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Abstract Weedy rice is a close relative of cultivated rice that devastates rice productivity worldwide. In the southern United States, two distinct strains have been historically predominant, but the 21 st century introduction of hybrid rice and herbicide resistant rice technologies has dramatically altered the weedy rice selective landscape. Here, we use whole-genome sequences of 48 contemporary weedy rice accessions to investigate the genomic consequences of crop-weed hybridization and selection for herbicide resistance. We find that population dynamics have shifted such that most contemporary weeds are now crop-weed hybrid derivatives, and that their genomes have subsequently evolved to be more like their weedy ancestors. Haplotype analysis reveals extensive adaptive introgression of cultivated alleles at the resistance gene ALS , but also uncovers evidence for convergent molecular evolution in accessions with no signs of hybrid origin. The results of this study suggest a new era of weedy rice evolution in the United States.
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Recent Crop‐To‐Weed Adaptive Introgression Has Reshaped the Genomic Composition and Geographical Structure of US Weedy Rice ( Oryza spp.)
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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- Award ID(s):
- 1947609
- PAR ID:
- 10586081
- Publisher / Repository:
- Wiley and Sons
- Date Published:
- Journal Name:
- Molecular Ecology
- ISSN:
- 0962-1083
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Weedy rice (Oryzaspp.) is a weedy relative of the cultivated rice that competes with the crop and causes significant production loss. The BHA (blackhull awned) US weedy rice group has evolved fromauscultivated rice and differs from its ancestors in several important weediness traits, including flowering time, plant height and seed shattering. Prior attempts to determine the genetic basis of weediness traits in plants using linkage mapping approaches have not often considered weed origins. However, the timing of divergence between crossed parents can affect the detection of quantitative trait loci (QTL) relevant to the evolution of weediness. Here, we used a QTL‐seq approach that combines bulked segregant analysis and high‐throughput whole genome resequencing to map the three important weediness traits in an F2population derived from a cross between BHA weedy rice with an ancestralauscultivar. We compared these QTLs with those previously detected in a cross of BHA with a more distantly related crop,indica. We identified multiple QTLs that overlapped with regions under selection during the evolution of weedy BHA rice and some candidate genes possibly underlying the evolution weediness traits in BHA. We showed that QTLs detected with ancestor–descendant crosses are more likely to be involved in the evolution of weediness traits than those detected from crosses of more diverged taxa.more » « less
- Free Publicly Accessible Full Text
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Accepted Manuscript
- Journal Article:
- https://doi.org/10.1111/mec.17604
