Traces of introgression from cAus into tropical japonica observed in African upland rice varieties
Asian rice Oryza sativa, first domesticated in East Asia, has considerable success in African fields. When and where this introduction occurred is unclear. Rice varieties of Asian origin may have evolved locally during and after migration to Africa, resulting in unique adaptations, particularly in r...
| Main Authors: | , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Springer
2023
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| Online Access: | https://hdl.handle.net/10568/163977 |
| _version_ | 1855539836429008896 |
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| author | Beye, Abdoulaye Billot, Claire Ronfort, Joëlle McNally, Kenneth L. Diouf, Diaga Glaszmann, Jean Christophe |
| author_browse | Beye, Abdoulaye Billot, Claire Diouf, Diaga Glaszmann, Jean Christophe McNally, Kenneth L. Ronfort, Joëlle |
| author_facet | Beye, Abdoulaye Billot, Claire Ronfort, Joëlle McNally, Kenneth L. Diouf, Diaga Glaszmann, Jean Christophe |
| author_sort | Beye, Abdoulaye |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Asian rice Oryza sativa, first domesticated in East Asia, has considerable success in African fields. When and where this introduction occurred is unclear. Rice varieties of Asian origin may have evolved locally during and after migration to Africa, resulting in unique adaptations, particularly in relation to upland cultivation as frequently practiced in Africa. Methods We investigated the genetic differentiation between Asian and African varieties using the 3000 Rice Genomes SNP dataset. African upland cultivars were first characterized using principal component analysis among 292 tropical Japonica accessions from Africa and Asia. The particularities of African accessions were then explored using two inference techniques, PCA-KDE for supervised classification and chromosome painting, and ELAI for individual allelic dosage monitoring. Key Results Ambiguities of local differentiation between Japonica and other groups pointed at genomic segments that potentially resulted from genetic exchange. Those specific to West African upland accessions were concentrated on chromosome 6 and featured several cAus introgression signals, including a large one between 17.9 and 21.7 Mb. We found iHS statistics in support of positive selection in this region and we provide a list of candidate genes enriched in GO terms that have regulatory functions involved in stress responses that could have facilitated adaptation to harsh upland growing conditions. |
| format | Journal Article |
| id | CGSpace163977 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1639772024-12-19T14:13:36Z Traces of introgression from cAus into tropical japonica observed in African upland rice varieties Beye, Abdoulaye Billot, Claire Ronfort, Joëlle McNally, Kenneth L. Diouf, Diaga Glaszmann, Jean Christophe introgression upland rice varieties africa Asian rice Oryza sativa, first domesticated in East Asia, has considerable success in African fields. When and where this introduction occurred is unclear. Rice varieties of Asian origin may have evolved locally during and after migration to Africa, resulting in unique adaptations, particularly in relation to upland cultivation as frequently practiced in Africa. Methods We investigated the genetic differentiation between Asian and African varieties using the 3000 Rice Genomes SNP dataset. African upland cultivars were first characterized using principal component analysis among 292 tropical Japonica accessions from Africa and Asia. The particularities of African accessions were then explored using two inference techniques, PCA-KDE for supervised classification and chromosome painting, and ELAI for individual allelic dosage monitoring. Key Results Ambiguities of local differentiation between Japonica and other groups pointed at genomic segments that potentially resulted from genetic exchange. Those specific to West African upland accessions were concentrated on chromosome 6 and featured several cAus introgression signals, including a large one between 17.9 and 21.7 Mb. We found iHS statistics in support of positive selection in this region and we provide a list of candidate genes enriched in GO terms that have regulatory functions involved in stress responses that could have facilitated adaptation to harsh upland growing conditions. 2023-12 2024-12-19T12:53:18Z 2024-12-19T12:53:18Z Journal Article https://hdl.handle.net/10568/163977 en Open Access Springer Beye, Abdoulaye; Billot, Claire; Ronfort, Joëlle; McNally, Kenneth L.; Diouf, Diaga and Glaszmann, Jean Christophe. 2023. Traces of introgression from cAus into tropical japonica observed in African upland rice varieties. Rice, Volume 16, no. 1 |
| spellingShingle | introgression upland rice varieties africa Beye, Abdoulaye Billot, Claire Ronfort, Joëlle McNally, Kenneth L. Diouf, Diaga Glaszmann, Jean Christophe Traces of introgression from cAus into tropical japonica observed in African upland rice varieties |
| title | Traces of introgression from cAus into tropical japonica observed in African upland rice varieties |
| title_full | Traces of introgression from cAus into tropical japonica observed in African upland rice varieties |
| title_fullStr | Traces of introgression from cAus into tropical japonica observed in African upland rice varieties |
| title_full_unstemmed | Traces of introgression from cAus into tropical japonica observed in African upland rice varieties |
| title_short | Traces of introgression from cAus into tropical japonica observed in African upland rice varieties |
| title_sort | traces of introgression from caus into tropical japonica observed in african upland rice varieties |
| topic | introgression upland rice varieties africa |
| url | https://hdl.handle.net/10568/163977 |
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