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Nawaz AH, Setthaya P, Feng C. Exploring Evolutionary Adaptations and Genomic Advancements to Improve Heat Tolerance in Chickens. Animals (Basel) 2024; 14:2215. [PMID: 39123741 PMCID: PMC11311085 DOI: 10.3390/ani14152215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
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.
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Affiliation(s)
- Ali Hassan Nawaz
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China;
| | - Phatthawin Setthaya
- Multidisciplinary Research Institute, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Chungang Feng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China;
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Desta TT, Wakeyo O. Breeding practice of indigenous village chickens, and traits and breed preferences of smallholder farmers. Vet Med Sci 2024; 10:e1517. [PMID: 38952253 PMCID: PMC11217597 DOI: 10.1002/vms3.1517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 05/18/2024] [Accepted: 06/10/2024] [Indexed: 07/03/2024] Open
Abstract
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.
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Affiliation(s)
- Takele Taye Desta
- Wolaita Sodo AgriculturalTechnical, VocationalEducation and Training CollegeSodoEthiopia
- Present address:
Department of Biology, College of Science and Mathematics EducationKotebe University of EducationAddis AbabaEthiopia
| | - Oli Wakeyo
- Wolaita Sodo AgriculturalTechnical, VocationalEducation and Training CollegeSodoEthiopia
- Present address:
College of Agriculture and Environmental ScienceArsi UniversityAselaEthiopia
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Yussif I, Kugonza DR, Okot MW, Amuge PO, Costa R, Dos Anjos F. Uganda chicken genetic resources: I. phenotypic and production characteristics. Front Genet 2023; 13:1033031. [PMID: 36761692 PMCID: PMC9902952 DOI: 10.3389/fgene.2022.1033031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/29/2022] [Indexed: 01/25/2023] Open
Abstract
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.
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Affiliation(s)
- Illyass Yussif
- College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda,*Correspondence: Illyass Yussif,
| | - Donald Rugira Kugonza
- College of Agricultural and Environmental Sciences, Makerere University, Kampala, Uganda
| | | | | | | | - Filomena Dos Anjos
- Faculty of Veterinary Medicine, Eduardo Mondlane University, Maputo, Mozambique
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Chebo C, Betsha S, Melesse A. Chicken genetic diversity, improvement strategies and impacts on egg productivity in Ethiopia: a review. WORLD POULTRY SCI J 2022. [DOI: 10.1080/00439339.2022.2067020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Chencha Chebo
- Department of Animal Science, Arba Minch University, College of Agricultural Sciences, Arba Minch, Ethiopia
- School of Animal & Range Sciences, Hawassa University, College of Agriculture, Hawassa, Ethiopia
| | - Simret Betsha
- School of Animal & Range Sciences, Hawassa University, College of Agriculture, Hawassa, Ethiopia
| | - Aberra Melesse
- School of Animal & Range Sciences, Hawassa University, College of Agriculture, Hawassa, Ethiopia
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Lawal RA, Hanotte O. Domestic chicken diversity: Origin, distribution, and adaptation. Anim Genet 2021; 52:385-394. [PMID: 34060099 DOI: 10.1111/age.13091] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2021] [Indexed: 12/13/2022]
Abstract
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.
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Affiliation(s)
- R A Lawal
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.,The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - O Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.,Centre for Tropical Livestock Genetics and Health, The Roslin Institute, Edinburgh, EH25 9RG, UK.,LiveGene, International Livestock Research Institute (ILRI), P.O. 5689, Addis Ababa, Ethiopia
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Sustainable intensification of indigenous village chicken production system: matching the genotype with the environment. Trop Anim Health Prod 2021; 53:337. [PMID: 34021847 DOI: 10.1007/s11250-021-02773-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/08/2021] [Indexed: 10/21/2022]
Abstract
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.
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Desta TT. The genetic basis and robustness of naked neck mutation in chicken. Trop Anim Health Prod 2021; 53:95. [PMID: 33415443 DOI: 10.1007/s11250-020-02505-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/03/2020] [Indexed: 10/22/2022]
Abstract
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.
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Affiliation(s)
- Takele Taye Desta
- Department of Biology, College of Natural and Computational Science, Kotebe Metropolitan University, Addis Ababa, Ethiopia.
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8
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Desta TT. Indigenous village chicken production: a tool for poverty alleviation, the empowerment of women, and rural development. Trop Anim Health Prod 2020; 53:1. [DOI: 10.1007/s11250-020-02433-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 10/06/2020] [Indexed: 11/30/2022]
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Banos G, Lindsay V, Desta TT, Bettridge J, Sanchez-Molano E, Vallejo-Trujillo A, Matika O, Dessie T, Wigley P, Christley RM, Kaiser P, Hanotte O, Psifidi A. Integrating Genetic and Genomic Analyses of Combined Health Data Across Ecotypes to Improve Disease Resistance in Indigenous African Chickens. Front Genet 2020; 11:543890. [PMID: 33193617 PMCID: PMC7581896 DOI: 10.3389/fgene.2020.543890] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 09/04/2020] [Indexed: 12/30/2022] Open
Abstract
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.
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Affiliation(s)
- Georgios Banos
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
- Scotland’s Rural College, Edinburgh, United Kingdom
- Centre for Tropical Livestock Genetics and Health, Edinburgh, United Kingdom
| | - Victoria Lindsay
- Royal Veterinary College, University of London, London, United Kingdom
| | - Takele T. Desta
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Judy Bettridge
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
- LiveGene – Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Addis Ababa, Ethiopia
- Natural Resources Institute, University of Greenwich, London, United Kingdom
| | | | | | - Oswald Matika
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Tadelle Dessie
- LiveGene – Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Paul Wigley
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Robert M. Christley
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Peter Kaiser
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Olivier Hanotte
- Centre for Tropical Livestock Genetics and Health, Edinburgh, United Kingdom
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- LiveGene – Centre for Tropical Livestock Genetics and Health, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Androniki Psifidi
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
- Centre for Tropical Livestock Genetics and Health, Edinburgh, United Kingdom
- Royal Veterinary College, University of London, London, United Kingdom
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Lawal RA, Martin SH, Vanmechelen K, Vereijken A, Silva P, Al-Atiyat RM, Aljumaah RS, Mwacharo JM, Wu DD, Zhang YP, Hocking PM, Smith J, Wragg D, Hanotte O. The wild species genome ancestry of domestic chickens. BMC Biol 2020; 18:13. [PMID: 32050971 PMCID: PMC7014787 DOI: 10.1186/s12915-020-0738-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/08/2020] [Indexed: 01/28/2023] Open
Abstract
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.
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Affiliation(s)
- Raman Akinyanju Lawal
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
- Present Address: The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA.
| | - Simon H Martin
- Present Address: Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
| | - Koen Vanmechelen
- Open University of Diversity - Mouth Foundation, Hasselt, Belgium
| | - Addie Vereijken
- Technology and Service B.V., Hendrix Genetics, P.O. Box 114, 5830 AC, Boxmeer, The Netherlands
| | - Pradeepa Silva
- Department of Animal Science, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | - Raed Mahmoud Al-Atiyat
- Genetics and Biotechnology, Animal Science Department, Agriculture Faculty, Mutah University, Karak, Jordan
| | | | - Joram M Mwacharo
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), P.O. Box 5689, ILRI-Ethiopia Campus, Addis Ababa, Ethiopia
| | - Dong-Dong Wu
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Ya-Ping Zhang
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Paul M Hocking
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - David Wragg
- Centre for Tropical Livestock Genetics and Health, The Roslin Institute, Edinburgh, EH25 9RG, UK
| | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
- Centre for Tropical Livestock Genetics and Health, The Roslin Institute, Edinburgh, EH25 9RG, UK.
- LiveGene, International Livestock Research Institute (ILRI), P. O. 5689, Addis Ababa, Ethiopia.
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12
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Otecko NO, Ogali I, Ng'ang'a SI, Mauki DH, Ogada S, Moraa GK, Lichoti J, Agwanda B, Peng MS, Ommeh SC, Zhang YP. Phenotypic and morphometric differentiation of indigenous chickens from Kenya and other tropical countries augments perspectives for genetic resource improvement and conservation. Poult Sci 2019; 98:2747-2755. [PMID: 30850827 PMCID: PMC6591685 DOI: 10.3382/ps/pez097] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 02/25/2019] [Indexed: 12/20/2022] Open
Abstract
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.
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Affiliation(s)
- Newton O Otecko
- Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Sino-Africa Joint Research Center, Jomo Kenyatta University of Agriculture and Technology, Nairobi 00200, Kenya
| | - Irene Ogali
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi 00200, Kenya.,Veterinary Research Institute, Kenya Agriculture and Livestock Research Organization, Nairobi 00200, Kenya
| | - Said I Ng'ang'a
- Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, 650223, China
| | - David H Mauki
- Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, 650223, China
| | - Stephen Ogada
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi 00200, Kenya.,Sino-Africa Joint Research Center, Jomo Kenyatta University of Agriculture and Technology, Nairobi 00200, Kenya
| | - Grace K Moraa
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi 00200, Kenya.,Sino-Africa Joint Research Center, Jomo Kenyatta University of Agriculture and Technology, Nairobi 00200, Kenya
| | - Jacqueline Lichoti
- Directorate of Veterinary Services, State Department of Livestock, Ministry of Agriculture, Livestock and Fisheries, Nairobi 00625, Kenya
| | - Bernard Agwanda
- Department of Zoology, National Museums of Kenya, Nairobi 00100, Kenya
| | - Min-Shen Peng
- Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, 650223, China
| | - Sheila C Ommeh
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi 00200, Kenya.,Sino-Africa Joint Research Center, Jomo Kenyatta University of Agriculture and Technology, Nairobi 00200, Kenya
| | - Ya-Ping Zhang
- Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, 650223, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
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Bettridge JM, Psifidi A, Terfa ZG, Desta TT, Lozano-Jaramillo M, Dessie T, Kaiser P, Wigley P, Hanotte O, Christley RM. The role of local adaptation in sustainable village chicken production. NATURE SUSTAINABILITY 2018; 1:574-582. [PMID: 30411000 PMCID: PMC6217978 DOI: 10.1038/s41893-018-0150-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 09/04/2018] [Indexed: 06/08/2023]
Abstract
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.
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Affiliation(s)
- Judy M. Bettridge
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, CH64 7TE, United Kingdom
- LiveGene - CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- International Livestock Research Institute, P.O. Box 30709-00100, Nairobi, Kenya
| | - Androniki Psifidi
- The Roslin Institute and Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
- Department of Clinical Sciences and Services, Royal Veterinary College, University of London, Hatfield, UK
| | - Zelalem G. Terfa
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, CH64 7TE, United Kingdom
- LiveGene - CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Takele T. Desta
- LiveGene - CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Maria Lozano-Jaramillo
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, NL-6700 AH Wageningen, the Netherlands
| | - Tadelle Dessie
- LiveGene - CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Pete Kaiser
- The Roslin Institute and Royal (Dick) School of Veterinary Science, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - Paul Wigley
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, CH64 7TE, United Kingdom
| | - Olivier Hanotte
- LiveGene - CTLGH, International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Robert M. Christley
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, CH64 7TE, United Kingdom
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Terfa ZG, Garikipati S, Kassie G, Bettridge JM, Christley RM. Eliciting preferences for attributes of Newcastle disease vaccination programmes for village poultry in Ethiopia. Prev Vet Med 2018; 158:146-151. [PMID: 30220388 PMCID: PMC6152585 DOI: 10.1016/j.prevetmed.2018.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 07/12/2018] [Accepted: 08/14/2018] [Indexed: 12/02/2022]
Abstract
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.
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Affiliation(s)
- Z G Terfa
- Management School, University of Liverpool, Chatham Street, Liverpool L69 7ZH, UK; Institute of Infection and Global Health, Department of Epidemiology and Population Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, Cheshire CH64 7TE, UK.
| | - S Garikipati
- Management School, University of Liverpool, Chatham Street, Liverpool L69 7ZH, UK
| | - G Kassie
- ICARDA, ICARDA c/o ILRI, P.O. Box 5689, Addis Ababa, Ethiopia
| | - J M Bettridge
- Institute of Infection and Global Health, Department of Epidemiology and Population Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, Cheshire CH64 7TE, UK
| | - R M Christley
- Institute of Infection and Global Health, Department of Epidemiology and Population Health, University of Liverpool, Leahurst Campus, Chester High Road, Neston, Cheshire CH64 7TE, UK
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15
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Lawal RA, Al-Atiyat RM, Aljumaah RS, Silva P, Mwacharo JM, Hanotte O. Whole-Genome Resequencing of Red Junglefowl and Indigenous Village Chicken Reveal New Insights on the Genome Dynamics of the Species. Front Genet 2018; 9:264. [PMID: 30079080 PMCID: PMC6062655 DOI: 10.3389/fgene.2018.00264] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/29/2018] [Indexed: 12/13/2022] Open
Abstract
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.
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Affiliation(s)
- Raman A. Lawal
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Raed M. Al-Atiyat
- Genetics and Biotechnology, Animal Science Department, Agriculture Faculty, Mutah University, Karak, Jordan
- Animal Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Riyadh S. Aljumaah
- Animal Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Pradeepa Silva
- Department of Animal Sciences, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | - Joram M. Mwacharo
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas, Addis Ababa, Ethiopia
| | - Olivier Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
- LiveGene – CTLGH, International Livestock Research Institute, Addis Ababa, Ethiopia
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16
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Goto T, Tsudzuki M. Genetic Mapping of Quantitative Trait Loci for Egg Production and Egg Quality Traits in Chickens: a Review. J Poult Sci 2017; 54:1-12. [PMID: 32908402 PMCID: PMC7477176 DOI: 10.2141/jpsa.0160121] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/24/2016] [Indexed: 12/11/2022] Open
Abstract
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.
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Affiliation(s)
- Tatsuhiko Goto
- Genetics, Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
- Present address: Department of Life Science and Agriculture, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido 080-8555, Japan
| | - Masaoki Tsudzuki
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
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17
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Psifidi A, Banos G, Matika O, Desta TT, Bettridge J, Hume DA, Dessie T, Christley R, Wigley P, Hanotte O, Kaiser P. Genome-wide association studies of immune, disease and production traits in indigenous chicken ecotypes. Genet Sel Evol 2016; 48:74. [PMID: 27687164 PMCID: PMC5041578 DOI: 10.1186/s12711-016-0252-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 09/15/2016] [Indexed: 12/24/2022] Open
Abstract
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.
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Affiliation(s)
- Androniki Psifidi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - Georgios Banos
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.,Scotland's Rural College, Easter Bush, Edinburgh, Midlothian, EH25 9RG, UK
| | - Oswald Matika
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Takele T Desta
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Judy Bettridge
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Liverpool, CH64 7TE, UK
| | - David A Hume
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Tadelle Dessie
- International Livestock Research Institute, P.O. Box 5689, Addis Ababa, Ethiopia
| | - Rob Christley
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Liverpool, CH64 7TE, UK
| | - Paul Wigley
- Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Liverpool, CH64 7TE, UK
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.,International Livestock Research Institute, P.O. Box 5689, Addis Ababa, Ethiopia
| | - Pete Kaiser
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
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18
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Dahloum L, Moula N, Halbouche M, Mignon-Grasteau S. Phenotypic characterization of the indigenous chickens <i>(Gallus gallus)</i> in the northwest of Algeria. Arch Anim Breed 2016. [DOI: 10.5194/aab-59-79-2016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
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.
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Wragg D, Mason AS, Yu L, Kuo R, Lawal RA, Desta TT, Mwacharo JM, Cho CY, Kemp S, Burt DW, Hanotte O. Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken. BMC Genomics 2015; 16:784. [PMID: 26466991 PMCID: PMC4607243 DOI: 10.1186/s12864-015-1954-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/02/2015] [Indexed: 12/11/2022] Open
Abstract
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.
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Affiliation(s)
- David Wragg
- Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
- Institut National de la Recherche Agronomique (INRA), UMR 1338 GenPhySE, 31326, Castanet-Tolosan, France.
| | - Andrew S Mason
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, Edinburgh, UK.
| | - Le Yu
- GAIC Co. Ltd. Jing Chen Buiding, Science Park, South Street, Chao Yang District, Beijing, People's Republic Popular of China.
| | - Richard Kuo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, Edinburgh, UK.
| | - Raman A Lawal
- Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
| | - Takele Taye Desta
- Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
| | - Joram M Mwacharo
- Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
- International Centre for Agricultural Research in Dry Areas, c/o International Livestock Research Institute, Addis Ababa, Ethiopia.
| | - Chang-Yeon Cho
- Animal Genetic Resources Station, National Institute of Animal Science, Namwon, Republic of Korea.
| | - Steve Kemp
- International Livestock Research Institute, Naivasha Road, P.O. Box 30709, Nairobi, Kenya.
| | - David W Burt
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, Edinburgh, UK.
| | - Olivier Hanotte
- Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
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Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res 2015; 145:78-179. [PMID: 26282327 PMCID: PMC5120589 DOI: 10.1159/000430927] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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