Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes

Abstract

Genealogical patterns in different genomic regions may be different due to the joint influence of gene flow and selection. The existence of two subspecies of cultivated rice provides a unique opportunity for analyzing these effects during domestication. We chose 66 accessions from the three rice taxa (about 22 each from Oryza sativa indica, O. sativa japonica, and O. rufipogon) for whole-genome sequencing. In the search for the signature of selection, we focus on low diversity regions (LDRs) shared by both cultivars. We found that the genealogical histories of these overlapping LDRs are distinct from the genomic background. While indica and japonica genomes generally appear to be of independent origin, many overlapping LDRs may have originated only once, as a result of selection and subsequent introgression. Interestingly, many such LDRs contain only one candidate gene of rice domestication, and several known domestication genes have indeed been “rediscovered” by this approach. In summary, we identified 13 additional candidate genes of domestication.

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 .…”

“…Recently, a demographic analysis of single-nucleotide polymorphisms (SNPs) detected from 630 gene fragments suggested a single domestication origin of rice 17 . Meanwhile, population genetics analyses of genome-wide data of cultivated and wild rice have tended to suggest that indica and japonica genomes generally appear to be of independent origin 18,19 , but many genomic segments bearing domestication alleles may have originated only once 18 . Despite these advances, wider sampling with population-scale whole-genome sequencing is needed to shed greater light on the evolutionary history of rice domestication.…”

Robust Identification of Local Adaptation from Allele Frequencies

“…Recently, pooled next-generation sequencing (NGS) of multiple individuals from a population has gained in popularity (e.g., Turner et al 2010Turner et al , 2011He et al 2011;Kolaczkowski et al 2011;Boitard et al 2012;Fabian et al 2012;Kofler et al 2012;Lamichhaney et al 2012;Orozco-terWengel et al 2012), as it offers a cost-efficient alternative to sequencing of single individuals. However, estimating allele frequencies from read counts sequenced from a pool implies a second level of sampling variance (Futschik and Schlötterer 2010;Zhu et al 2012), which needs to be considered in population genetic analyses.…”

Rice in Thailand: The Archaeobotanical Contribution

“…Genetic studies remain divided as to whether rice domestication had a single origin or multiple origins (He et al 2011;Molina et al 2011;Sang and Ge 2007). The multiple-origins model proposes two centres of domestication, one in China ca.…”