Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice

Michael Reagon, Carrie S. Thurber, Briana L. Gross, Kenneth M. Olsen, Yulin Jia, Ana L. Caicedo

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102 Scopus citations

Abstract

Background. Weedy rice (red rice), a conspecific weed of cultivated rice (Oryza sativa L.), is a significant problem throughout the world and an emerging threat in regions where it was previously absent. Despite belonging to the same species complex as domesticated rice and its wild relatives, the evolutionary origins of weedy rice remain unclear. We use genome-wide patterns of single nucleotide polymorphism (SNP) variation in a broad geographic sample of weedy, domesticated, and wild Oryza samples to infer the origin and demographic processes influencing U.S. weedy rice evolution. Results. We find greater population structure than has been previously reported for U.S. weedy rice, and that the multiple, genetically divergent populations have separate origins. The two main U.S. weedy rice populations share genetic backgrounds with cultivated O. sativa varietal groups not grown commercially in the U.S., suggesting weed origins from domesticated ancestors. Hybridization between weedy groups and between weedy rice and local crops has also led to the evolution of distinct U.S. weedy rice populations. Demographic simulations indicate differences among the main weedy groups in the impact of bottlenecks on their establishment in the U.S., and in the timing of divergence from their cultivated relatives. Conclusions. Unlike prior research, we did not find unambiguous evidence for U.S. weedy rice originating via hybridization between cultivated and wild Oryza species. Our results demonstrate the potential for weedy life-histories to evolve directly from within domesticated lineages. The diverse origins of U.S. weedy rice populations demonstrate the multiplicity of evolutionary forces that can influence the emergence of weeds from a single species complex.

Original languageEnglish (US)
Article number180
JournalBMC evolutionary biology
Volume10
Issue number1
DOIs
StatePublished - 2010

Bibliographical note

Funding Information:
We are grateful to D. Gealy for providing weedy rice accessions and S.R. McCouch for providing several cultivated rice accessions used in this study. We also thank members of the Caicedo, Olsen labs, and anonymous reviewers that provided comments that much improved that manuscript. This project was funded by a grant from the U.S. National Science Foundation Plant Genome Research Program (DBI-0638820) to ALC, KMO and YJ.

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