IBD sharing patterns as intra-breed admixture indicators in small ruminants
cg.contact | anne.blondeau@unilim.fr | en_US |
cg.contributor.center | International Center for Agricultural Research in the Dry Areas - ICARDA | en_US |
cg.contributor.center | University of KwaZulu-Natal - UKZN | en_US |
cg.contributor.center | Agricultural Research Council South Africa - ARC South Africa | en_US |
cg.contributor.center | Utrecht University - UU | en_US |
cg.contributor.center | Chinese Academy of Agricultural Sciences - CAAS | en_US |
cg.contributor.center | Center for Tropical Livestock Genetics and Health - CLTGH | en_US |
cg.contributor.center | University of Limoges - UNILIM | en_US |
cg.contributor.center | Misurata University | en_US |
cg.contributor.center | Académie de Limoges | en_US |
cg.contributor.crp | CGIAR Research Program on Livestock Agri-Food Systems - Livestock | en_US |
cg.contributor.funder | International Center for Agricultural Research in the Dry Areas - ICARDA | en_US |
cg.contributor.project | Communication and Documentation Information Services (CODIS) | en_US |
cg.contributor.project-lead-institute | International Center for Agricultural Research in the Dry Areas - ICARDA | en_US |
cg.creator.id | Mwacharo, Joram: 0000-0001-6981-8140 | en_US |
cg.identifier.doi | https://dx.doi.org/10.1038/s41437-023-00658-x | en_US |
cg.isijournal | ISI Journal | en_US |
cg.issn | 0018-067X | en_US |
cg.journal | Heredity | en_US |
cg.subject.agrovoc | sheep | en_US |
cg.subject.agrovoc | goats | en_US |
cg.subject.agrovoc | animal breeding | en_US |
cg.subject.agrovoc | haplotypes | en_US |
cg.subject.agrovoc | goats | en_US |
cg.subject.agrovoc | sheep | en_US |
cg.subject.impactArea | Climate adaptation and mitigation | en_US |
cg.subject.impactArea | Nutrition, health and food security | en_US |
cg.subject.impactArea | Poverty reduction, livelihoods and jobs | en_US |
cg.subject.impactArea | Environmental health and biodiversity | en_US |
cg.subject.sdg | SDG 1 - No poverty | en_US |
cg.subject.sdg | SDG 2 - Zero hunger | en_US |
cg.subject.sdg | SDG 3 - Good health and well-being | en_US |
cg.subject.sdg | SDG 11 - Sustainable cities and communities | en_US |
cg.subject.sdg | SDG 13 - Climate action | en_US |
dc.contributor | Mwacharo, Joram | en_US |
dc.contributor | Li, Meng-Hua | en_US |
dc.contributor | Ahbara, Abulgasim | en_US |
dc.contributor | Catherine Muchadeyi, Farai | en_US |
dc.contributor | Dzomba, Edgar | en_US |
dc.contributor | Lenstra, Johannes | en_US |
dc.contributor | Silva, Anne da | en_US |
dc.creator | Da Silva, Stéphane | en_US |
dc.date.accessioned | 2023-11-22T16:16:44Z | |
dc.date.available | 2023-11-22T16:16:44Z | |
dc.description.abstract | In 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.format | en_US | |
dc.identifier | https://mel.cgiar.org/reporting/downloadmelspace/hash/19d1921b75607f13fb07bea7e113727e/v/a91d9d59c08c573a745d0a845bce095e | en_US |
dc.identifier.citation | Stéphane 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.status | Open access | en_US |
dc.identifier.uri | https://hdl.handle.net/20.500.11766/68805 | |
dc.language | en | en_US |
dc.publisher | Springer Nature [academic journals on nature.com] (Fully open access journals) | en_US |
dc.relation | Colli, Licia et al. (2020). Data from: Signatures of selection and environmental adaptation across the goat genome post-domestication [Dataset]. Dryad. | en_US |
dc.relation | Moreno-Romieux, C., Tortereau, F., Raoul, J., & Servin, B. (2017). High density genotypes of French Sheep populations [Data set]. In BMC Genomics (Vol. 19, Number 71). Zenodo. | en_US |
dc.relation | Lenstra, 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.relation | International Sheep Genomics Consortium | en_US |
dc.relation | Zewdu 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.relation | Abulgasim 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.uri | https://doi.org/10.5061/dryad.v8g21pt | en_US |
dc.relation.uri | https://doi.org/10.5281/zenodo.237116 | en_US |
dc.relation.uri | https://doi.org/10.23644/uu.8947346 | en_US |
dc.relation.uri | http://www.sheephapmap.org/ | en_US |
dc.relation.uri | http://www.animalgenome.org/repository/pub/KORE2017.1122 | en_US |
dc.relation.uri | https://doi.org/10.3389/fgene.2018.00699 | en_US |
dc.rights | CC-BY-4.0 | en_US |
dc.source | Heredity;(2023) | en_US |
dc.subject | admixture | en_US |
dc.subject | identity by descent | en_US |
dc.title | IBD sharing patterns as intra-breed admixture indicators in small ruminants | en_US |
dc.type | Journal Article | en_US |
dcterms.available | 2023-11-03 | en_US |
mel.impact-factor | 3.8 | en_US |