Domesticated Asian rice (Oryza sativa) is one of the oldest domesticated crop species in the world, having fed more people than any other plant in human history. We report the patterns of DNA sequence variation in rice and its wild ancestor, O. rufipogon, across 111 randomly chosen gene fragments, and use these to infer the evolutionary dynamics that led to the origins of rice. There is a genome-wide excess of high-frequency derived single nucleotide polymorphisms (SNPs) in O. sativa varieties, a pattern that has not been reported for other crop species. We developed several alternative models to explain contemporary patterns of polymorphisms in rice, including a (i) selectively neutral population bottleneck model, (ii) bottleneck plus migration model, (iii) multiple selective sweeps model, and (iv) bottleneck plus selective sweeps model. We find that a simple bottleneck model, which has been the dominant demographic model for domesticated species, cannot explain the derived nucleotide polymorphism site frequency spectrum in rice. Instead, a bottleneck model that incorporates selective sweeps, or a more complex demographic model that includes subdivision and gene flow, are more plausible explanations for patterns of variation in domesticated rice varieties. If selective sweeps are indeed the explanation for the observed nucleotide data of domesticated rice, it suggests that strong selection can leave its imprint on genome-wide polymorphism patterns, contrary to expectations that selection results only in a local signature of variation. Domesticated Asian rice is one of the oldest and most important crops in the world. Two main rice evolutionary lineages have been identified, and are thought to have been independently domesticated in Asia. We have examined patterns of DNA sequence variation in the genomes of rice and its wild ancestor to make inferences about the origin of domesticated rice. Population bottlenecks (a reduction in the size of the founding population) in the evolutionary transition from wild to cultivated species has long been thought to be the dominant force shaping patterns of molecular evolution during domestication. We find that the nucleotide variation patterns in rice are inconsistent with a simple bottleneck model. Rice genetic variation, however, can be explained by either a model that incorporates both a bottleneck and migration among rice variety groups, or a model that incorporates a bottleneck and multiple rounds of artificial selection on rice. Selection by humans is believed to have played an important role during crop domestication, and these results may suggest that strong, recurrent selection can leave a signal that can be observed throughout the genomes of domesticated species.

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.

Despite its status as one of the world's major crops, linkage disequilibrium (LD) patterns have not been systematically characterized across the genome of Asian rice (Oryza sativa). Such information is critical to fully exploit the genome sequence for mapping complex traits using association techniques. Here we characterize LD in five 500-kb regions of the rice genome in three major cultivated rice varieties (indica, tropical japonica, and temperate japonica) and in the wild ancestor of Asian rice, Oryza rufipogon. Using unlinked SNPs to determine the amount of background linkage disequilibrium in each population, we find that the extent of LD is greatest in temperate japonica (probably >500 kb), followed by tropical japonica (∼150 kb) and indica (∼75 kb). LD extends over a shorter distance in O. rufipogon (≪40 kb) than in any of the O. sativa groups assayed here. The differences in the extent of LD among these groups are consistent with differences in outcrossing and recombination rate estimates. As well as heterogeneity between groups, our results suggest variation in LD patterns among genomic regions. We demonstrate the feasibility of genomewide association mapping in cultivated Asian rice using a modest number of SNPs.

Domestication is a co-evolutionary process that occurs when wild plants are brought into cultivation by humans, leading to origin of new species and/or differentiated populations that are critical for human survival. Darwin used domesticated species as early models for evolution, highlighting their variation and the key role of selection in species differentiation. Over the last two decades, a growing synthesis of plant genetics, genomics, and archaeobotany has led to challenges to old orthodoxies and the advent of fresh perspectives on how crop domestication and diversification proceed. I discuss four new insights into plant domestication - that in general domestication is a protracted process, that unconscious (natural) selection plays a prominent role, that interspecific hybridization may be an important mechanism for crop species diversification and range expansion, and that similar genes across multiple species underlies parallel/convergent phenotypic evolution between domesticated taxa. Insights into the evolutionary origin and diversification of crop species can help us in developing new varieties (and possibly even new species) to deal with current and future environmental challenges in a sustainable manner.