Origins and geographic diversification of African rice (Oryza glaberrima).
Rice is a staple food for the majority of the world's population. Whereas Asian rice (Oryza sativa) has been extensively studied, the exact origins of African rice (Oryza glaberrima) are still contested. Previous studies have supported either a centric or a non-centric geographic origin of Afri...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2019-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0203508 |
| _version_ | 1818588236067373056 |
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| author | Margaretha A Veltman Jonathan M Flowers Tinde R van Andel M Eric Schranz |
| author_facet | Margaretha A Veltman Jonathan M Flowers Tinde R van Andel M Eric Schranz |
| author_sort | Margaretha A Veltman |
| collection | DOAJ |
| description | Rice is a staple food for the majority of the world's population. Whereas Asian rice (Oryza sativa) has been extensively studied, the exact origins of African rice (Oryza glaberrima) are still contested. Previous studies have supported either a centric or a non-centric geographic origin of African rice domestication. Here we review the evidence for both scenarios through a critical reassessment of 206 whole genome sequences of domesticated and wild African rice. While genetic diversity analyses support a severe bottleneck caused by domestication, signatures of recent and strong positive selection do not unequivocally point to candidate domestication genes, suggesting that domestication proceeded differently than in Asian rice-either by selection on different alleles, or different modes of selection. Population structure analysis revealed five genetic clusters localising to different geographic regions. Isolation by distance was identified in the coastal populations, which could account for parallel adaptation in geographically separated demes. Although genome-wide phylogenetic relationships support an origin in the eastern cultivation range followed by diversification along the Atlantic coast, further analysis of domestication genes shows distinct haplotypes in the southwest-suggesting that at least one of several key domestication traits might have originated there. These findings shed new light on an old controversy concerning plant domestication in Africa by highlighting the divergent roots of African rice cultivation, including a separate centre of domestication activity in the Guinea Highlands. We thus suggest that the commonly accepted centric origin of African rice must be reconsidered in favour of a non-centric or polycentric view. |
| first_indexed | 2024-12-16T09:21:32Z |
| format | Article |
| id | doaj.art-046d184724124255bfd03780105178aa |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-16T09:21:32Z |
| publishDate | 2019-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-046d184724124255bfd03780105178aa2022-12-21T22:36:44ZengPublic Library of Science (PLoS)PLoS ONE1932-62032019-01-01143e020350810.1371/journal.pone.0203508Origins and geographic diversification of African rice (Oryza glaberrima).Margaretha A VeltmanJonathan M FlowersTinde R van AndelM Eric SchranzRice is a staple food for the majority of the world's population. Whereas Asian rice (Oryza sativa) has been extensively studied, the exact origins of African rice (Oryza glaberrima) are still contested. Previous studies have supported either a centric or a non-centric geographic origin of African rice domestication. Here we review the evidence for both scenarios through a critical reassessment of 206 whole genome sequences of domesticated and wild African rice. While genetic diversity analyses support a severe bottleneck caused by domestication, signatures of recent and strong positive selection do not unequivocally point to candidate domestication genes, suggesting that domestication proceeded differently than in Asian rice-either by selection on different alleles, or different modes of selection. Population structure analysis revealed five genetic clusters localising to different geographic regions. Isolation by distance was identified in the coastal populations, which could account for parallel adaptation in geographically separated demes. Although genome-wide phylogenetic relationships support an origin in the eastern cultivation range followed by diversification along the Atlantic coast, further analysis of domestication genes shows distinct haplotypes in the southwest-suggesting that at least one of several key domestication traits might have originated there. These findings shed new light on an old controversy concerning plant domestication in Africa by highlighting the divergent roots of African rice cultivation, including a separate centre of domestication activity in the Guinea Highlands. We thus suggest that the commonly accepted centric origin of African rice must be reconsidered in favour of a non-centric or polycentric view.https://doi.org/10.1371/journal.pone.0203508 |
| spellingShingle | Margaretha A Veltman Jonathan M Flowers Tinde R van Andel M Eric Schranz Origins and geographic diversification of African rice (Oryza glaberrima). PLoS ONE |
| title | Origins and geographic diversification of African rice (Oryza glaberrima). |
| title_full | Origins and geographic diversification of African rice (Oryza glaberrima). |
| title_fullStr | Origins and geographic diversification of African rice (Oryza glaberrima). |
| title_full_unstemmed | Origins and geographic diversification of African rice (Oryza glaberrima). |
| title_short | Origins and geographic diversification of African rice (Oryza glaberrima). |
| title_sort | origins and geographic diversification of african rice oryza glaberrima |
| url | https://doi.org/10.1371/journal.pone.0203508 |
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