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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #241497
Title: Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice

Author
item REAGON, MICHAEL - University Of Massachusetts
item THURBER, CARRIE - Washington University
item GROSS, BRIANA - Washington University
item OLSEN, KENNETH - Washington University
item Jia, Yulin
item CAICEDO, ANA - University Of Massachusetts

Submitted to: BMC Evolutionary Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/2/2010
Publication Date: 6/15/2010
Citation: Reagon, M., Thurber, C.S., Gross, B.L., Olsen, K.M., Jia, Y., Caicedo, A.L. 2010. Genomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice. BMC Evolutionary Biology. 10(180):1-16.

Interpretive Summary: Weedy rice has been a major constraint for rice production in the US and the world. In the present study we investigated the origin of US weedy rice use genome-wide patterns of single nucleotide polymorphism (SNP) variation. Separate origins of multiple, genetically divergent populations of U.S. weedy rice were identified. Similar genetic backgrounds of the two morphologically diverse U.S. weedy rice populations were identified in cultivated O. sativa varieties not grown commercially in the U.S. This finding suggests that these two main weedy populations originated from domesticated ancestors. Furthermore, evidence of hybridization between weedy groups and between weedy rice and local crops was found to play a small, but detectable role in U.S. weedy rice evolution. The SNP data also identify the differences among the main weedy groups in the impact of bottlenecks on their establishment in the U.S., and differences in the timing of divergence from their cultivated relatives.

Technical Abstract: Weedy rice is a significant problem in cultivated rice fields throughout the world, and is an emerging threat in regions where it was previously absent. Prior research has classified weedy rice as the same species as Asian cultivated rice (Oryza sativa L.). This close genetic relationship makes control of the weed particularly difficult. 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 origin and demographic processes influencing weed evolution. We found greater population structure than has been previously reported for U.S. weedy rice, and that multiple, genetically divergent populations have separate origins. The two main U.S. weedy rice populations are largely differentiated morphologically, and share a genetic background with cultivated O. sativa varieties not grown commercially in the U.S., suggesting an origin from domesticated ancestors. Hybridization between weedy groups and between weedy rice and local crops has played a small, but detectable role in U.S. weedy rice evolution. Demographic simulations indicate differences among the main weedy groups in the impact of bottlenecks on their establishment in the U.S., and differences in the timing of divergence from their cultivated relatives.