Abstract
While the domestication history of Asian rice has been extensively studied, details of the evolution of African rice remain elusive. The inner Niger delta has been suggested as the center of origin but molecular data to support this hypothesis is lacking. Here, we present a comprehensive analysis of the evolutionary and domestication history of African rice. By analyzing whole genome re-sequencing data from 282 individuals of domesticated African rice Oryza glaberrima and its progenitor O. barthii, we hypothesize a non-centric (i.e. multiregional) domestication origin for African rice. Our analyses showed genetic structure within O. glaberrima that has a geographical association. 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 were either mislabeled or may actually represent feral wild-domesticated hybrids. 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. In addition, measurements of panicle threshability, a key early domestication trait for seed shattering, were consistent with the gene phylogeographic results. We suggest seed non-shattering was selected from multiple genotypes, possibly arising from different geographical regions. Based on our evidence, O. glaberrima was not domesticated from a single centric location but was a result of diffuse process where multiple regions contributed key alleles for different domestication traits.
Highlights
Domestication of crop species represents a key co-evolutionary transition, in which wild plant species were cultivated by humans and eventually gave rise to new species whose propagation were dependent on human action [1,2,3]
Together with 92 O. glaberrima genomes that were previously re-sequenced [14], which originated mostly from the coastal region (S1B Fig), the 172 O. glaberrima genomes analyzed in this study represent a wide geographical range from West and Central Africa
We re-sequenced the genomes of 16 O. barthii samples randomly selected from this area, which includes the areas from coastal west Africa, inner Niger delta, and the lower Niger basin (S1C Fig)
Summary
Domestication of crop species represents a key co-evolutionary transition, in which wild plant species were cultivated by humans and eventually gave rise to new species whose propagation were dependent on human action [1,2,3]. The evolutionary origin(s) of various crop species have been the subject of considerable interest Studying it has broadened our understanding of the early dynamics associated with crop species origins and divergence, the nature of human/ plant interactions, and the genetic basis of domestication. Within the genus Oryza, crop domestication has occurred at least twice—once in Asia and separately in Africa. In Asia, the wild rice O. rufipogon was domesticated into the Asian rice O. sativa approximately 9,000 years ago [4]. In West Africa, the wild rice O. barthii was independently domesticated into the African rice O. glaberrima about 3,000 years ago [4]. Recent archaeological studies have suggested that a third independent domestication event occurred in South America during pre-Columbian times, but this crop species is no longer cultivated [5]
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