Abstract
Background: The domestication of Asian rice (Oryza sativa) was a complex process punctuated by episodes of introgressive hybridization among and between subpopulations. Deep genetic divergence between the two main varietal groups (Indica and Japonica) suggests domestication from at least two distinct wild populations. However, genetic uniformity surrounding key domestication genes across divergent subpopulations suggests cultural exchange of genetic material among ancient farmers. Methodology/Principal Findings: In this study, we utilize a novel 1,536 SNP panel genotyped across 395 diverse accessions of O. sativa to study genome-wide patterns of polymorphism, to characterize population structure, and to infer the introgression history of domesticated Asian rice. Our population structure analyses support the existence of five major subpopulations (indica, aus, tropical japonica, temperate japonica and GroupV) consistent with previous analyses. Our introgression analysis shows that most accessions exhibit some degree of admixture, with many individuals within a population sharing the same introgressed segment due to artificial selection. Admixture mapping and association analysis of amylose content and grain length illustrate the potential for dissecting the genetic basis of complex traits in domesticated plant populations. Conclusions/Significance: Genes in these regions control a myriad of traits including plant stature, blast resistance, and amylose content. These analyses highlight the power of population genomics in agricultural systems to identify functionally important regions of the genome and to decipher the role of human-directed breeding in refashioning the genomes of a domesticated species.
| Original language | English (US) |
|---|---|
| Article number | e10780 |
| Journal | PloS one |
| Volume | 5 |
| Issue number | 5 |
| DOIs | |
| State | Published - 2010 |
Bibliographical note
Funding Information:We thank Teresa Hancock and Daniel Wood, supported by this grant through the University of Arkansas at the Rice Research and Extension Center, Stuttgart, AR for their outstanding technical assistance collecting phenotypic information and managing the seed stocks. We thank Weiwei Zhai from Beijing Institute of Genomics for comments and suggestions on the manuscript. We acknowledge the assistance of Melissa Jia in the Genomics Core Facility at the Dale Bumpers National Rice Research Center, Stuttgart, AR for running the grain quality markers. We thank Ken McNally and Jan Leach of the OryzaSNP project for early access to the OryzaSNP data. We are grateful to Lois Swales for help formatting the manuscript.
