The complex geography of domestication of the African rice Oryza glaberrima
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Abstract
Abstract While the domestication history of Asian rice has been extensively studied, details of the evolution of African rice remains elusive. The inner Niger delta has been suggested as the center of origin but molecular data for its support are lacking. Here, we present the most comprehensive analysis to date on the evolutionary and domestication history of African rice. By analyzing whole genome re-sequencing data from 282 individuals in domesticated African rice Oryza glaberrima and its progenitor O. barthii , we hypothesize a non-centric domestication origin for African rice. Our analyses show geographically based population structure in O. glaberrima , as well as significant evidence of admixture between genetic groups. Furthermore, we have evidence that the previously hypothesized O. barthii progenitor populations in West Africa have evolutionary signatures similar to domesticated rice and carried causal domestication mutations, suggesting those progenitors may actually represent feral wild-domesticated hybrid rice. Demography modeling suggested the inland O. glaberrima had a protracted period of bottlenecking that preceded the coastal population by 800–1,800 years. Phylogeographic analysis of genes involved in the core domestication process suggests that the origins of causal domestication mutations could be traced to wild progenitors in multiple different locations in West and Central Africa. Based on our evidence, we hypothesize O. glaberrima was not domesticated from a single centric location but was rather a diffuse process where multiple regions contributed key alleles for different domestication traits. Author Summary For many crops it is not clear how they got domesticated from their wild progenitors. Transition from a wild to domesticated state required a series of genetic changes, and studying the evolutionary origin of these domestication-causing mutations are key to understanding the domestication origins of a crop. Moreover, population relationships within a crop holds insight into the evolutionary history of domestication and whether there was gene flow between different genetic groups. In this study, we investigate the domestication history of Oryza glaberrima , a rice species that was domesticated in West Africa independently from the Asian rice species O. sativa . Using genome-wide data from a large sample of domesticated and wild African rice samples we did not find evidence that supported the established domestication model for O. glaberrima —a single domestication origin. Rather, our evidence suggests the domestication process for African rice was initiated in multiple regions of West Africa, caused potentially by the local environmental and cultivation preference of people. Admixture between different genetic groups had facilitated the exchange and spread of core domestication mutations. Hence domestication of African rice was a multi-regional process.
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The findings, in combination with recent genomic analyses of African rice, African yam, and pearl millet, suggest West Africa as a major cradle of both animal and plant domestication.
“Our findings in combination with recent genomic analyses of African rice (Cubry et al. 2018; Choi et al. 2019), African yam (Scarcelli et al. 2019), and pearl millet suggest West Africa as a major cradle of both animal and plant domestication.”
From Genomic Analyses Unveil Helmeted Guinea Fowl (<i>Numida meleagris</i>) Domestication in West Africa (2021) · cites this paper as Choi et al. 2019
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Interspecific Breeding of African Rice with Asian Rice and Intraspecific Breeding of African Rice
Shaibu, A. A., Yadav, S., Amoah, N. K. A., Futakuchi, K., Zenna, N., Namaky, R. E., & Semwal, V. K. (2026) · Springer eBooks · doi:10.1007/978-3-032-22733-1_7
Numaguchi, K., Lim, S., Orn, C., Higashikubo, Y., Saito, H., Sato, Y., Ishikawa, R., Gutaker, R. M., & Ishii, T. (2026) · Journal of Experimental Botany · doi:10.1093/jxb/erag411
Self-citationWang, P., Shen, Q., Chen, Y., Song, C., Shi, T., Ma, P., Dong, G., Chen, J., Chen, Q., Sun, W., et al. (2026) · Medicinal Plant Biology · doi:10.48130/mpb-0026-0020
- Authors
- Choi, J. Y., Zaidem, M., Gutaker, R., Dorph, K., Singh, R. K., & Purugganan, M. D.
- Affiliations
- New York University (US)
- International Rice Research Institute (PH)
- New York University Abu Dhabi (AE)
- Corresponding author
- Purugganan, Michael D.
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2019-03-07
- Volume
- 15
- Issue
- 3
- Pages
- e1007414
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC6424484
- OpenAlex
- W2949760494
- Cited by
- 66
- References
- 124
- Citations by year
- 2026: 11 · 2025: 4 · 2024: 5 · 2023: 10 · 2022: 9 · 2021: 8 · 2020: 15 · 2019: 3 · 2018: 1
- FWCI
- 5.27
- Type
- journal article
- Language
- en
- Update notices
- new_version (2019-03-19)
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- CGSPace A Repository of Agricultural Research Outputs (Consultative Group for International Agricultural Research) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Greater South Information System
- Funders
- National Science Foundation (IOS-1546218)
- Zegar Family Foundation (A16-0051)
- NYU Abu Dhabi Research Institute (G1205)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Rice Cultivation and Yield Improvement
- Keywords
- Oryza glaberrima, Oryza barthii, crop domestication, domestication center, seed shattering, phylogeography, genetic structure, wild progenitor, Inner Niger Delta, West Africa, Central Africa
- MeSH terms
- Domestication, Africa, Western, Edible Grain, Geography, Oryza, Seeds, Species Specificity, Genetic Variation, Crops, Agricultural, DNA, Plant, Genome, Plant, Polymorphism, Single Nucleotide, Phylogeography
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