Fine scale genomic signals of admixture and alien introgression among Asian rice landraces
Modern rice cultivars are adapted to a range of environmental conditions and human preferences. At the root of this diversity is a marked genetic structure, owing to multiple foundation events. Admixture and recurrent introgression from wild sources have played upon this base to produce the myriad a...
| Autores principales: | , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Oxford University Press
2019
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| Acceso en línea: | https://hdl.handle.net/10568/164696 |
| _version_ | 1855534086196559872 |
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| author | Santos, João D. Chebotarov, Dmytro McNally, Kenneth L. Bartholomé, Jérôme Droc, Gaëtan Billot, Claire Glaszmann, Jean Christophe |
| author_browse | Bartholomé, Jérôme Billot, Claire Chebotarov, Dmytro Droc, Gaëtan Glaszmann, Jean Christophe McNally, Kenneth L. Santos, João D. |
| author_facet | Santos, João D. Chebotarov, Dmytro McNally, Kenneth L. Bartholomé, Jérôme Droc, Gaëtan Billot, Claire Glaszmann, Jean Christophe |
| author_sort | Santos, João D. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Modern rice cultivars are adapted to a range of environmental conditions and human preferences. At the root of this diversity is a marked genetic structure, owing to multiple foundation events. Admixture and recurrent introgression from wild sources have played upon this base to produce the myriad adaptations existing today. Genome-wide studies bring support to this idea, but understanding the history and nature of particular genetic adaptations requires the identification of specific patterns of genetic exchange. In this study, we explore the patterns of haplotype similarity along the genomes of a subset of rice cultivars available in the 3,000 Rice Genomes data set. We begin by establishing a custom method of classification based on a combination of dimensionality reduction and kernel density estimation. Through simulations, the behaviour of this classifier is studied under scenarios of varying genetic divergence, admixture and alien introgression. Finally, the method is applied to local haplotypes along the genome of a Core set of Asian Landraces. Taking the Japonica, Indica and cAus groups as references, we find evidence of reciprocal introgressions covering 2.6% of reference genomes on average. Structured signals of introgression among reference accessions are discussed. We extend the analysis to elucidate the genetic structure of the group circum-Basmati: we delimit regions of Japonica, cAus and Indica origin, as well as regions outlier to these groups (13% on average). Finally, the approach used highlights regions of partial to complete loss of structure that can be attributed to selective pressures during domestication. |
| format | Journal Article |
| id | CGSpace164696 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1646962025-12-08T09:54:28Z Fine scale genomic signals of admixture and alien introgression among Asian rice landraces Santos, João D. Chebotarov, Dmytro McNally, Kenneth L. Bartholomé, Jérôme Droc, Gaëtan Billot, Claire Glaszmann, Jean Christophe Modern rice cultivars are adapted to a range of environmental conditions and human preferences. At the root of this diversity is a marked genetic structure, owing to multiple foundation events. Admixture and recurrent introgression from wild sources have played upon this base to produce the myriad adaptations existing today. Genome-wide studies bring support to this idea, but understanding the history and nature of particular genetic adaptations requires the identification of specific patterns of genetic exchange. In this study, we explore the patterns of haplotype similarity along the genomes of a subset of rice cultivars available in the 3,000 Rice Genomes data set. We begin by establishing a custom method of classification based on a combination of dimensionality reduction and kernel density estimation. Through simulations, the behaviour of this classifier is studied under scenarios of varying genetic divergence, admixture and alien introgression. Finally, the method is applied to local haplotypes along the genome of a Core set of Asian Landraces. Taking the Japonica, Indica and cAus groups as references, we find evidence of reciprocal introgressions covering 2.6% of reference genomes on average. Structured signals of introgression among reference accessions are discussed. We extend the analysis to elucidate the genetic structure of the group circum-Basmati: we delimit regions of Japonica, cAus and Indica origin, as well as regions outlier to these groups (13% on average). Finally, the approach used highlights regions of partial to complete loss of structure that can be attributed to selective pressures during domestication. 2019-05-01 2024-12-19T12:54:12Z 2024-12-19T12:54:12Z Journal Article https://hdl.handle.net/10568/164696 en Open Access Oxford University Press Santos, João D; Chebotarov, Dmytro; McNally, Kenneth L; Bartholomé, Jérôme; Droc, Gaëtan; Billot, Claire and Glaszmann, Jean Christophe. 2019. Fine scale genomic signals of admixture and alien introgression among Asian rice landraces. Genome Biology and Evolution, volume 11, no. 5; pages 1358-1373. |
| spellingShingle | Santos, João D. Chebotarov, Dmytro McNally, Kenneth L. Bartholomé, Jérôme Droc, Gaëtan Billot, Claire Glaszmann, Jean Christophe Fine scale genomic signals of admixture and alien introgression among Asian rice landraces |
| title | Fine scale genomic signals of admixture and alien introgression among Asian rice landraces |
| title_full | Fine scale genomic signals of admixture and alien introgression among Asian rice landraces |
| title_fullStr | Fine scale genomic signals of admixture and alien introgression among Asian rice landraces |
| title_full_unstemmed | Fine scale genomic signals of admixture and alien introgression among Asian rice landraces |
| title_short | Fine scale genomic signals of admixture and alien introgression among Asian rice landraces |
| title_sort | fine scale genomic signals of admixture and alien introgression among asian rice landraces |
| url | https://hdl.handle.net/10568/164696 |
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