Optical mapping compendium of structural variants across global cattle breeds
Structural variants (SV) have been linked to important bovine disease phenotypes, but due to the difficulty of their accurate detection with standard sequencing approaches, their role in shaping important traits across cattle breeds is largely unexplored. Optical mapping is an alternative approach f...
| Autores principales: | , , , , , , , , , , , , , , , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2022
|
| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/125135 |
| _version_ | 1855535157125054464 |
|---|---|
| author | Talenti, A. Powell, J. Wragg, D. Chepkwony, Maurine Fisch, A. Ferreira, B.R. Mercadante, Maria E.Z. Santos, I.M. Ezeasor, C.K. Obishakin, E.T. Muhanguzi, D. Amanyire, W. Silwamba, I. Muma, J.B. Mainda, G. Kelly, R.F. Toye, Philip G. Connelley, T. Prendergast, J. |
| author_browse | Amanyire, W. Chepkwony, Maurine Connelley, T. Ezeasor, C.K. Ferreira, B.R. Fisch, A. Kelly, R.F. Mainda, G. Mercadante, Maria E.Z. Muhanguzi, D. Muma, J.B. Obishakin, E.T. Powell, J. Prendergast, J. Santos, I.M. Silwamba, I. Talenti, A. Toye, Philip G. Wragg, D. |
| author_facet | Talenti, A. Powell, J. Wragg, D. Chepkwony, Maurine Fisch, A. Ferreira, B.R. Mercadante, Maria E.Z. Santos, I.M. Ezeasor, C.K. Obishakin, E.T. Muhanguzi, D. Amanyire, W. Silwamba, I. Muma, J.B. Mainda, G. Kelly, R.F. Toye, Philip G. Connelley, T. Prendergast, J. |
| author_sort | Talenti, A. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Structural variants (SV) have been linked to important bovine disease phenotypes, but due to the difficulty of their accurate detection with standard sequencing approaches, their role in shaping important traits across cattle breeds is largely unexplored. Optical mapping is an alternative approach for mapping SVs that has been shown to have higher sensitivity than DNA sequencing approaches. The aim of this project was to use optical mapping to develop a high-quality database of structural variation across cattle breeds from different geographical regions, to enable further study of SVs in cattle. To do this we generated 100X Bionano optical mapping data for 18 cattle of nine different ancestries, three continents and both cattle sub-species. In total we identified 13,457 SVs, of which 1,200 putatively overlap coding regions. This resource provides a high-quality set of optical mapping-based SV calls that can be used across studies, from validating DNA sequencing-based SV calls to prioritising candidate functional variants in genetic association studies and expanding our understanding of the role of SVs in cattle evolution. |
| format | Journal Article |
| id | CGSpace125135 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1251352024-05-01T08:18:56Z Optical mapping compendium of structural variants across global cattle breeds Talenti, A. Powell, J. Wragg, D. Chepkwony, Maurine Fisch, A. Ferreira, B.R. Mercadante, Maria E.Z. Santos, I.M. Ezeasor, C.K. Obishakin, E.T. Muhanguzi, D. Amanyire, W. Silwamba, I. Muma, J.B. Mainda, G. Kelly, R.F. Toye, Philip G. Connelley, T. Prendergast, J. cattle breeds Structural variants (SV) have been linked to important bovine disease phenotypes, but due to the difficulty of their accurate detection with standard sequencing approaches, their role in shaping important traits across cattle breeds is largely unexplored. Optical mapping is an alternative approach for mapping SVs that has been shown to have higher sensitivity than DNA sequencing approaches. The aim of this project was to use optical mapping to develop a high-quality database of structural variation across cattle breeds from different geographical regions, to enable further study of SVs in cattle. To do this we generated 100X Bionano optical mapping data for 18 cattle of nine different ancestries, three continents and both cattle sub-species. In total we identified 13,457 SVs, of which 1,200 putatively overlap coding regions. This resource provides a high-quality set of optical mapping-based SV calls that can be used across studies, from validating DNA sequencing-based SV calls to prioritising candidate functional variants in genetic association studies and expanding our understanding of the role of SVs in cattle evolution. 2022-10-13 2022-10-20T11:14:26Z 2022-10-20T11:14:26Z Journal Article https://hdl.handle.net/10568/125135 en Open Access Springer Talenti, A., Powell, J., Wragg, D., Chepkwony, M., Fisch, A., Ferreira, B.R., Mercadante, M.E.Z., Santos, I.M., Ezeasor, C.K., Obishakin, E.T., Muhanguzi, D., Amanyire, W., Silwamba, I., Muma, J.B., Mainda, G., Kelly, R.F., Toye, P., Connelley, T. and Prendergast, J. 2022. Optical mapping compendium of structural variants across global cattle breeds. Scientific Data 9:618. |
| spellingShingle | cattle breeds Talenti, A. Powell, J. Wragg, D. Chepkwony, Maurine Fisch, A. Ferreira, B.R. Mercadante, Maria E.Z. Santos, I.M. Ezeasor, C.K. Obishakin, E.T. Muhanguzi, D. Amanyire, W. Silwamba, I. Muma, J.B. Mainda, G. Kelly, R.F. Toye, Philip G. Connelley, T. Prendergast, J. Optical mapping compendium of structural variants across global cattle breeds |
| title | Optical mapping compendium of structural variants across global cattle breeds |
| title_full | Optical mapping compendium of structural variants across global cattle breeds |
| title_fullStr | Optical mapping compendium of structural variants across global cattle breeds |
| title_full_unstemmed | Optical mapping compendium of structural variants across global cattle breeds |
| title_short | Optical mapping compendium of structural variants across global cattle breeds |
| title_sort | optical mapping compendium of structural variants across global cattle breeds |
| topic | cattle breeds |
| url | https://hdl.handle.net/10568/125135 |
| work_keys_str_mv | AT talentia opticalmappingcompendiumofstructuralvariantsacrossglobalcattlebreeds AT powellj opticalmappingcompendiumofstructuralvariantsacrossglobalcattlebreeds AT wraggd opticalmappingcompendiumofstructuralvariantsacrossglobalcattlebreeds AT chepkwonymaurine opticalmappingcompendiumofstructuralvariantsacrossglobalcattlebreeds AT fischa opticalmappingcompendiumofstructuralvariantsacrossglobalcattlebreeds AT ferreirabr opticalmappingcompendiumofstructuralvariantsacrossglobalcattlebreeds AT mercadantemariaez opticalmappingcompendiumofstructuralvariantsacrossglobalcattlebreeds AT santosim opticalmappingcompendiumofstructuralvariantsacrossglobalcattlebreeds AT ezeasorck opticalmappingcompendiumofstructuralvariantsacrossglobalcattlebreeds AT obishakinet opticalmappingcompendiumofstructuralvariantsacrossglobalcattlebreeds AT muhanguzid opticalmappingcompendiumofstructuralvariantsacrossglobalcattlebreeds AT amanyirew opticalmappingcompendiumofstructuralvariantsacrossglobalcattlebreeds AT silwambai opticalmappingcompendiumofstructuralvariantsacrossglobalcattlebreeds AT mumajb opticalmappingcompendiumofstructuralvariantsacrossglobalcattlebreeds AT maindag opticalmappingcompendiumofstructuralvariantsacrossglobalcattlebreeds AT kellyrf opticalmappingcompendiumofstructuralvariantsacrossglobalcattlebreeds AT toyephilipg opticalmappingcompendiumofstructuralvariantsacrossglobalcattlebreeds AT connelleyt opticalmappingcompendiumofstructuralvariantsacrossglobalcattlebreeds AT prendergastj opticalmappingcompendiumofstructuralvariantsacrossglobalcattlebreeds |