Genomic resources to guide improvement of the shea tree
A defining component of agroforestry parklands across Sahelo-Sudanian Africa (SSA), the shea tree (Vitellaria paradoxa) is central to sustaining local livelihoods and the farming environments of rural communities. Despite its economic and cultural value, however, not to mention the ecological roles...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
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Frontiers Media
2021
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/115285 |
| _version_ | 1855521230548893696 |
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| author | Hale, I. Ma, X. Melo, A.T.O. Padi, Francis K Hendre, P.S. Kingan, S.B. Sullivan, S.T. Chen, S. Boffa, J.-M. Muchugi, Alice Danquah, A. Barnor, M.T. Jamnadass, Ramni H. Peer, Y. van de Deynze, A. van |
| author_browse | Barnor, M.T. Boffa, J.-M. Chen, S. Danquah, A. Deynze, A. van Hale, I. Hendre, P.S. Jamnadass, Ramni H. Kingan, S.B. Ma, X. Melo, A.T.O. Muchugi, Alice Padi, Francis K Peer, Y. van de Sullivan, S.T. |
| author_facet | Hale, I. Ma, X. Melo, A.T.O. Padi, Francis K Hendre, P.S. Kingan, S.B. Sullivan, S.T. Chen, S. Boffa, J.-M. Muchugi, Alice Danquah, A. Barnor, M.T. Jamnadass, Ramni H. Peer, Y. van de Deynze, A. van |
| author_sort | Hale, I. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | A defining component of agroforestry parklands across Sahelo-Sudanian Africa (SSA), the shea tree (Vitellaria paradoxa) is central to sustaining local livelihoods and the farming environments of rural communities. Despite its economic and cultural value, however, not to mention the ecological roles it plays as a dominant parkland species, shea remains semi-domesticated with virtually no history of systematic genetic improvement. In truth, shea’s extended juvenile period makes traditional breeding approaches untenable; but the opportunity for genome-assisted breeding is immense, provided the foundational resources are available. Here we report the development and public release of such resources. Using the FALCON-Phase workflow, 162.6 Gb of long-read PacBio sequence data were assembled into a 658.7 Mbp, chromosome-scale reference genome annotated with 38,505 coding genes. Whole genome duplication (WGD) analysis based on this gene space revealed clear signatures of two ancient WGD events in shea’s evolutionary past, one prior to the Astrid-Rosid divergence (116–126 Mya) and the other at the root of the order Ericales (65–90 Mya). In a first genome-wide look at the suite of fatty acid (FA) biosynthesis genes that likely govern stearin content, the primary determinant of shea butter quality, relatively high copy numbers of six key enzymes were found (KASI, KASIII, FATB, FAD2, FAD3, and FAX2), some likely originating in shea’s more recent WGD event. To help translate these findings into practical tools for characterization, selection, and genome-wide association studies (GWAS), resequencing data from a shea diversity panel was used to develop a database of more than 3.5 million functionally annotated, physically anchored SNPs. Two smaller, more curated sets of suggested SNPs, one for GWAS (104,211 SNPs) and the other targeting FA biosynthesis genes (90 SNPs), are also presented. With these resources, the hope is to support national programs across the shea belt in the strategic, genome-enabled conservation and long-term improvement of the shea tree for SSA. |
| format | Journal Article |
| id | CGSpace115285 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | Frontiers Media |
| publisherStr | Frontiers Media |
| record_format | dspace |
| spelling | CGSpace1152852024-05-01T08:16:28Z Genomic resources to guide improvement of the shea tree Hale, I. Ma, X. Melo, A.T.O. Padi, Francis K Hendre, P.S. Kingan, S.B. Sullivan, S.T. Chen, S. Boffa, J.-M. Muchugi, Alice Danquah, A. Barnor, M.T. Jamnadass, Ramni H. Peer, Y. van de Deynze, A. van plant genetics trees forestry A defining component of agroforestry parklands across Sahelo-Sudanian Africa (SSA), the shea tree (Vitellaria paradoxa) is central to sustaining local livelihoods and the farming environments of rural communities. Despite its economic and cultural value, however, not to mention the ecological roles it plays as a dominant parkland species, shea remains semi-domesticated with virtually no history of systematic genetic improvement. In truth, shea’s extended juvenile period makes traditional breeding approaches untenable; but the opportunity for genome-assisted breeding is immense, provided the foundational resources are available. Here we report the development and public release of such resources. Using the FALCON-Phase workflow, 162.6 Gb of long-read PacBio sequence data were assembled into a 658.7 Mbp, chromosome-scale reference genome annotated with 38,505 coding genes. Whole genome duplication (WGD) analysis based on this gene space revealed clear signatures of two ancient WGD events in shea’s evolutionary past, one prior to the Astrid-Rosid divergence (116–126 Mya) and the other at the root of the order Ericales (65–90 Mya). In a first genome-wide look at the suite of fatty acid (FA) biosynthesis genes that likely govern stearin content, the primary determinant of shea butter quality, relatively high copy numbers of six key enzymes were found (KASI, KASIII, FATB, FAD2, FAD3, and FAX2), some likely originating in shea’s more recent WGD event. To help translate these findings into practical tools for characterization, selection, and genome-wide association studies (GWAS), resequencing data from a shea diversity panel was used to develop a database of more than 3.5 million functionally annotated, physically anchored SNPs. Two smaller, more curated sets of suggested SNPs, one for GWAS (104,211 SNPs) and the other targeting FA biosynthesis genes (90 SNPs), are also presented. With these resources, the hope is to support national programs across the shea belt in the strategic, genome-enabled conservation and long-term improvement of the shea tree for SSA. 2021-09-09 2021-10-01T09:19:57Z 2021-10-01T09:19:57Z Journal Article https://hdl.handle.net/10568/115285 en Open Access Frontiers Media Hale, I., Ma, X., Melo, A.T.O., Padi, F.K., Hendre, P.S., Kingan, S.B., Sullivan, S.T., Chen, S., Boffa, J.-M., Muchugi, A., Danquah, A., Barnor, M.T., Jamnadass, R., Van de Peer, Y. and Van Deynze, A. 2021. Genomic resources to guide improvement of the shea tree. Frontiers in Plant Science 12:720670. |
| spellingShingle | plant genetics trees forestry Hale, I. Ma, X. Melo, A.T.O. Padi, Francis K Hendre, P.S. Kingan, S.B. Sullivan, S.T. Chen, S. Boffa, J.-M. Muchugi, Alice Danquah, A. Barnor, M.T. Jamnadass, Ramni H. Peer, Y. van de Deynze, A. van Genomic resources to guide improvement of the shea tree |
| title | Genomic resources to guide improvement of the shea tree |
| title_full | Genomic resources to guide improvement of the shea tree |
| title_fullStr | Genomic resources to guide improvement of the shea tree |
| title_full_unstemmed | Genomic resources to guide improvement of the shea tree |
| title_short | Genomic resources to guide improvement of the shea tree |
| title_sort | genomic resources to guide improvement of the shea tree |
| topic | plant genetics trees forestry |
| url | https://hdl.handle.net/10568/115285 |
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