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

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dc.contributor.authorFleming, Damarius S.en
dc.contributor.authorWeigend, Steffenen
dc.contributor.authorSimianer, Henneren
dc.contributor.authorWeigend, Annetten
dc.contributor.authorRothschild, Max F.en
dc.contributor.authorSchmidt, Carl J.en
dc.contributor.authorAshwell, Christopher M.en
dc.contributor.authorPersia, Michael E.en
dc.contributor.authorReecy, Jamesen
dc.contributor.authorLamont, Susan J.en
dc.contributor.departmentAnimal and Poultry Sciencesen
dc.date.accessioned2019-12-20T18:33:29Zen
dc.date.available2019-12-20T18:33:29Zen
dc.date.issued2017-05en
dc.description.abstractGlobal 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 FST, 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.en
dc.description.notesThe authors thank the Synbreed diversity panel consortium and its collaborators for graciously providing the data on the multiple breeds used in these analyses: Egypt-Asmaa Abushady, Faculty of Agriculture, Ain Shams University, Cairo; Ethiopia-Raed Al-Atiyat, King Saud University, Riyadh and Olivier Hanotte, School of Biology, University of Nottingham, United Kingdom; Sudan-Mohyeldein Berima, University of Khartoum Shambat Centre, North Sudan; Tanzania-Charles Lyimo, Sokoine University of Agriculture, Morogoro; Zimbabwe-Farai Muchdeyi, University of Harare; Finland and Norway-Miika Tapio and Asko Maki-Tanila, Natural Resources Institute Finland (Luke), Jokioinen; and Iceland and Poland-samples were taken from the Development of Strategy and Application of Molecular Tools to Assess Biodiversity in Chicken Genetic Resources (AVIANDIV) project (http://w3.tzv.fal.de/). The authors also acknowledge the technical support and expertise provided by Elyn Fritz-Waters for assistance in the creation of in-house scripts for analysis and Dorian Garrick and students for assistance with GenSel program usage. Funding was provided by a United States Department of Agriculture (USDA), National Institute of Food and Agriculture, Agriculture and Food Research Initiative Climate Change Award (#2011-67003-30228) and a USDA National Needs training grant (#2001-38420-20050) to D.S.F. The authors declare that there are no competing interests.en
dc.description.sponsorshipUnited States Department of Agriculture (USDA), National Institute of Food and Agriculture, Agriculture and Food Research Initiative [2011-67003-30228]; USDAUnited States Department of Agriculture (USDA) [2001-38420-20050]en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1534/g3.117.041228en
dc.identifier.eissn2160-1836en
dc.identifier.issue5en
dc.identifier.pmid28341699en
dc.identifier.urihttp://hdl.handle.net/10919/96172en
dc.identifier.volume7en
dc.language.isoenen
dc.publisherGenetics Society of Americaen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjecttoleranceen
dc.subjectselective pressureen
dc.subjectgenomic variationen
dc.subjectadaptationen
dc.subjectenvironmenten
dc.titleGenomic Comparison of Indigenous African and Northern European Chickens Reveals Putative Mechanisms of Stress Tolerance Related to Environmental Selection Pressureen
dc.title.serialG3-Genes Genomes Geneticsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen

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