Signature of artificial selection and ecological landscape on morphological structures of Ethiopian village chickens

Exploring Evolutionary Adaptations and Genomic Advancements to Improve Heat Tolerance in Chickens

Climate change poses a significant threat to the poultry industry, especially in hot climates that adversely affect chicken growth, development, and productivity through heat stress. This literature review evaluates the evolutionary background of chickens with the specific genetic characteristics that can help chickens to cope with hot conditions. Both natural selection and human interventions have influenced the genetic characteristics of the breeds used in the current poultry production system. The domestication of chickens from the Red junglefowl (Gallus gallus) has resulted in the development of various breeds with distinct genetic differences. Over the past few years, deliberate breeding for desirable traits (such as meat production and egg quality) in chickens has resulted in the emergence of various economically valuable breeds. However, this selective breeding has also caused a decrease in the genetic diversity of chickens, making them more susceptible to environmental stressors like heat stress. Consequently, the chicken breeds currently in use may possess a limited ability to adapt to challenging conditions, such as extreme heat. This review focuses on evaluating potential genes and pathways responsible for heat tolerance, including heat shock response, antioxidant defense systems, immune function, and cellular homeostasis. This article will also discuss the physiological and behavioral responses of chicken varieties that exhibit genetic resistance to heat, such as the naked neck and dwarf traits in different indigenous chickens. This article intends to review the current genomic findings related to heat tolerance in chickens that used methods such as the genome-wide association study (GWAS) and quantitative trait loci (QTL) mapping, offering valuable insights for the sustainability of poultry in the face of global warming.

Breeding practice of indigenous village chickens, and traits and breed preferences of smallholder farmers

BACKGROUND

Indigenous village chickens, or (IVCs), significantly contribute to rural livelihoods. Although natural selection has a disproportionate impact on the genetic structure of IVCs, farmers have developed locally tailored breeding practices to get the most out of their flocks.

OBJECTIVES

Small-scale farmers' insights on trait breed preferences and family flock breeding practices are presented in this cross-sectional study.

METHODS

A cross-sectional study was conducted in two agroecological zones using face-to-face individual interviews with 119 general informants.

RESULTS

Farmers prefer IVCs because they are multipurpose birds. Unlike policymakers, who usually underestimate the importance of IVCs, small-scale farmers acknowledge the coexistence of local and commercial chickens. Only 15.7% of farmers recruited homegrown cocks, whereas 47.9% outsourced breeding cocks from local markets and 36.4% from neighbours (χ-squared = 15.976, df = 2, p = 0.0003395). About 49.2% of small-scale farmers believed that consanguineous mating-induced inbreeding has only trivial effects. High flock turnover significantly reduces inbreeding. Regardless of the low production capacity, small-scale farmers prefer local (rank = 1.47) chickens to commercial (rank = 1.61). For cocks, fertility and growth traits were highly sought after, whereas for hens, maternal instincts and laying performance were prioritized. Compared to the highlands, the lowlands had a longer egg storage period (t = 2.677, df = 117, p = 0.009, 95% CI: -3.7607, -0.5622).

CONCLUSIONS

This study documented the wisdom of small-scale farmers and encouraged the incorporation of their insights into a sustainable genetic improvement program.

Uganda chicken genetic resources: I. phenotypic and production characteristics

The extent of diversity in the indigenous chicken breeds of Uganda was assessed for their potential utilisation in breeding programmes. A total of 293 indigenous-chicken-keeping households in villages across 35 districts forming 12 sub-regions of the four regions were randomly sampled for 586 mature chickens of both sexes. While only 20.8% of households were headed by women, 40.6% of indigenous chicken keepers were women. The production objectives mainly focused on chickens as sources of income from sales and household food. The chickens were predominantly managed in a scavenging (94.2%) feeding system in a mainly (96.9%) mixed crop-livestock system. The average flock size was 19.80 ± 1.21 chickens with 3.83 ± 0.29 laying hens, each producing an average of 13.41 ± 0.20 eggs/clutch and 40.3 ± 0.6 eggs/annum of 5.20 ± 0.03-month egg production age. Normal-feather strains predominated (>90%), with scattered incidences of naked neck, frizzles, polydactyl, and ptilopody traits in both sexes. Dark (49.0% hen; 43.8% cock) and white (38.3% hen; 42.4% cock) skin colours were most common among the chickens compared to yellow skin. However, yellow-coloured shanks were proportionally the most observed (41% cock; 29% hen). Orange and brown iris (eye) colours were the most common in both sexes. The hens commonly had small round earlobes with varying colours, while cocks had large oval-shaped, mainly red (70%) earlobes. The single-comb type was dominant in both sexes, with wattles almost universally present. Frizzle and polydactyl allele frequencies were significantly lower (p < 0.05) than the expected Mendelian proportions, indicating a possible state of endangerment. Meanwhile, the estimated allele frequencies of ptilopody, tufted-crest, and rose comb alleles in the population were similar (p > 0.05) to the expected Mendelian frequencies. However, these strains did not show any significant (p > 0.05) influence on the body weight or the linear morphometric estimates except for being marginally higher than the normal strains. The phenotypic correlations of body weight and morphometric traits ranged from 0.457 to 0.668 and 0.292 to 0.454 in cocks and hens, respectively. These findings provide hints about the prospects for improved performance with modifications in the production environment. The wide phenotypic diversity would support management efforts for their sustainable utilisation and preservation.

Domestic chicken diversity: Origin, distribution, and adaptation

Chicken is the most numerous among the domesticated livestock species. Across cultures, religions, and societies, chicken is widely accepted with little or no taboo compared to other domestic animals. Its adaptability to diverse environmental conditions and demonstrated potential for breeding improvement provide a unique genetic resource for addressing the challenges of food security in a world impacted by climatic change and human population growth. Recent studies, shedding new knowledge on the chicken genomes, have helped reconstruct its past evolutionary history. Here, we review the literature concerning the origin, dispersion, and adaptation of domestic chicken. We highlight the role of human and natural selection in shaping the diversity of the species and provide a few examples of knowledge gaps that may be the focus of future research.

Sustainable intensification of indigenous village chicken production system: matching the genotype with the environment

The multi-purpose indigenous village chickens (IVCs) are kept in low- and middle-income countries. IVCs are hardy and are resilient to disease, hostile environment, global warming, and climate change. The IVCs are a little impacted by anthropogenic effects; consequently, they possess high genetic and phenotypic diversity. Likewise, the genetic structure of IVCs is principally shaped by natural selection, which enables them to accumulate high genetic polymorphism and to adaptively radiate. Regardless of this, the genetic wealth of IVCs has been eroded by indiscriminate crossbreeding. Emerging infectious and non-infectious diseases, flawed assumptions, predation, inadequate nutrition, poorly maintained night enclosures, and underdeveloped market infrastructure, and the overlooked multiple-use values and unique attributes of IVCs have threatened their mere survival. The IVCs lay a few eggs and produce less meat, which cannot meet the growing (existing) demand. However, the demand for IVC products is growing attributable to the flavor and texture of eggs and meat, and they are well-aligned with the subsistence farming system. The several use values and ecosystem services provided by IVCs have been increasingly realized. Enhanced production can be attained through sustainable use of local (genetic) resources and by scaling up and out best practices. Genetic improvement needs to mainly rely upon IVC genetic resources and should have to match the genotype with the environment. Moreover, it has to maintain the genetic polymorphism that has been accumulated for time immemorial to respond to unanticipated changes in the production system and consumers' demand. In this review, enhanced management, selection strategies, and genetic crosses including the crossing of commercial chickens with red junglefowl have been proposed to sustainably intensify the IVC production system.

The genetic basis and robustness of naked neck mutation in chicken

Chicken is a homeothermic animal; consequently, regardless of fluctuation in weather conditions, it maintains constant body temperature. However, in hot regions and seasons, chickens suffer from heat stress. To dissipate excess heat, besides modifying the environment, which is costly, however, chickens with efficient heat dissipation capacity might be utilized. Naked neck chickens have a higher capacity for heat loss attributable to reduced feather mass. The naked neck mutation (Na) was originated from a large insertion (~ 180 bp) integrated ~ 260-kb downstream of a protein-coding gene-GDF7 (Growth Differentiation Factor 7). Na possesses a cis-regulatory function and upregulates the expression of GDF7-a gene that exhibits a tissue-specific effect by the sensitizing action of retinoic acid. Na suppresses the development of feathers in the neck and vent. Na shows autosomal incomplete dominance and regulates several developmental processes. Na usually segregates at low frequency, which might be attributed to limited socio-cultural preferences. Specifically, in hot and humid regions, although to a varying extent, Na enhances performance, immunocompetence, and resilience to disease both in the homozygous and heterozygous state. Occasionally, naked neck chickens (especially the homozygous ones) lose comparative advantage in cool environments. Homozygous Na also results in high embryo death and reduced hatchability and diminishes floating and flying capacity. Nevertheless, selective breeding of naked neck chickens for fertility traits enhances the performance and welfare of chickens in hot and humid regions. The comparative advantage of Na needs to be studied not only from a temperature perspective and under controlled experiment but also from humidity, body weight, feed intake (absolute and relative to body weight), age, agroecology insights, and under field condition. Due to the incomplete dominant expression pattern of Na, studies need to separately report their findings for homozygous and heterozygous naked neck chicken.

Integrating Genetic and Genomic Analyses of Combined Health Data Across Ecotypes to Improve Disease Resistance in Indigenous African Chickens

Poultry play an important role in the agriculture of many African countries. The majority of chickens in sub-Saharan Africa are indigenous, raised in villages under semi-scavenging conditions. Vaccinations and biosecurity measures rarely apply, and infectious diseases remain a major cause of mortality and reduced productivity. Genomic selection for disease resistance offers a potentially sustainable solution but this requires sufficient numbers of individual birds with genomic and phenotypic data, which is often a challenge to collect in the small populations of indigenous chicken ecotypes. The use of information across-ecotypes presents an attractive possibility to increase the relevant numbers and the accuracy of genomic selection. In this study, we performed a joint analysis of two distinct Ethiopian indigenous chicken ecotypes to investigate the genomic architecture of important health and productivity traits and explore the feasibility of conducting genomic selection across-ecotype. Phenotypic traits considered were antibody response to Infectious Bursal Disease (IBDV), Marek's Disease (MDV), Fowl Cholera (PM) and Fowl Typhoid (SG), resistance to Eimeria and cestode parasitism, and productivity [body weight and body condition score (BCS)]. Combined data from the two chicken ecotypes, Horro (n = 384) and Jarso (n = 376), were jointly analyzed for genetic parameter estimation, genome-wide association studies (GWAS), genomic breeding value (GEBVs) calculation, genomic predictions, whole-genome sequencing (WGS), and pathways analyses. Estimates of across-ecotype heritability were significant and moderate in magnitude (0.22-0.47) for all traits except for SG and BCS. GWAS identified several significant genomic associations with health and productivity traits. The WGS analysis revealed putative candidate genes and mutations for IBDV (TOLLIP, ANGPTL5, BCL9, THEMIS2), MDV (GRM7), SG (MAP3K21), Eimeria (TOM1L1) and cestodes (TNFAIP1, ATG9A, NOS2) parasitism, which warrant further investigation. Reliability of GEBVs increased compared to within-ecotype calculations but accuracy of genomic prediction did not, probably because the genetic distance between the two ecotypes offset the benefit from increased sample size. However, for some traits genomic prediction was only feasible in across-ecotype analysis. Our results generally underpin the potential of genomic selection to enhance health and productivity across-ecotypes. Future studies should establish the required minimum sample size and genetic similarity between ecotypes to ensure accurate joint genomic selection.

The wild species genome ancestry of domestic chickens

BACKGROUND

Hybridisation and introgression play key roles in the evolutionary history of animal species. They are commonly observed within several orders in wild birds. The domestic chicken Gallus gallus domesticus is the most common livestock species. More than 65 billion chickens are raised annually to produce meat and 80 million metric tons of egg for global human consumption by the commercial sector. Unravelling the origin of its genetic diversity has major application for sustainable breeding improvement programmes.

RESULTS

In this study, we report genome-wide analyses for signatures of introgression between indigenous domestic village chicken and the four wild Gallus species. We first assess the genome-wide phylogeny and divergence time across the genus Gallus. Genome-wide sequence divergence analysis supports a sister relationship between the Grey junglefowl G. sonneratii and Ceylon junglefowl G. lafayettii. Both species form a clade that is sister to the Red junglefowl G. gallus, with the Green junglefowl G. varius the most ancient lineage within the genus. We reveal extensive bidirectional introgression between the Grey junglefowl and the domestic chicken and to a much lesser extent with the Ceylon junglefowl. We identify a single case of Green junglefowl introgression. These introgressed regions include genes with biological functions related to development and immune system.

CONCLUSIONS

Our study shows that while the Red junglefowl is the main ancestral species, introgressive hybridisation episodes have impacted the genome and contributed to the diversity of the domestic chicken, although likely at different levels across its geographic range.

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 role of local adaptation in sustainable village chicken production

Village chickens are ubiquitous in smallholder farming systems, contributing to household, local and national economies under diverse environmental, economic and cultural settings. However, they are raised in challenging environments where productivity is low while mortality is high. There is much interest in utilizing indigenous genetic resources to produce a chicken resilient to its environment, whilst providing the basis of an economically sustainable enterprise. Globally, however, a wide variety of interventions have so far proved unable to deliver sustainable improvements. Here, we show that regional differences in trait preferences and parasite burden are associated with distinct chicken genepools, likely in response to interacting natural and human-driven (economic and social) selection pressures. Drivers of regional differences include marketing opportunities, cultural preferences, agro-ecologies and parasite populations, and are evident in system adaptations, such as management practices, population dynamics and bird genotypes. Our results provide sound multidisciplinary evidence to support previous observations that sustainable poultry development interventions for smallholder farmers, including breeding programs, should be locally tailored and designed for flexible implementation.

Eliciting preferences for attributes of Newcastle disease vaccination programmes for village poultry in Ethiopia

Newcastle disease (NCD) is an important disease of poultry, directly affecting the livelihoods of poor farmers across developing countries. Research has identified promising innovations in NCD vaccine development and field trials among village poultry have been promising. However, NCD vaccination is not currently part of village poultry extension programmes in many developing countries. Understanding the preferences for, and relative importance of, different attributes of potential vaccination programmes to prevent NCD will be crucial in designing acceptable and sustainable prevention programmes. This research employed the discrete choice experiment approach to elicit farmers' preference for attributes of NCD vaccination programmes for village poultry in rural Ethiopia. The choice experiment survey was conducted on 450 smallholder farmers. The relative importance of attributes of NCD vaccines to farmers was estimated using a random parameter logit regression model. The preferred NCD vaccine programme had greater bird-level protection (i.e. greater capacity to reduce mortality should NCD occur in a flock), was delivered by animal health development agents, and could be administered via drinking water. Results from simulations on changes in attribute levels revealed that bird-level protection capacity and delivery of vaccine by animal heath extension affect farmers' preferences more than other attributes. These findings suggest that it is important to ensure NCD vaccine programmes offer reasonable capacity to protect against mortality. It also suggests the need to understand farmers' preferred vaccine delivery mechanisms and route of vaccine administration for a wider acceptance of vaccine.

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.

Genetic Mapping of Quantitative Trait Loci for Egg Production and Egg Quality Traits in Chickens: a Review

Chickens display a wide spectrum of phenotypic variations in quantitative traits such as egg-related traits. Quantitative trait locus (QTL) analysis is a statistical method used to understand the relationship between phenotypic (trait measurements) and genotypic data (molecular markers). We have performed QTL analyses for egg-related traits using an original resource population based on the Japanese Large Game (Oh-Shamo) and the White Leghorn breeds of chickens. In this article, we summarize the results of our extensive QTL analyses for 11 and 66 traits for egg production and egg quality, respectively. We reveal that at least 30 QTL regions on 17 different chromosomes affect phenotypic variation in egg-related traits. Each locus had an age-specific effect on traits, and a variety in effects was also apparent, such as additive, dominance, and epistatic-interaction effects. Although genome-wide association study (GWAS) is suitable for gene-level resolution mapping of GWAS loci with additive effects, QTL mapping studies enable us to comprehensively understand genetic control, such as chromosomal regions, genetic contribution to phenotypic variance, mode of inheritance, and age-specificity of both common and rare alleles. QTL analyses also describe the relationship between genotypes and phenotypes in experimental populations. Accumulation of QTL information, including GWAS loci, is also useful for studies of population genomics approached without phenotypic data in order to validate the identified genomic signatures of positive selection. The combination of QTL studies and next-generation sequencing techniques with uncharacterized genetic resources will enhance current understanding of the relationship between genotypes and phenotypes in livestock animals.

Genome-wide association studies of immune, disease and production traits in indigenous chicken ecotypes

Background

The majority of chickens in sub-Saharan Africa are indigenous ecotypes, well adapted to the local environment and raised in scavenging production systems. Although they are generally resilient to disease challenge, routine vaccination and biosecurity measures are rarely applied and infectious diseases remain a major cause of mortality and reduced productivity. Management and genetic improvement programmes are hampered by lack of routine data recording. Selective breeding based on genomic technologies may provide the means to enhance sustainability. In this study, we investigated the genetic architecture of antibody response to four major infectious diseases [infectious bursal disease (IBDV), Marek’s disease (MDV), fowl typhoid (SG), fowl cholera (PM)] and resistance to Eimeria and cestode parasitism, along with two production traits [body weight and body condition score (BCS)] in two distinct indigenous Ethiopian chicken ecotypes. We conducted variance component analyses, genome-wide association studies, and pathway and selective sweep analyses.

Results

The large majority of birds was found to have antibody titres for all pathogens and were infected with both parasites, suggesting almost universal exposure. We derived significant moderate to high heritabilities for IBDV, MDV and PM antibody titres, cestodes infestation, body weight and BCS. We identified single nucleotide polymorphisms (SNPs) with genome-wide significance for each trait. Based on these associations, we identified for each trait, pathways, networks and functional gene clusters that include plausible candidate genes. Selective sweep analyses revealed a locus on chromosome 18 associated with viral antibody titres and resistance to Eimeria parasitism that is within a positive selection signal. We found no significant genetic correlations between production, immune and disease traits, implying that selection for altered antibody response and/or disease resistance will not affect production.

Conclusions

We confirmed the presence of genetic variability and identified SNPs significantly associated with immune, disease and production traits in indigenous village chickens. Results underpin the feasibility of concomitant genetic improvement for enhanced antibody response, resistance to parasitism and productivity within and across indigenous chicken ecotypes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-016-0252-7) contains supplementary material, which is available to authorized users.

Phenotypic characterization of the indigenous chickens <i>(Gallus gallus)</i> in the northwest of Algeria

Abstract. This study was conducted to characterize local chickens in the northwest of Algeria based on some phenotypic traits and to look at prediction of body weight from morphometric measurements (linear body). The results indicated that the predominant comb colour was dark red (77.8 %), followed by light red (22.2 %). Tarsus colour was either white (40.9 %), grey (31 %), yellow (15.39 %), dark (8.05 %), or green (4.51 %). Most chickens (81.7 %) had orange eyes, while 10.37 and 7.92 % had yellow and dark-brown eyes, respectively. The dominant earlobe colour was white (73.96 %), followed by red (16.81 %). The remaining proportion included yellow and red-mottled yellow and black earlobes. Proportions of the adaptive genes were low. Incidences of Na, F, Pti, Cr, R, and P genes were 8.82, 0.45, 1.22, 5.54, 3.35, and 4.7 %, respectively. The calculated gene frequencies ranged from 0.002 to 0.045. Variations were also found in quantitative morphological traits. Sex-associated differences (P < 0.001) were observed in almost all the parameters evaluated with higher values recorded for males. Phenotypic correlations of body weight and biometric traits ranged from −0.13 to 0.88 and −0.15 to 0.97 for males and females, respectively. From the factor analysis with varimax rotation of the intercorrelated traits, three principal components which accounted for 71.6 and 73.2 % of the total variance were extracted in males and females, respectively. Orthogonal body shape characters derived from the factor analysis accounted for 84.3 and 94.2 % of the variation in body weight of males and females, respectively. Information obtained from this study could be useful in an appropriate management, breeding programmes for selection and utilization of Algerian chicken genetic resources.

Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken

BACKGROUND

EAV-HP is an ancient retrovirus pre-dating Gallus speciation, which continues to circulate in modern chicken populations, and led to the emergence of avian leukosis virus subgroup J causing significant economic losses to the poultry industry. We mapped EAV-HP integration sites in Ethiopian village chickens, a Silkie, Taiwan Country chicken, red junglefowl Gallus gallus and several inbred experimental lines using whole-genome sequence data.

RESULTS

An average of 75.22 ± 9.52 integration sites per bird were identified, which collectively group into 279 intervals of which 5 % are common to 90 % of the genomes analysed and are suggestive of pre-domestication integration events. More than a third of intervals are specific to individual genomes, supporting active circulation of EAV-HP in modern chickens. Interval density is correlated with chromosome length (P < 2.31(-6)), and 27 % of intervals are located within 5 kb of a transcript. Functional annotation clustering of genes reveals enrichment for immune-related functions (P < 0.05).

CONCLUSIONS

Our results illustrate a non-random distribution of EAV-HP in the genome, emphasising the importance it may have played in the adaptation of the species, and provide a platform from which to extend investigations on the co-evolutionary significance of endogenous retroviral genera with their hosts.