breeds. In total, 636 genomes (43 populations) were sequenced from chickens of American, Chinese, Indonesian, and European origin. Evaluated populations included wild junglefowl, rural indigenous chickens, breeds that have been widely used to improve modern western poultry populations and current commercial stocks bred for efficient meat and egg production. In‐depth characterizations of the genome structure and genomic relationships among these populations were performed, and population admixture events were investigated. In addition, the genomic architectures of several domestication traits and central documented events in the recent breeding history were explored. Our results provide detailed insights into the contributions from population admixture events described in the historical literature to the genomic variation in the domestic chicken. In particular, we find that the genomes of modern chicken stocks used for meat production both in eastern (Asia) and western (Europe/US) agriculture are dominated by contributions from heavy Asian breeds. Further, by exploring the link between genomic selective divergence and pigmentation, connections to functional genes feather coloring were confirmed.

Investigating genetic diversity and population phylogeny of five Chongqing local chicken populations autosomal using microsatellites

The genetic diversity and population structures of five Chongqing local chicken populations were investigated using by 24 microsatellite markers. Results revealed that the mean number of alleles (N_A) ranged from 7.08 (Daninghe chicken, DN) to 8.46 (Nanchuan chicken, NC). The highest observed heterozygosity (H_O) and expected heterozygosity (H_E) were observed in DN (H_O = 0.7252; H_E = 0.7409) and the lowest H_O and H_E were observed in XS (Xiushan native chicken [XS], H_O = 0.5910 and H_E = 0.6697). The inbreeding coefficient (F_IS) within population ranged from 0.022 (DN) to 0.119 (XS). Among the 24 microsatellite markers, four loci (MCW0111, MCW0016, ADL0278, and MCW0104) deviated from the Hardy-Weinberg equilibrium in all the studied populations. The results of population polygenetic analysis based on Nei's genetic distance and STRUCTURE software showed that the clustering of the five populations was incomplete consistent with geographical distribution. Moreover, a large number of gene flows were widespread among different populations, suggesting that genetic material exchanges occurred due to human activities and migration which was also verified by PCoA. In summary, this study preliminarily showed that Chongqing local chicken populations had rich genetic diversity and remarkable genetic divergence, but still high risk in conversion. These findings would be useful to the management of conservation strategies and the utilization of local chicken populations in further.

A Descriptive Study of Keel Bone Fractures in Hens and Roosters from Four Non-Commercial Laying Breeds Housed in Furnished Cages

The presence of keel bone fractures (KBF) in laying hens has been documented and discussed by several authors, nevertheless the causative factors behind KBF remain uncertain. High prevalence of KBF have been reported in all commercial egg production systems, in different genetic lines and at different ages. Several of the proposed causal mechanisms behind KBF are linked to selection for efficient production. It is, therefore, of interest to explore whether less selected breeds have a lower occurrence of keel bone fractures compared to reports from highly selected, modern laying hen breeds. Thus, the aim of the current study was to investigate keel bones of hens from four non-commercial layer breeds. Birds were housed in furnished cages and keel bones examined at 30 and 63 weeks of age, using a portable X-ray equipment. The results from this descriptive study indicate a low prevalence of KBF at both ages in all four breeds, with only five KBF detected in 213 X-ray pictures taken from 126 birds. Of these, four of the KBF were observed in the most genetically selected breed, with an early onset of lay. None of the roosters examined exhibited KBF. The overall low numbers of KBF found indicate that genetic factors may be involved in KBF and, thus that selective breeding may help to reduce the susceptibility to KBF. Finally, this study highlights the importance of poultry conservation to secure genetic diversity, which may be an important resource in future selection schemes.

Effects of Maternal Stress on Measures of Anxiety and Fearfulness in Different Strains of Laying Hens

Maternal stress can affect the offspring of birds, possibly due to hormone deposition in the egg. Additionally, phenotypic diversity resulting from domestication and selection for productivity has created a variety of poultry lines that may cope with stress differently. In this study, we investigated the effects of maternal stress on the behavior of different strains of laying hens and the role of corticosterone as its mediator. For this, fertilized eggs of five genetic lines-two brown (Brown 1 and 2), two white (White 1 and 2), and one pure line White Leghorn-were reared identically as four flocks of 27 birds (24F: 3M) per strain. Each strain was equally separated into two groups: Maternal Stress ("MS"), where hens were subjected to a series of daily acute psychological stressors for 8 days before egg collection, and "Control," which received routine husbandry. Fertile eggs from both treatments were collected at three different ages forming different offspring groups that were treated as replicates; additional eggs from Control were injected either with corticosterone diluted in a vehicle solution ("CORT") or just "Vehicle." Eggs from each replicate were incubated and hatched, and offspring (N = 1,919) were brooded under identical conditions. To measure the effects of maternal stress on anxiety and fear-like behavior, offspring were subjected to a social isolation test (SI) between 5 and 10 days of age and a tonic immobility test (TI) at 9 weeks of age. Compared to Control, MS decreased the number of distress vocalizations emitted by White 2 in SI. No effects of MS were observed in TI, and no effects of CORT were observed in any tests. Overall, brown lines vocalized more in SI and remained in TI for a longer duration than white strains, suggesting genetic differences in fear behavior. Females vocalized more than males in TI and showed a trend toward significance for the same trait in SI. Overall, results suggest that the effects of maternal stress on fearfulness are not directly mediated by corticosterone. Moreover, it highlights behavioral differences across various strains of laying hens, suggesting that fear responses are highly dependent on genotype.

Effects of prenatal stress and genetics on embryonic survival and offspring growth of laying hens

Early-life exposure to stressors can shape the phenotype of the offspring resulting in changes that may affect their prehatch and posthatch development. This can be modeled indirectly through maternal exposure to stressors (natural model) or by offspring exposure to stress hormones (pharmacological model). In this study, both models were used to investigate the effects of genetic line on hatchability, late embryonic mortality, sex ratio, and body weight until 17 wk of age. To form the parent stock, fertilized eggs of 4 commercial genetic lines — two brown (brown 1 and 2), two white (white 1 and 2), and a pure line White Leghorn — were incubated, hatched, and housed identically in 4 flocks of 27 birds (24 females and 3 males) per strain. Each strain was equally separated into 2 groups: “maternal stress,” where hens were subjected to a series of acute psychological stressors (e.g., physical restraint, transportation) for 8 D before egg collection, and “control,” where hens received routine husbandry. At 3 maternal ages, fertile eggs from both treatments were collected, and additional eggs from the control group were injected with corticosterone (10 ng/mL egg content) (“CORT”). A “vehicle” treatment was included to account for effects of egg manipulation. Each maternal age comprised a replicate over time. Eggs were incubated and hatched, and the offspring (N = 1,919) were brooded until 17 wk under identical conditions. The results show that prenatal stress interacted with strain to decrease embryonic survival and growth. Among all strains, brown 2 was consistently the most affected line in both prehatch and posthatch development. Our study shows that embryonic survival and offspring growth are mostly affected by the pharmacological model and that strain differences may increase susceptibility to prenatal stress. Moreover, it suggests that the natural stressor model may be useful for quantifying the response of the mother to stressors, whereas the pharmacological model may be useful for quantifying the response of the embryo to increased levels of corticosterone.

Behavioural consequences of divergent selection on general locomotor activity in chickens

General locomotor activity is a highly variable phenotypic trait of animals. In domestic chickens it is different within and between breeds. The general locomotor activity is a substantially heritable trait and has been shown to be correlated with several other behavioural traits, such as for example feather pecking and anxiety in chickens. However, whether there is a relation between different levels of general locomotor activity and behavioural changes remained unclear. Therefore, a selection line model system has been established, where hens from the same founder population were selected over eight generations for either high or low general locomotor activity. The selection led to significant increases, respectively decreases in general locomotor activity and differences in growth. We here tested 128 hens of the 8^th generation in three behavioural tests. We assumed fearfulness to be affected from selection on general locomotor activity, which we tested in a tonic immobility test. Socio-positive and socio-negative behaviours were tested in respective test paradigms. Fearfulness was higher in hens selected for high general locomotor activity. Social behavioural traits and feather pecking were not affected by selection for general locomotor activity. Evolutionary mechanisms that link fear and general locomotor activity are discussed and also why social behaviours and feather pecking seems not to be affected from selection on general locomotor activity. Our results provide interesting new insights on how selection on one trait, general locomotor activity, affects the behavioural phenotype in other dimensions too.

Phenotypic and morphometric differentiation of indigenous chickens from Kenya and other tropical countries augments perspectives for genetic resource improvement and conservation

Indigenous chickens at the Swahili coast and other traditional migratory corridors in Kenya represent important populations that are inconclusively characterized. Using a comprehensive dataset of Kenyan indigenous chickens and additional mined data of chickens from 8 African and 5 Asian countries, we performed univariate and multivariate assessments to uncover the underlying phenotypic and morphometric variability. Kenyan indigenous chickens expressed differentiation of several qualitative and quantitative traits, both among different counties in the Swahili coast, and among coastal, western, and northern migratory corridors. There was a substantial population stratification of these chickens, particularly distinctive clustering of chickens from Marsabit, Lamu, and Kilifi counties. The pooled dataset further clarified a closer phenotypic and morphometric proximity of chickens within different geographical regions. We additionally revealed a preponderance of bantam and rumpless traits to hot and humid locales, and feathered shanks to cooler regions. Currently, most chicken breeding programs in developing countries rely on phenotypic and morphometric properties. Hence, the high chicken diversity and population stratification observed in our study, possibly shaped by natural and artificial selective pressures, reveal opportunities for complementary phenotypic and genotypic assessments to identify resources for effective breed improvement and conservation strategies of indigenous chickens in the tropics.

The SYNBREED chicken diversity panel: a global resource to assess chicken diversity at high genomic resolution

BACKGROUND

Since domestication, chickens did not only disperse into the different parts of the world but they have also undergone significant genomic changes in this process. Many breeds, strains or lines have been formed and those represent the diversity of the species. However, other than the natural evolutionary forces, management practices (including those that threaten the persistence of genetic diversity) following domestication have shaped the genetic make-up of and diversity between today's chicken breeds. As part of the SYNBREED project, samples from a wide variety of chicken populations have been collected across the globe and were genotyped with a high density SNP array. The panel consists of the wild type, commercial layers and broilers, indigenous village/local type and fancy chicken breeds. The SYNBREED chicken diversity panel (SCDP) is made available to serve as a public basis to study the genetic structure of chicken diversity. In the current study we analyzed the genetic diversity between and within the populations in the SCDP, which is important for making informed decisions for effective management of farm animal genetic resources.

RESULTS

Many of the fancy breeds cover a wide spectrum and clustered with other breeds of similar supposed origin as shown by the phylogenetic tree and principal component analysis. However, the fancy breeds as well as the highly selected commercial layer lines have reduced genetic diversity within the population, with the average observed heterozygosity estimates lower than 0.205 across their breeds' categories and the average proportion of polymorphic loci lower than 0.680. We show that there is still a lot of genetic diversity preserved within the wild and less selected African, South American and some local Asian and European breeds with the average observed heterozygosity greater than 0.225 and the average proportion of polymorphic loci larger than 0.720 within their breeds' categories.

CONCLUSIONS

It is important that such highly diverse breeds are maintained for the sustainability and flexibility of future chicken breeding. This diversity panel provides opportunities for exploitation for further chicken molecular genetic studies. With the possibility to further expand, it constitutes a very useful community resource for chicken genetic diversity research.

Leveraging Available Resources and Stakeholder Involvement for Improved Productivity of African Livestock in the Era of Genomic Breeding

The African continent is home to diverse populations of livestock breeds adapted to harsh environmental conditions with more than 70% under traditional systems of management. Animal productivity is less than optimal in most cases and is faced with numerous challenges including limited access to adequate nutrition and disease management, poor institutional capacities and lack of adequate government policies and funding to develop the livestock sector. Africa is home to about 1.3 billion people and with increasing demand for animal proteins by an ever growing human population, the current state of livestock productivity creates a significant yield gap for animal products. Although a greater section of the population, especially those living in rural areas depend largely on livestock for their livelihoods; the potential of the sector remains underutilized and therefore unable to contribute significantly to economic development and social wellbeing of the people. With current advances in livestock management practices, breeding technologies and health management, and with inclusion of all stakeholders, African livestock populations can be sustainably developed to close the animal protein gap that exists in the continent. In particular, advances in gene technologies, and application of genomic breeding in many Western countries has resulted in tremendous gains in traits like milk production with the potential that, implementation of genomic selection and other improved practices (nutrition, healthcare, etc.) can lead to rapid improvement in traits of economic importance in African livestock populations. The African livestock populations in the context of this review are limited to cattle, goat, pig, poultry, and sheep, which are mainly exploited for meat, milk, and eggs. This review examines the current state of livestock productivity in Africa, the main challenges faced by the sector, the role of various stakeholders and discusses in-depth strategies that can enable the application of genomic technologies for rapid improvement of livestock traits of economic importance.

Bidirectional Selection for Body Weight on Standing Genetic Variation in a Chicken Model

Experimental populations of model organisms provide valuable opportunities to unravel the genomic impact of selection in a controlled system. The Virginia body weight chicken lines represent a unique resource to investigate signatures of selection in a system where long-term, single-trait, bidirectional selection has been carried out for more than 60 generations. At 55 generations of divergent selection, earlier analyses of pooled genome resequencing data from these lines revealed that 14.2% of the genome showed extreme differentiation between the selected lines, contained within 395 genomic regions. Here, we report more detailed analyses of these data exploring the regions displaying within- and between-line genomic signatures of the bidirectional selection applied in these lines. Despite the strict selection regime for opposite extremes in body weight, this did not result in opposite genomic signatures between the lines. The lines often displayed a duality of the sweep signatures, where an extended region of homozygosity in one line, in contrast to mosaic pattern of heterozygosity in the other line. These haplotype mosaics consisted of short, distinct haploblocks of variable between-line divergence, likely the results of a complex demographic history involving bottlenecks, introgressions and moderate inbreeding. We demonstrate this using the example of complex haplotype mosaicism in the growth1 QTL. These mosaics represent the standing genetic variation available at the onset of selection in the founder population. Selection on standing genetic variation can thus result in different signatures depending on the intensity and direction of selection.

Avian Toll-like receptor allelic diversity far exceeds human polymorphism: an insight from domestic chicken breeds

Immune genes show remarkable levels of adaptive variation shaped by pathogen-mediated selection. Compared to humans, however, population polymorphism in animals has been understudied. To provide an insight into immunogenetic diversity in birds, we sequenced complete protein-coding regions of all Toll-like receptor (TLR) genes with direct orthology between mammals and birds (TLR3, TLR4, TLR5 and TLR7) in 110 domestic chickens from 25 breeds and compared their variability with a corresponding human dataset. Chicken TLRs (chTLRs) exhibit on average nine-times higher nucleotide diversity than human TLRs (hTLRs). Increased potentially functional non-synonymous variability is found in chTLR ligand-binding ectodomains. While we identified seven sites in chTLRs under positive selection and found evidence for convergence between alleles, no selection or convergence was detected in hTLRs. Up to six-times more alleles were identified in fowl (70 chTLR4 alleles vs. 11 hTLR4 alleles). In chTLRs, high numbers of alleles are shared between the breeds and the allelic frequencies are more equal than in hTLRs. These differences may have an important impact on infectious disease resistance and host-parasite co-evolution. Though adaptation through high genetic variation is typical for acquired immunity (e.g. MHC), our results show striking levels of intraspecific polymorphism also in poultry innate immune receptors.

Genetic diversity of 21 experimental chicken lines with diverse origins and genetic backgrounds

The genetic characteristics and diversity of 21 experimental chicken lines registered with the National BioResource Project of Japan were examined using mitochondrial D-loop sequences and 54 microsatellite DNA markers. A total of 12 haplotypes were detected in the 500-bp mitochondrial DNA sequences of the hypervariable segment I for 349 individuals of 21 lines. The 12 haplotypes belonged to three (A, D, and E) haplogroups, out of the eight (A‒H) common haplogroups in domestic chickens and red junglefowls. The haplogroups A and D were widely represented in indigenous chickens in the Asian and Pacific regions, and the haplogroup E was the most prevalent in domestic chickens. Genetic clustering by discriminant analysis of principal components with microsatellite markers divided 681 individuals of 21 lines into three groups that consisted of Fayoumi-, European-, and Asian- derived lines. In each of the cladograms constructed with Nei's genetic distances based on allele frequencies and the membership coefficients provided by STRUCTURE and with the genetic distance based on the proportion of shared alleles, the genetic relationships coincided well with the breeding histories of the lines. Microsatellite markers showed remarkably lower genetic heterozygosities (less than 0.1 observed heterozygosity) for eight lines (GSP, GSN/1, YL, PNP, BM-C, WL-G, BL-E, and #413), which have been maintained as closed colonies for more than 40 years (except for #413), indicating their usefulness as experimental chicken lines in laboratory animal science research.

Population genetic analyses of seven Chinese indigenous chicken breeds in a context of global breeds

Jiangxi province in China is rich in indigenous chicken breeds, which have diverse phenotypes and represent a valuable genetic resource for further genetic improvement of modern breeds. Here, we conducted a series of analyses to reveal genetic diversity, phylogenetic relationships and population structure of seven chicken breeds in Jiangxi province in the context of nine non-local chicken breeds, using 600K SNP data. We show that Jiangxi indigenous breeds have more abundant nucleotide diversity than do European local and commercial breeds. Among Jiangxi breeds, Dongxiang Blue-eggshell (DX) and Chongren Partride (CR) display remarkably reduced genetic diversity, as the two breeds exhibit increased inbreeding coefficients, runs of homozygosity, extent of linkage disequilibrium and reduced expected heterozygosity. DX, CR and Taihe Silkie (TH) represent three ancestral lineages of the Jiangxi chicken and display genetic differentiation from the other four Jiangxi breeds, which show a signature of admixture with European commercial breeds. These findings provide insight for the establishment of an efficient conservation program for Jiangxi chicken breeds. Considering the current status of genetic diversity and ancestral representativeness, particular attention should be paid to DX, CR and TH chickens.

Use of geographic information system tools to predict animal breed suitability for different agro-ecological zones

Predicting breed-specific environmental suitability has been problematic in livestock production. Native breeds have low productivity but are thought to be more robust to perform under local conditions than exotic breeds. Attempts to introduce genetically improved exotic breeds are generally unsuccessful, mainly due to the antagonistic environmental conditions. Knowledge of the environmental conditions that are shaping the breed would be needed to determine its suitability to different locations. Here, we present a methodology to predict the suitability of breeds for different agro-ecological zones using Geographic Information Systems tools and predictive habitat distribution models. This methodology was tested on the current distribution of two introduced chicken breeds in Ethiopia: the Koekoek, originally from South Africa, and the Fayoumi, originally from Egypt. Cross-validation results show this methodology to be effective in predicting breed suitability for specific environmental conditions. Furthermore, the model predicts suitable areas of the country where the breeds could be introduced. The specific climatic parameters that explained the potential distribution of each of the breeds were similar to the environment from which the breeds originated. This novel methodology finds application in livestock programs, allowing for a more informed decision when designing breeding programs and introduction programs, and increases our understanding of the role of the environment in livestock productivity.

Comparison of genotype imputation strategies using a combined reference panel for chicken population

Using whole-genome sequence (WGS) data are supposed to be optimal for genome-wide association studies and genomic predictions. However, sequencing thousands of individuals of interest is expensive. Imputation from single nucleotide polymorphisms panels to WGS data is an attractive approach to obtain highly reliable WGS data at low cost. Here, we conducted a genotype imputation study with a combined reference panel in yellow-feather dwarf broiler population. The combined reference panel was assembled by sequencing 24 key individuals of a yellow-feather dwarf broiler population (internal reference panel) and WGS data from 311 chickens in public databases (external reference panel). Three scenarios were investigated to determine how different factors affect the accuracy of imputation from 600 K array data to WGS data, including: genotype imputation with internal, external and combined reference panels; the number of internal reference individuals in the combined reference panel; and different reference sizes and selection strategies of an external reference panel. Results showed that imputation accuracy from 600 K to WGS data were 0.834±0.012, 0.920±0.007 and 0.982±0.003 for the internal, external and combined reference panels, respectively. Increasing the reference size from 50 to 250 improved the accuracy of genotype imputation from 0.848 to 0.974 for the combined reference panel and from 0.647 to 0.917 for the external reference panel. The selection strategies for the external reference panel had no impact on the accuracy of imputation using the combined reference panel. However, if only an external reference panel with reference size &gt;50 was used, the selection strategy of minimizing the average distance to the closest leaf had the greatest imputation accuracy compared with other methods. Generally, using a combined reference panel provided greater imputation accuracy, especially for low-frequency variants. In conclusion, the optimal imputation strategy with a combined reference panel should comprehensively consider genetic diversity of the study population, availability and properties of external reference panels, sequencing and computing costs, and frequency of imputed variants. This work sheds light on how to design and execute genotype imputation with a combined external reference panel in a livestock population.

More Than Eggs - Relationship Between Productivity and Learning in Laying Hens

The intense selection of chickens for production traits, such as egg laying, is thought to cause undesirable side effects and changes in behavior. Trade-offs resulting from energy expenditure in productivity may influence other traits: in order to sustain energetic costs for high egg production, energy expenditure may be redirected away from specific behavioral traits. For example, such energetic trade-offs may change the hens' cognitive abilities. Therefore, we hypothesized highly productive laying hens to show reduced learning performance in comparison to moderate productive lines. We examined the learning ability of four chicken lines that differed in laying performance (200 versus 300 eggs/year) and phylogenetic origin (brown/white layer; respectively, within performance). In total 61 hens were tested in semi-automated Skinner boxes in a three-phase learning paradigm (initial learning, reversal learning, extinction). To measure the hens' learning performance within each phase, we compared the number of active decisions needed to fulfill a learning criteria (80% correct choices for learning, 70% no responses at extinction) using linear models. Differences between the proportions of hens per line that reached criterion on each phase of the learning tasks were analyzed by using a Kaplan-Meier (KM) survival analysis. A greater proportion of high productive hens achieved the learning criteria on each phase compared to less productive hens (Chi2 3 = 8.25, p = 0.041). Furthermore, high productive hens accomplished the learning criteria after fewer active decisions in the initial phase (p = 0.012) and in extinction (p = 0.004) compared to the less selected lines. Phylogenetic origin was associated with differences in learning in extinction. Our results contradict our hypothesis and indicate that the selection for productivity traits has led to changes in learning behavior and the high productive laying hens possessed a better learning strategy compared to moderate productive hens in a feeding-rewarding context. This better performance may be a response to constraints resulting from high selection as it may enable these hens to efficiently acquire additional energy resources. Underlying mechanisms for this may be directly related to differences in neuronal structure or indirectly to foraging strategies and changes in personality traits such as fearfulness and sociality.

Distinguishing industrial meat from that of indigenous chickens with molecular markers

The aim of investigation was to evaluate a traceability system to detect industrial chicken meat among indigenous products, considering issues that could affect assignment accuracy. The dataset included 2 Italian indigenous meat breeds, namely Bionda Piemontese (2 ecotypes) and Bianca di Saluzzo, one broiler line, and 3 layer lines. Assignment tests were performed using a standard panel of 28 microsatellite loci. To evaluate effects of inbreeding and substructure on assignment accuracy, a simulated dataset was prepared. Broilers and layers belong to homogeneous populations and never enter the clusters of indigenous breeds. Ambiguity or misallocation are expected between the Bionda ecotypes and between the 2 indigenous breeds, but it is unlikely that niche products provided by Bionda and Bianca will compete with one another. Non-random mating reduces accuracy, but only populations having weak genetic differentiation are involved, namely those that are less interesting to discriminate. The dataset can be used as a reference population to distinguish commercial meat from indigenous meat with great accuracy. Misallocations increase as number of loci decreases, but only within or between the indigenous breeds. A subpanel of the most resolving 14 loci keeps sufficient informative content to provide accuracy and to correctly allocate additional test samples within the reference population. This analytical tool is economically sustainable as a method to detect fraud or mislabeling. Adoption of a monitoring system should increase the value of typical products because the additional burden of molecular analyses would improve commercial grade and perception of quality.

Efficiency of different strategies to mitigate ascertainment bias when using SNP panels in diversity studies

Background

Single nucleotide polymorphism (SNP) panels have been widely used to study genomic variations within and between populations. Methods of SNP discovery have been a matter of debate for their potential of introducing ascertainment bias, and genetic diversity results obtained from the SNP genotype data can be misleading. We used a total of 42 chicken populations where both individual genotyped array data and pool whole genome resequencing (WGS) data were available. We compared allele frequency distributions and genetic diversity measures (expected heterozygosity (H_e), fixation index (F_ST) values, genetic distances and principal components analysis (PCA)) between the two data types. With the array data, we applied different filtering options (SNPs polymorphic in samples of two Gallus gallus wild populations, linkage disequilibrium (LD) based pruning and minor allele frequency (MAF) filtering, and combinations thereof) to assess their potential to mitigate the ascertainment bias.

Results

Rare SNPs were underrepresented in the array data. Array data consistently overestimated H_e compared to WGS data, however, with a similar ranking of the breeds, as demonstrated by Spearman’s rank correlations ranging between 0.956 and 0.985. LD based pruning resulted in a reduced overestimation of H_e compared to the other filters and slightly improved the relationship with the WGS results. The raw array data and those with polymorphic SNPs in the wild samples underestimated pairwise F_ST values between breeds which had low F_ST (<0.15) in the WGS, and overestimated this parameter for high WGS F_ST (>0.15). LD based pruned data underestimated F_ST in a consistent manner. The genetic distance matrix from LD pruned data was more closely related to that of WGS than the other array versions. PCA was rather robust in all array versions, since the population structure on the PCA plot was generally well captured in comparison to the WGS data.

Conclusions

Among the tested filtering strategies, LD based pruning was found to account for the effects of ascertainment bias in the relatively best way, producing results which are most comparable to those obtained from WGS data and therefore is recommended for practical use.

Electronic supplementary material

The online version of this article (doi: 10.1186/s12864-017-4416-9) contains supplementary material, which is available to authorized users.

Genomic Comparison of Indigenous African and Northern European Chickens Reveals Putative Mechanisms of Stress Tolerance Related to Environmental Selection Pressure

Global climate change is increasing the magnitude of environmental stressors, such as temperature, pathogens, and drought, that limit the survivability and sustainability of livestock production. Poultry production and its expansion is dependent upon robust animals that are able to cope with stressors in multiple environments. Understanding the genetic strategies that indigenous, noncommercial breeds have evolved to survive in their environment could help to elucidate molecular mechanisms underlying biological traits of environmental adaptation. We examined poultry from diverse breeds and climates of Africa and Northern Europe for selection signatures that have allowed them to adapt to their indigenous environments. Selection signatures were studied using a combination of population genomic methods that employed F_ST, integrated haplotype score (iHS), and runs of homozygosity (ROH) procedures. All the analyses indicated differences in environment as a driver of selective pressure in both groups of populations. The analyses revealed unique differences in the genomic regions under selection pressure from the environment for each population. The African chickens showed stronger selection toward stress signaling and angiogenesis, while the Northern European chickens showed more selection pressure toward processes related to energy homeostasis. The results suggest that chromosomes 2 and 27 are the most diverged between populations and the most selected upon within the African (chromosome 27) and Northern European (chromosome 2) birds. Examination of the divergent populations has provided new insight into genes under possible selection related to tolerance of a population’s indigenous environment that may be baselines for examining the genomic contribution to tolerance adaptions.

Maternal genealogical patterns of chicken breeds sampled in Europe

The aim of this study was to investigate the maternal genealogical pattern of chicken breeds sampled in Europe. Sequence polymorphisms of 1256 chickens of the hypervariable region (D-loop) of mitochondrial DNA (mtDNA) were used. Median-joining networks were constructed to establish evolutionary relationships among mtDNA haplotypes of chickens, which included a wide range of breeds with different origin and history. Chicken breeds which have had their roots in Europe for more than 3000 years were categorized by their founding regions, encompassing Mediterranean type, East European type and Northwest European type. Breeds which were introduced to Europe from Asia since the mid-19th century were classified as Asian type, and breeds based on crossbreeding between Asian breeds and European breeds were classified as Intermediate type. The last group, Game birds, included fighting birds from Asia. The classification of mtDNA haplotypes was based on Liu et al.'s (2006) nomenclature. Haplogroup E was the predominant clade among the European chicken breeds. The results showed, on average, the highest number of haplotypes, highest haplotype diversity, and highest nucleotide diversity for Asian type breeds, followed by Intermediate type chickens. East European and Northwest European breeds had lower haplotype and nucleotide diversity compared to Mediterranean, Intermediate, Game and Asian type breeds. Results of our study support earlier findings that chicken breeds sampled in Europe have their roots in the Indian subcontinent and East Asia. This is consistent with historical and archaeological evidence of chicken migration routes to Europe.

Effects of Long-term Graded L-arginine Supply on Growth Development, Egg Laying and Egg Quality in Four Genetically Diverse Purebred Layer Lines

The present study was conducted to examine effects of long-term graded L-arginine supply on growth development, egg laying and egg quality in four genetically diverse purebred layer lines. The study comprised a rearing trial from hatch to week 16 and a following laying performance trial from week 17 to 41. After hatch 150 one-day-old female chicks of each genotype were distributed to three diets. The experimental diets were equivalent to 70, 100 and 200% L-arginine of age-specific recommended level (National Research Council, 1994) and were offered ad libitum to chicks (hatch to week 7), pullets (week 8 to 16) and hens (week 17 to 41). However, hens' diets were quite low in crude protein. After a pre-laying period from week 17 to 21 thirty-six pullets of each group were used further in the laying performance trial. Independent of chicken's genetic background, insufficient L-arginine supply caused lower body weight, daily weight gain and daily feed intake during the rearing (p<0.001) and induced lower laying intensity and daily egg mass production in the laying period (p<0.05). Parameters fitted to Gompertz function suggested higher adult body weight in L-arginine supplemented birds compared to insufficient supplied ones (p<0.01). Groups fed with insufficient L-arginine reached age of maximum daily weight gain later and showed lowest maximum daily weight gain (p<0.001). As a consequence of limitations in dietary L-arginine and crude protein, high performing genotypes decreased strongly in body weight, daily feed intake and performance compared to the low performing genotypes. In conclusion, L-arginine modified the amount of weight gain and feed intake, especially in growing chicks and pullets independent of genetic background. The high performing hens were more nutritionally stressed than the low performing ones, because concentrations of dietary crude protein were relatively low.