IBD sharing patterns as intra-breed admixture indicators in small ruminants

cg.contactanne.blondeau@unilim.fren_US
cg.contributor.centerInternational Center for Agricultural Research in the Dry Areas - ICARDAen_US
cg.contributor.centerUniversity of KwaZulu-Natal - UKZNen_US
cg.contributor.centerAgricultural Research Council South Africa - ARC South Africaen_US
cg.contributor.centerUtrecht University - UUen_US
cg.contributor.centerChinese Academy of Agricultural Sciences - CAASen_US
cg.contributor.centerCenter for Tropical Livestock Genetics and Health - CLTGHen_US
cg.contributor.centerUniversity of Limoges - UNILIMen_US
cg.contributor.centerMisurata Universityen_US
cg.contributor.centerAcadémie de Limogesen_US
cg.contributor.crpCGIAR Research Program on Livestock Agri-Food Systems - Livestocken_US
cg.contributor.funderInternational Center for Agricultural Research in the Dry Areas - ICARDAen_US
cg.contributor.projectCommunication and Documentation Information Services (CODIS)en_US
cg.contributor.project-lead-instituteInternational Center for Agricultural Research in the Dry Areas - ICARDAen_US
cg.creator.idMwacharo, Joram: 0000-0001-6981-8140en_US
cg.identifier.doihttps://dx.doi.org/10.1038/s41437-023-00658-xen_US
cg.isijournalISI Journalen_US
cg.issn0018-067Xen_US
cg.journalHeredityen_US
cg.subject.agrovocsheepen_US
cg.subject.agrovocgoatsen_US
cg.subject.agrovocanimal breedingen_US
cg.subject.agrovochaplotypesen_US
cg.subject.agrovocgoatsen_US
cg.subject.agrovocsheepen_US
cg.subject.impactAreaClimate adaptation and mitigationen_US
cg.subject.impactAreaNutrition, health and food securityen_US
cg.subject.impactAreaPoverty reduction, livelihoods and jobsen_US
cg.subject.impactAreaEnvironmental health and biodiversityen_US
cg.subject.sdgSDG 1 - No povertyen_US
cg.subject.sdgSDG 2 - Zero hungeren_US
cg.subject.sdgSDG 3 - Good health and well-beingen_US
cg.subject.sdgSDG 11 - Sustainable cities and communitiesen_US
cg.subject.sdgSDG 13 - Climate actionen_US
dc.contributorMwacharo, Joramen_US
dc.contributorLi, Meng-Huaen_US
dc.contributorAhbara, Abulgasimen_US
dc.contributorCatherine Muchadeyi, Faraien_US
dc.contributorDzomba, Edgaren_US
dc.contributorLenstra, Johannesen_US
dc.contributorSilva, Anne daen_US
dc.creatorDa Silva, Stéphaneen_US
dc.date.accessioned2023-11-22T16:16:44Z
dc.date.available2023-11-22T16:16:44Z
dc.description.abstractIn this study, we investigated how IBD patterns shared between individuals of the same breed could be informative of its admixture level, with the underlying assumption that the most admixed breeds, i.e. the least genetically isolated, should have a much more fragmented genome. We considered 111 goat breeds (i.e. 2501 individuals) and 156 sheep breeds (i.e. 3304 individuals) from Europe, Africa and Asia, for which beadchip SNP genotypes had been performed. We inferred the breed’s level of admixture from: (i) the proportion of the genome shared by breed’s members (i.e. “genetic integrity level” assessed from ADMIXTURE software analyses), and (ii) the “AV index” (calculated from Reynolds’ genetic distances), used as a proxy for the “genetic distinctiveness”. In both goat and sheep datasets, the statistical analyses (comparison of means, Spearman correlations, LM and GAM models) revealed that the most genetically isolated breeds, also showed IBD profiles made up of more shared IBD segments, which were also longer. These results pave the way for further research that could lead to the development of admixture indicators, based on the characterization of intra-breed shared IBD segments, particularly effective as they would be independent of the knowledge of the whole genetic landscape in which the breeds evolve. Finally, by highlighting the fragmentation experienced by the genomes subjected to crossbreeding carried out over the last few generations, the study reminds us of the need to preserve local breeds and the integrity of their adaptive architectures that have been shaped over the centuries.en_US
dc.formatPDFen_US
dc.identifierhttps://mel.cgiar.org/reporting/downloadmelspace/hash/19d1921b75607f13fb07bea7e113727e/v/a91d9d59c08c573a745d0a845bce095een_US
dc.identifier.citationStéphane Da Silva, Joram Mwacharo, Meng-Hua Li, Abulgasim Ahbara, Farai Catherine Muchadeyi, Edgar Dzomba, Johannes Lenstra, Anne da Silva. (3/11/2023). IBD sharing patterns as intra-breed admixture indicators in small ruminants. Heredity.en_US
dc.identifier.statusOpen accessen_US
dc.identifier.urihttps://hdl.handle.net/20.500.11766/68805
dc.languageenen_US
dc.publisherSpringer Nature [academic journals on nature.com] (Fully open access journals)en_US
dc.relationColli, Licia et al. (2020). Data from: Signatures of selection and environmental adaptation across the goat genome post-domestication [Dataset]. Dryad.en_US
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dc.relationLenstra, J.A. (Hans); Ciani, Elena; Mastrangelo, Salvatore; Marroni, Fabio; Silva, Anne Blondeau da; Ferenčaković, Maja; et al. (2020). 50K SNP genotypes of southeast European sheep. Utrecht University. Dataset.en_US
dc.relationInternational Sheep Genomics Consortiumen_US
dc.relationZewdu Edea, Tadelle Dessie, Hailu Dadi, Kyoung-Tag Do and Kwan-Suk Kim. (2017). Genetic diversity and population structure of Ethiopian sheep populations revealed by high-density SNP markers. Front Genet. 2017 Dec 22;8:218.en_US
dc.relationAbulgasim Ahbara, Hussain Bahbahani, Faisal Almathen, Mohammed Al Abri, Mukhtar Omar Agoub, Ayelle Abeba, Adebabay Kebede, Hassan Hussein Musa, Salvatore Mastrangelo, Fabio Pilla, Elena Ciani, Olivier Hanotte, Joram M. Mwacharo. (2018). Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep. Frontier in Genetics.en_US
dc.relation.urihttps://doi.org/10.5061/dryad.v8g21pten_US
dc.relation.urihttps://doi.org/10.5281/zenodo.237116en_US
dc.relation.urihttps://doi.org/10.23644/uu.8947346en_US
dc.relation.urihttp://www.sheephapmap.org/en_US
dc.relation.urihttp://www.animalgenome.org/repository/pub/KORE2017.1122en_US
dc.relation.urihttps://doi.org/10.3389/fgene.2018.00699en_US
dc.rightsCC-BY-4.0en_US
dc.sourceHeredity;(2023)en_US
dc.subjectadmixtureen_US
dc.subjectidentity by descenten_US
dc.titleIBD sharing patterns as intra-breed admixture indicators in small ruminantsen_US
dc.typeJournal Articleen_US
dcterms.available2023-11-03en_US
mel.impact-factor3.8en_US

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