Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice

Abstract

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.

The Evolutionary History of Ehrhartoideae, Oryzeae, and Oryza

“…5b (Caicedo et al 2007). In addition, too many loci had SNPs that were at a high frequency in O. sativa.…”

Genetic Diversity of Isolated Populations of Indonesian Landraces of Rice (Oryza sativa L.) Collected in East Kalimantan on the Island of Borneo

“…The genetic diversity of cultivated rice germplasm on a global scale has been well characterized using molecular markers (Caicedo et al 2007;Garris et al 2005;Glaszmann 1987;Yang et al 1994;Yu et al 2003). To encompass the entire range of rice diversity, these studies have sampled rice varieties from many different rice-growing countries around the world.…”

“…In contrast, the accelerated evolution provided by intense artificial selection and seed exchanges among local farmers has led to dramatic changes in the genetics of cultivated crops in a relatively short time frame (<10,000 years). While the story of rice domestication is still being unraveled based on interpretations of geographic and phylogenetic data (Caicedo et al 2007;Londo et al 2006) and analysis of cloned domestication genes (Kovach et al 2007;), it appears that rice was domesticated from diverse gene pools and that gene flow among sub-populations and with wild ancestral populations has created a complex series of events leading to the modern day fabric of rice diversity (Sang and Ge 2007;Sweeney and McCouch 2007), although the possibility of a single domestication event is still debated (Gao and Innan 2008;Vaughan et al 2008). While the relationships between the earliest domesticates and indigenous landraces surviving in rice-growing regions today are still unclear, signatures of shared ancestry, selection, and introgression are written in the genomes of traditional varieties.…”

A map of rice genome variation reveals the origin of cultivated rice

“…Despite the fact that rice is a major cereal and a model system for plant biology, the evolutionary origins and domestication processes of cultivated rice have long been debated. The puzzles about rice domestication include: (1) where the geographic origin of cultivated rice was, (2) which types of O. rufipogon served as its direct wild progenitor, and (3) whether the two subspecies of cultivated rice, indica and japonica, are derived from a single or multiple domestications.A wide range of genetic and archaeological studies have been carried out to examine the phylogenetic relationships of rice, and investigate the demographic history of rice domestication [10][11][12][13][14][15][16][17][18][19] . Molecular phylogenetic analyses indicated that indica and japonica originated independently 3,10,20 .…”

“…A wide range of genetic and archaeological studies have been carried out to examine the phylogenetic relationships of rice, and investigate the demographic history of rice domestication [10][11][12][13][14][15][16][17][18][19] . Molecular phylogenetic analyses indicated that indica and japonica originated independently 3,10,20 .…”