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

    Fingerprint

    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

    Veltman, M. A., Flowers, J., van Andel, T. R., & Eric Schranz, M. (2019). Origins and geographic diversification of African rice (Oryza glaberrima). PloS one, 14(3), [e0203508]. https://doi.org/10.1371/journal.pone.0203508

    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, MA, Flowers, J, van Andel, TR & Eric Schranz, M 2019, 'Origins and geographic diversification of African rice (Oryza glaberrima)', PloS one, vol. 14, no. 3, e0203508. https://doi.org/10.1371/journal.pone.0203508
    Veltman MA, Flowers J, van Andel TR, Eric Schranz M. Origins and geographic diversification of African rice (Oryza glaberrima). PloS one. 2019 Mar 1;14(3). e0203508. https://doi.org/10.1371/journal.pone.0203508
    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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