Whole genome diversity of indigenous chicken populations in Ethiopia

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cg.authorship.typesCGIAR and developing country instituteen
cg.authorship.typesCGIAR and advanced research instituteen
cg.contributor.affiliationAddis Ababa Universityen
cg.contributor.affiliationAmhara Regional Agricultural Research Institute, Ethiopiaen
cg.contributor.affiliationInternational Livestock Research Instituteen
cg.contributor.affiliationUniversity of Edinburghen
cg.contributor.affiliationUniversity of Nottinghamen
cg.coverage.countryEthiopia
cg.coverage.iso3166-alpha2ET
cg.coverage.regionAfrica
cg.coverage.regionEastern Africa
cg.creator.identifierTadelle Dessie: 0000-0002-1630-0417
cg.creator.identifierOlivier Hanotte: 0000-0002-2877-4767
cg.howPublishedGrey Literatureen
cg.subject.ilriANIMAL BREEDINGen
cg.subject.ilriBREEDSen
cg.subject.ilriCHICKENSen
cg.subject.ilriPOULTRYen
cg.subject.ilriLIVESTOCKen
cg.subject.ilriINDIGENOUS BREEDSen
cg.subject.ilriGENETICSen
dc.contributor.authorKebede, A.en
dc.contributor.authorTesfaye, K.en
dc.contributor.authorBelay. G.en
dc.contributor.authorVallejo, A.en
dc.contributor.authorDessie, Tadelleen
dc.contributor.authorSpark, N.en
dc.contributor.authorHanotte, Olivier H.en
dc.contributor.authorRaman, L..en
dc.contributor.authorGheyas, Almas A.en
dc.date.accessioned2020-01-03T11:10:14Zen
dc.date.available2020-01-03T11:10:14Zen
dc.identifier.urihttps://hdl.handle.net/10568/106374
dc.titleWhole genome diversity of indigenous chicken populations in Ethiopiaen
dcterms.abstractIndigenous chicken makes most of the world’s poultry genetic diversity particularly in developing countries. These local breeds, which are well- adapted to extensive husbandry systems and suitable for resource-poor poultry farmers endowed with very limited means, should be thoroughly studied as a basis for enhancing their use and conservation. Understanding the link between genomic diversity and adaptability is opening the door to marker-assisted breed improvement programs. Here, we report the genomic diversity of Ethiopian indigenous chicken through discovery and characterization of 21 million SNPs (72% novel) from 27 indigenous chicken populations (n = 260 birds) using whole genome sequencing. In each population around 10 to12 million SNPs are present, of which, 40 - 47% are heterozygote. The mean SNP density for all population across all autosomes is 20 ± 5 per kb. It much lower, for he Z chromosome (mean = 21) and the W chromosomes (mean = 0.4). Principal component and admixture analyses suggest the presence of four ancestral gene pools across the populations. Over 46% of the SNPs are located within genes, of which exonic and intronic SNPs account for 1.59% and 43.94%, respectively; while 31% of the exonic SNPs are non-synonymous. A large proportion of SNPs has low alternative allele frequency (AAF < 10%), although this proportion is higher in exon for potentially harmful categories like missense and stop gain/loss (> 60%) compared to neutral genes (40-45%). Genes with deleterious missense variants are included within several important biological pathways including innate immunity. This study confirms the existence of significant genomic diversity in indigenous chicken populations of Ethiopia, with most of the variants previously undescribed in commercial breeds.en
dcterms.accessRightsLimited Access
dcterms.audienceScientistsen
dcterms.bibliographicCitationKebede, A., Tesfaye, K., Belay, G., Vallejo, A., Dessie, T., Spark, N., Hanotte, O., Raman, L., and Gheyas, A. 2019. Whole genome diversity of indigenous chicken populations in Ethiopia. Paper presented at the Seventh All Africa conference on Animal Agriculture, Accra, Ghana, 29 July-2 August 2019.en
dcterms.issued2019-08-02
dcterms.languageen
dcterms.subjectanimal breedingen
dcterms.subjectbreedsen
dcterms.subjectchickensen
dcterms.subjectpoultryen
dcterms.subjectindigenous breedsen
dcterms.subjectgeneticsen
dcterms.typeConference Paper

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