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Nat Genet. 2014 Sep;46(9):982-8. doi: 10.1038/ng.3044. Epub 2014 Jul 27.

The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication.

Author information

1
1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2].
2
1] Plant Genome and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany. [2].
3
1] Dow AgroSciences, Indianapolis, Indiana, USA. [2].
4
1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2] Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA.
5
Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA.
6
Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.
7
1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2] DuPont Pioneer, Johnston, Iowa, USA.
8
Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy.
9
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
10
1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2] US Arid Land Agricultural Research Center, Maricopa, Arizona, USA.
11
Africa Rice Center, Cotonou, Benin.
12
Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA.
13
Department of Geography, Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA.
14
Laboratoire Génome et Développement des Plantes, UMR CNRS/Institut de Recherche pour le Développement/l'Université de Perpignan Via Domitia, Université de Perpignan, Perpignan, France.
15
Institute of Plant Biology, University of Zurich, Zurich, Switzerland.
16
Department of Biology, University of Maryland, College Park, Maryland, USA.
17
Plant Genome and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany.
18
Dow AgroSciences, Indianapolis, Indiana, USA.

Abstract

The cultivation of rice in Africa dates back more than 3,000 years. Interestingly, African rice is not of the same origin as Asian rice (Oryza sativa L.) but rather is an entirely different species (i.e., Oryza glaberrima Steud.). Here we present a high-quality assembly and annotation of the O. glaberrima genome and detailed analyses of its evolutionary history of domestication and selection. Population genomics analyses of 20 O. glaberrima and 94 Oryza barthii accessions support the hypothesis that O. glaberrima was domesticated in a single region along the Niger river as opposed to noncentric domestication events across Africa. We detected evidence for artificial selection at a genome-wide scale, as well as with a set of O. glaberrima genes orthologous to O. sativa genes that are known to be associated with domestication, thus indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes.

PMID:
25064006
DOI:
10.1038/ng.3044
[Indexed for MEDLINE]

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