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

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dc.contributor.authorReagon, Michael
dc.contributor.authorThurber, Carrie
dc.contributor.authorGross, Brian
dc.contributor.authorOlsen, Kenneth
dc.contributor.authorJia, Yulin
dc.contributor.authorCaicedo, Ana
dc.contributor.departmentUniversity of Massachusetts - Amherst
dc.contributor.departmentUniversity of Massachusetts - Amherst
dc.contributor.departmentWashington University in St Louis
dc.contributor.departmentWashington University in St Louis
dc.contributor.departmentUniversity of Massachusetts - Amherst
dc.date2023-09-23T17:07:23.000
dc.date.accessioned2024-04-26T08:41:14Z
dc.date.available2024-04-26T08:41:14Z
dc.date.issued2010-06-15
dc.descriptionThis article was harvested from BioMedCentral. <a href="http://creativecommons.org/licenses/by/3.0/deed.en_US"><img src="http://i.creativecommons.org/l/by/3.0/80x15.png" /></a><br />This work is licensed under a <a href="http://creativecommons.org/licenses/by/3.0/deed.en_US">Creative Commons Attribution 3.0 Unported License</a>.
dc.description.abstractBackground: 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.
dc.identifier.doihttps://doi.org/10.1186/1471-2148-10-180
dc.identifier.urihttps://hdl.handle.net/20.500.14394/4292
dc.relation.ispartofBMC Evolutionary Biology
dc.relation.urlhttps://works.bepress.com/ana_caicedo/1/download/
dc.source.issue180
dc.source.issue10
dc.source.issue10
dc.source.statuspublished
dc.subjectBiology
dc.subjectGenomics
dc.subjectMolecular Genetics
dc.titleGenomic patterns of nucleotide diversity in divergent populations of U.S. weedy rice
dc.typearticle
dc.typearticle
digcom.contributor.authorReagon, Michael
digcom.contributor.authorisAuthorOfPublication|email:cthurber@cns.umass.edu|institution:University of Massachusetts - Amherst|Thurber, Carrie
digcom.contributor.authorGross, Brian
digcom.contributor.authorOlsen, Kenneth
digcom.contributor.authorJia, Yulin
digcom.contributor.authorisAuthorOfPublication|email:caicedo@bio.umass.edu|institution:University of Massachusetts - Amherst|Caicedo, Ana
digcom.identifierbiology_faculty_pubs/619
digcom.identifier.contextkey9684405
digcom.identifier.submissionpathbiology_faculty_pubs/619
dspace.entity.typePublication
relation.isAuthorOfPublicationc5a14c39-9f74-4968-a900-482a22bab8a2
relation.isAuthorOfPublication.latestForDiscoveryc5a14c39-9f74-4968-a900-482a22bab8a2
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