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

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cg.authorship.typesCGIAR and advanced research instituteen
cg.contributor.affiliationInternational Livestock Research Instituteen
cg.contributor.affiliationWageningen University & Researchen
cg.contributor.affiliationUniversity of Nottinghamen
cg.contributor.donorWageningen University and Researchen
cg.contributor.donorKoepon Foundationen
cg.contributor.donorBill & Melinda Gates Foundationen
cg.contributor.donorCGIAR Trust Funden
cg.contributor.initiativeSustainable Animal Productivity
cg.coverage.countryEthiopia
cg.coverage.iso3166-alpha2ET
cg.coverage.regionAfrica
cg.coverage.regionEastern Africa
cg.creator.identifierFasil Getachew Kebede: 0000-0003-2719-5576
cg.creator.identifierTadelle Dessie: 0000-0002-1630-0417
cg.creator.identifierOlivier Hanotte: 0000-0002-2877-4767
cg.howPublishedFormally Publisheden
cg.identifier.doihttps://doi.org/10.1186/s12864-024-10193-6en
cg.isijournalISI Journalen
cg.issn1471-2164en
cg.issue1en
cg.journalBMC Genomicsen
cg.reviewStatusPeer Reviewen
cg.subject.actionAreaResilient Agrifood Systems
cg.subject.ilriANIMAL BREEDINGen
cg.subject.ilriCHICKENSen
cg.subject.ilriGENETICSen
cg.subject.ilriINDIGENOUS BREEDSen
cg.subject.impactAreaPoverty reduction, livelihoods and jobs
cg.volume25en
dc.contributor.authorGetachew, Fasilen
dc.contributor.authorDerks, M.F.L.en
dc.contributor.authorDessie, Tadelleen
dc.contributor.authorHanotte, Olivier H.en
dc.contributor.authorBarros, C.P.en
dc.contributor.authorCrooijmans, R.P.M.A.en
dc.contributor.authorKomen, H.en
dc.contributor.authorBastiaansen, J.W.M.en
dc.date.accessioned2024-05-16T11:48:47Zen
dc.date.available2024-05-16T11:48:47Zen
dc.identifier.urihttps://hdl.handle.net/10568/141869
dc.titleLandscape genomics reveals regions associated with adaptive phenotypic and genetic variation in Ethiopian indigenous chickensen
dcterms.abstractClimate change is a threat to sustainable livestock production and livelihoods in the tropics. It has adverse impacts on feed and water availability, disease prevalence, production, environmental temperature, and biodiversity. Unravelling the drivers of local adaptation and understanding the underlying genetic variation in random mating indigenous livestock populations informs the design of genetic improvement programmes that aim to increase productivity and resilience. In the present study, we combined environmental, genomic, and phenotypic information of Ethiopian indigenous chickens to investigate their environmental adaptability. Through a hybrid sampling strategy, we captured wide biological and ecological variabilities across the country. Our environmental dataset comprised mean values of 34 climatic, vegetation and soil variables collected over a thirty-year period for 260 geolocations. Our biological dataset included whole genome sequences and quantitative measurements (on eight traits) from 513 individuals, representing 26 chicken populations spread along 4 elevational gradients (6–7 populations per gradient). We performed signatures of selection analyses ( and XP-EHH) to detect footprints of natural selection, and redundancy analyses (RDA) to determine genotype-environment and genotype-phenotype-associations. RDA identified 1909 outlier SNPs linked with six environmental predictors, which have the highest contributions as ecological drivers of adaptive phenotypic variation. The same method detected 2430 outlier SNPs that are associated with five traits. A large overlap has been observed between signatures of selection identified by and XP-EHH showing that both methods target similar selective sweep regions. Average genetic differences measured by are low between gradients, but XP-EHH signals are the strongest between agroecologies. Genes in the calcium signalling pathway, those associated with the hypoxia-inducible factor (HIF) transcription factors, and sports performance (GALNTL6) are under selection in high-altitude populations. Our study underscores the relevance of landscape genomics as a powerful interdisciplinary approach to dissect adaptive phenotypic and genetic variation in random mating indigenous livestock populations.en
dcterms.accessRightsOpen Access
dcterms.audienceCGIARen
dcterms.audienceDonorsen
dcterms.audienceScientistsen
dcterms.available2024-03-18
dcterms.bibliographicCitationGetachew, F., Derks, M.F.L., Dessie, T., Hanotte, O., Barros, C.P., Crooijmans, R.P.M.A., Komen, H. and Bastiaansen, J.W.M. 2024. Landscape genomics reveals regions associated with adaptive phenotypic and genetic variation in Ethiopian indigenous chickens. BMC Genomics 25:284.en
dcterms.issued2024
dcterms.languageen
dcterms.licenseCC-BY-4.0
dcterms.publisherSpringer Science and Business Media LLCen
dcterms.subjectanimal breedingen
dcterms.subjectgeneticsen
dcterms.subjectchickensen
dcterms.subjectindigenous breedsen
dcterms.typeJournal Article

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