Abstract
BackgroundWeedy 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.ResultsWe 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.ConclusionsUnlike 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.
Highlights
Introduction to US.bPost domesticationc DomesticationdPrior to domesticationeBHA1 - aus SH - indica0.001 a The approximate likelihood is shown, calculated out of total number of simulations for each scenario. b τs = τf and ranges from 30 to 400 years. c τf = 1000 - 7000 d τf = 7000 - 12000 e τf = 12000 - 50000 A
Conspecific weeds may evolve from standing genetic variation in wild relatives [7], or cultivated germplasm [e.g. [9]], though examples of weeds evolving directly from crops are rare
Thirty-three single nucleotide polymorphism (SNP) had more than two alleles, primarily (73%) due to alternative states present in the outgroup species (O. barthii or O. meridionalis)
Summary
Despite belonging to the same species complex as domesticated rice and its wild relatives, the evolutionary origins of weedy rice remain unclear. Among the most widespread and costly agricultural pests are the numerous weeds that have evolved from within the same complex of interfertile species as domesticated plants [1,2,3]. The evolutionary success of conspecific weeds is often attributed to acquisition of traits associated with wild plants (e.g. dormancy), presumably selected against in crops. These weeds often exhibit characteristics typical of domesticated. The larger complex of interfertile species within which conspecific weeds evolve includes the crop, wild relatives, and other feral weeds [6]. The short evolutionary time scales involved make it less likely that novel mutations are significant to weed evolution, exceptions are known [e.g. [10]]
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