IBD sharing patterns as intra-breed admixture indicators in small ruminants
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 goa...
| Main Authors: | , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Springer Nature [academic journals on nature.com]
2025
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/169017 |
| _version_ | 1855527000185241600 |
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| author | Da Silva, Stéphane Mwacharo, Joram Li, Meng-Hua Ahbara, Abulgasim Catherine Muchadeyi, Farai Dzomba, Edgar Lenstra, Johannes Silva, Anne da |
| author_browse | Ahbara, Abulgasim Catherine Muchadeyi, Farai Da Silva, Stéphane Dzomba, Edgar Lenstra, Johannes Li, Meng-Hua Mwacharo, Joram Silva, Anne da |
| author_facet | Da Silva, Stéphane Mwacharo, Joram Li, Meng-Hua Ahbara, Abulgasim Catherine Muchadeyi, Farai Dzomba, Edgar Lenstra, Johannes Silva, Anne da |
| author_sort | Da Silva, Stéphane |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. |
| format | Journal Article |
| id | CGSpace169017 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Springer Nature [academic journals on nature.com] |
| publisherStr | Springer Nature [academic journals on nature.com] |
| record_format | dspace |
| spelling | CGSpace1690172026-01-15T02:09:54Z IBD sharing patterns as intra-breed admixture indicators in small ruminants Da Silva, Stéphane Mwacharo, Joram Li, Meng-Hua Ahbara, Abulgasim Catherine Muchadeyi, Farai Dzomba, Edgar Lenstra, Johannes Silva, Anne da sheep goats animal breeding haplotypes goats sheep admixture identity by descent 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. 2025-01-14T20:15:31Z 2025-01-14T20:15:31Z Journal Article https://hdl.handle.net/10568/169017 en https://doi.org/10.5061/dryad.v8g21pt https://doi.org/10.5281/zenodo.237116 https://doi.org/10.23644/uu.8947346 http://www.sheephapmap.org/ http://www.animalgenome.org/repository/pub/KORE2017.1122 https://doi.org/10.3389/fgene.2018.00699 Open Access application/pdf Springer Nature [academic journals on nature.com] 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, 132, pp. 30-42. |
| spellingShingle | sheep goats animal breeding haplotypes goats sheep admixture identity by descent Da Silva, Stéphane Mwacharo, Joram Li, Meng-Hua Ahbara, Abulgasim Catherine Muchadeyi, Farai Dzomba, Edgar Lenstra, Johannes Silva, Anne da IBD sharing patterns as intra-breed admixture indicators in small ruminants |
| title | IBD sharing patterns as intra-breed admixture indicators in small ruminants |
| title_full | IBD sharing patterns as intra-breed admixture indicators in small ruminants |
| title_fullStr | IBD sharing patterns as intra-breed admixture indicators in small ruminants |
| title_full_unstemmed | IBD sharing patterns as intra-breed admixture indicators in small ruminants |
| title_short | IBD sharing patterns as intra-breed admixture indicators in small ruminants |
| title_sort | ibd sharing patterns as intra breed admixture indicators in small ruminants |
| topic | sheep goats animal breeding haplotypes goats sheep admixture identity by descent |
| url | https://hdl.handle.net/10568/169017 |
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