Origins and geographic diversification of African rice (Oryza glaberrima)

Margaretha A. Veltman, Jonathan Flowers, Tinde R. van Andel, M. Eric Schranz

Research output: Contribution to journalArticle

Abstract

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.

Original languageEnglish (US)
Article numbere0203508
JournalPLoS ONE
Volume14
Issue number3
DOIs
StatePublished - Mar 1 2019

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Oryza glaberrima
domestication
Genes
Coastal zones
rice
Genome
Guinea
Population
genome
Oryza
staple foods
Domestication
provenance
Oryza sativa
haplotypes
Haplotypes
population structure
highlands
genes
alleles

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Origins and geographic diversification of African rice (Oryza glaberrima). / Veltman, Margaretha A.; Flowers, Jonathan; van Andel, Tinde R.; Eric Schranz, M.

In: PLoS ONE, Vol. 14, No. 3, e0203508, 01.03.2019.

Research output: Contribution to journalArticle

Veltman, Margaretha A. ; Flowers, Jonathan ; van Andel, Tinde R. ; Eric Schranz, M. / Origins and geographic diversification of African rice (Oryza glaberrima). In: PLoS ONE. 2019 ; Vol. 14, No. 3.
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