A cattle graph genome incorporating global breed diversity
Despite only 8% of cattle being found in Europe, European breeds dominate current genetic resources. This adversely impacts cattle research in other important global cattle breeds, especially those from Africa for which genomic resources are particularly limited, despite their disproportionate impor...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2022
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/118171 |
| _version_ | 1855529507797073920 |
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| author | Talenti, A. Powell, J. Hemmink, Johanneke D. Cook, Elizabeth A.J. Wragg, D. Jayaraman, S. Paxton, E. Ezeasor, C.K. Obishakin, E.T. Agusi, E.R. Tijjani, A. Amanyire, W. Muhanguzi, D. Marshall, Karen Fisch, A. Ferreira, B.R. Qasim, A. Chaudhry, U. Wiener, P. Toye, Philip G. Morrison, L.J. Connelley, T. Prendergast, J.G.D. |
| author_browse | Agusi, E.R. Amanyire, W. Chaudhry, U. Connelley, T. Cook, Elizabeth A.J. Ezeasor, C.K. Ferreira, B.R. Fisch, A. Hemmink, Johanneke D. Jayaraman, S. Marshall, Karen Morrison, L.J. Muhanguzi, D. Obishakin, E.T. Paxton, E. Powell, J. Prendergast, J.G.D. Qasim, A. Talenti, A. Tijjani, A. Toye, Philip G. Wiener, P. Wragg, D. |
| author_facet | Talenti, A. Powell, J. Hemmink, Johanneke D. Cook, Elizabeth A.J. Wragg, D. Jayaraman, S. Paxton, E. Ezeasor, C.K. Obishakin, E.T. Agusi, E.R. Tijjani, A. Amanyire, W. Muhanguzi, D. Marshall, Karen Fisch, A. Ferreira, B.R. Qasim, A. Chaudhry, U. Wiener, P. Toye, Philip G. Morrison, L.J. Connelley, T. Prendergast, J.G.D. |
| author_sort | Talenti, A. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Despite only 8% of cattle being found in Europe, European breeds dominate current genetic resources. This adversely impacts cattle research in other important global cattle breeds, especially those from Africa for which genomic resources are particularly limited, despite their disproportionate importance to the continent's economies. To mitigate this issue, we have generated assemblies of African breeds, which have been integrated with genomic data for 294 diverse cattle into a graph genome that incorporates global cattle diversity. We illustrate how this more representative reference assembly contains an extra 116.1 Mb (4.2%) of sequence absent from the current Hereford sequence and consequently inaccessible to current studies. We further demonstrate how using this graph genome increases read mapping rates, reduces allelic biases and improves the agreement of structural variant calling with independent optical mapping data. Consequently, we present an improved, more representative, reference assembly that will improve global cattle research. |
| format | Journal Article |
| id | CGSpace118171 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1181712024-01-17T12:58:34Z A cattle graph genome incorporating global breed diversity Talenti, A. Powell, J. Hemmink, Johanneke D. Cook, Elizabeth A.J. Wragg, D. Jayaraman, S. Paxton, E. Ezeasor, C.K. Obishakin, E.T. Agusi, E.R. Tijjani, A. Amanyire, W. Muhanguzi, D. Marshall, Karen Fisch, A. Ferreira, B.R. Qasim, A. Chaudhry, U. Wiener, P. Toye, Philip G. Morrison, L.J. Connelley, T. Prendergast, J.G.D. cattle animal breeding genomics Despite only 8% of cattle being found in Europe, European breeds dominate current genetic resources. This adversely impacts cattle research in other important global cattle breeds, especially those from Africa for which genomic resources are particularly limited, despite their disproportionate importance to the continent's economies. To mitigate this issue, we have generated assemblies of African breeds, which have been integrated with genomic data for 294 diverse cattle into a graph genome that incorporates global cattle diversity. We illustrate how this more representative reference assembly contains an extra 116.1 Mb (4.2%) of sequence absent from the current Hereford sequence and consequently inaccessible to current studies. We further demonstrate how using this graph genome increases read mapping rates, reduces allelic biases and improves the agreement of structural variant calling with independent optical mapping data. Consequently, we present an improved, more representative, reference assembly that will improve global cattle research. 2022-02-17 2022-02-18T15:42:56Z 2022-02-18T15:42:56Z Journal Article https://hdl.handle.net/10568/118171 en Open Access Springer Talenti, A., Powell, J., Hemmink, J.D., Cook, E.A.J., Wragg, D., Jayaraman, S., Paxton, E., Ezeasor, C., Obishakin, E.T., Agusi, E.R., Tijjani, A., Amanyire, W., Muhanguzi, D., Marshall, K., Fisch, A., Ferreira, B.R., Qasim, A., Chaudhry, U., Wiener, P., Toye, P., Morrison, L.J., Connelley, T. and Prendergast, J.G.D. 2022. A cattle graph genome incorporating global breed diversity. Nature Communications 13: 910. |
| spellingShingle | cattle animal breeding genomics Talenti, A. Powell, J. Hemmink, Johanneke D. Cook, Elizabeth A.J. Wragg, D. Jayaraman, S. Paxton, E. Ezeasor, C.K. Obishakin, E.T. Agusi, E.R. Tijjani, A. Amanyire, W. Muhanguzi, D. Marshall, Karen Fisch, A. Ferreira, B.R. Qasim, A. Chaudhry, U. Wiener, P. Toye, Philip G. Morrison, L.J. Connelley, T. Prendergast, J.G.D. A cattle graph genome incorporating global breed diversity |
| title | A cattle graph genome incorporating global breed diversity |
| title_full | A cattle graph genome incorporating global breed diversity |
| title_fullStr | A cattle graph genome incorporating global breed diversity |
| title_full_unstemmed | A cattle graph genome incorporating global breed diversity |
| title_short | A cattle graph genome incorporating global breed diversity |
| title_sort | cattle graph genome incorporating global breed diversity |
| topic | cattle animal breeding genomics |
| url | https://hdl.handle.net/10568/118171 |
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