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, 108 (20), 8351-6

Molecular Evidence for a Single Evolutionary Origin of Domesticated Rice

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Molecular Evidence for a Single Evolutionary Origin of Domesticated Rice

Jeanmaire Molina et al. Proc Natl Acad Sci U S A.

Abstract

Asian rice, Oryza sativa, is one of world's oldest and most important crop species. Rice is believed to have been domesticated ∼9,000 y ago, although debate on its origin remains contentious. A single-origin model suggests that two main subspecies of Asian rice, indica and japonica, were domesticated from the wild rice O. rufipogon. In contrast, the multiple independent domestication model proposes that these two major rice types were domesticated separately and in different parts of the species range of wild rice. This latter view has gained much support from the observation of strong genetic differentiation between indica and japonica as well as several phylogenetic studies of rice domestication. We reexamine the evolutionary history of domesticated rice by resequencing 630 gene fragments on chromosomes 8, 10, and 12 from a diverse set of wild and domesticated rice accessions. Using patterns of SNPs, we identify 20 putative selective sweeps on these chromosomes in cultivated rice. Demographic modeling based on these SNP data and a diffusion-based approach provide the strongest support for a single domestication origin of rice. Bayesian phylogenetic analyses implementing the multispecies coalescent and using previously published phylogenetic sequence datasets also point to a single origin of Asian domesticated rice. Finally, we date the origin of domestication at ∼8,200-13,500 y ago, depending on the molecular clock estimate that is used, which is consistent with known archaeological data that suggests rice was first cultivated at around this time in the Yangtze Valley of China.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Schematics of the single- (A) vs. double- (B) founder models. (A) In the single domestication event, both domesticated subspecies originated from the same O. rufipogon ancestral population. (B) In the double-founder model, indica and tropical japonica were domesticated independently from different O. rufipogon populations. O. rufipogon, O. sativa ssp. indica, and O. sativa ssp. tropical japonica are indicated by the subscripts r, I, and j, respectively. The times τB and τ represent the length of the bottleneck and time thereafter during the two-population epoch. Likewise, τ2B and τ2 represent the length of time of the bottleneck and time thereafter for the three-population epoch. Symmetric migration (μ) between the populations is represented by arrows, and N is the population size.
Fig. 2.
Fig. 2.
Summary of selective sweep mapping results. Candidate selective sweep regions identified in each test for selection for (A) chromosome 8, (B) chromosome 10, and (C) chromosome 12. Results for different subspecies are indicated by red for indica and blue for tropical japonica. CLR, composite likelihood ratio test based on the multipopulation allele frequency spectrum; DIV, diversity test based on regions of no variation; TJ, tropical japonica; IND. Vertical bars in the CLR track correspond to single fragments, because it was calculated for each fragment separately. Colors in the track correspond to the respective population, with black bars indicating a sweep in both indica and tropical japonica. The four shared sweep regions are marked with a dot.
Fig. 3.
Fig. 3.
Results from *BEAST analyses of phylogenetic datasets. Nodes supported with high posterior probability (≥95%) by all datasets are shown with a dot. I, J, R, and N represent indica, tropical japonica, O. rufipogon, and O. nivara, respectively. The numbers above the bars in the graphs indicate the percentage of trees in the posterior probability distribution with a given topology or that support a single origin of rice. (A) Alternative species trees and their proportions in the posterior distribution resulting from analyses of the Tang et al. (17) (red) and Zhu et al. (38) (yellow) data. (B) Only one well-supported species tree was recovered from the Rakshit et al. (19) data. (C) All trees in the posterior distribution, despite inclusion of the five main cultivar groups [aromatics (Ar), Aus, temperate japonica (TmJ), tropical japonica (TrJ), and indica (I)] in an analysis of the Yu et al. (39) dataset, support a single origin for domesticated taxa. Ri and Rc indicate O. rufipogon from India/Indochina and China, respectively.

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