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ABSTRACT Weedy rice is a close relative of cultivated rice (Oryza sativa) that infests rice fields worldwide and drastically reduces yields. To combat this agricultural pest, rice farmers in the southern US began to grow herbicide‐resistant (HR) rice cultivars in the early 2000s, which permitted the application of herbicides that selectively targeted weedy rice without harming the crop. The widespread adoption of HR rice coincided with increased reliance on hybrid rice cultivars in place of traditional inbred varieties. Although both cultivated and weedy rice are predominantly self‐fertilising, the combined introductions of HR and hybrid rice dramatically altered the opportunities and selective pressure for crop‐weed hybridization and adaptive introgression. In this study, we generated genotyping‐by‐sequencing data for 178 weedy rice samples collected from across the rice growing region of the southern US; these were analysed together with previously published rice and weedy rice genome sequences to determine the recent genomic and population genetic consequences of adaptive introgression and selection for herbicide resistance in US weedy rice populations. We find a reshaped geographical structure of southern US weedy rice as well as purging of crop‐derived alleles in some weed strains of crop‐weed hybrid origin. Furthermore, we uncover evidence that related weedy rice strains have made use of different genetic mechanisms to respond to selection. Lastly, we identify widespread presence of HR alleles in both hybrid‐derived and nonadmixed samples, which further supports an overall picture of weedy rice evolution and adaptation through diverse genetic mechanisms.
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Convergent evolution of root system architecture in two independently evolved lineages of weedy rice
Summary Root system architecture (RSA) is a critical aspect of plant growth and competitive ability. Here we used two independently evolved strains of weedy rice, a de‐domesticated form of rice, to study the evolution of weed‐associatedRSAtraits and the extent to which they evolve through shared or different genetic mechanisms.We characterised 98 two‐dimensional and three‐dimensionalRSAtraits in 671 plants representing parents and descendants of two recombinant inbred line populations derived from two weed × crop crosses. A random forest machine learning model was used to assess the degree to which root traits can predict genotype and the most diagnostic traits for doing so. We used quantitative trait locus (QTL)mapping to compare genetic architecture between the weed strains.The two weeds were distinguishable from the crop in similar and predictable ways, suggesting independent evolution of a ‘weedy’RSAphenotype. Notably, comparativeQTLmapping revealed little evidence for shared underlying genetic mechanisms.Our findings suggest that despite the double bottlenecks of domestication and de‐domestication, weedy rice nonetheless shows genetic flexibility in the repeated evolution of weedyRSAtraits. Whereas the root growth of cultivated rice may facilitate interactions among neighbouring plants, the weedy rice phenotype may minimise below‐ground contact as a competitive strategy.
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- Award ID(s):
- 1638507
- PAR ID:
- 10461458
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- New Phytologist
- Volume:
- 223
- Issue:
- 2
- ISSN:
- 0028-646X
- Page Range / eLocation ID:
- p. 1031-1042
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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