Genomic evidence of human selection on Vavilovian mimicry

Ye, Chu-Yu; Tang, Wei; Wu, Dongya; Lu, Jia; Qiu, Jie; Chen, Meihong; Mao, Limin; Lin, Feng; Xu, Haiming; Yu, Xiaoyue; Lu, Yongliang; Wang, Yonghong; Olsen, Kenneth M.; Timko, Michael P.; Fan, Longjiang

doi:10.1038/s41559-019-0976-1

Cited by 38 publications

(38 citation statements)

References 66 publications

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“…The ratios were not significantly different between subgenomes A T and B T in E. oryzicola (Figure 4A and 4B), and the ratios for subgenomes A H and B H were still not different after hexaploidization (Figure 4A and 4B). To further confirm this observation, we calculated the pN/pS ratio based on SNPs in E. crus-galli populations collected in our previous work (Ye et al, 2019) (for details see Methods), and also found no significant differences between the two subgenomes (Figure 4B). Taken together, these results suggest symmetric evolution of subgenomes under similar selection pressure during Echinochloa polyploidization.…”

Section: Symmetric Selection On Subgenomes During Echinochloa Polyploidizationsupporting

confidence: 62%

“…pS is the number of polymorphic synonymous positions divided by the number of possible synonymous sites. Thirty E. crus-galli lines with genome resequencing data were selected for pN/pS calculation (Ye et al, 2019). SNP calling was performed using the method described previously with the exception that the new STB08 genome assembly was used (Ye et al, 2019).…”

Section: Gene Family Identificationmentioning

confidence: 99%

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The Genomes of the Allohexaploid Echinochloa crus-galli and Its Progenitors Provide Insights into Polyploidization-Driven Adaptation

Mao

et al. 2020

Molecular Plant

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The hexaploid species Echinochloa crus-galli is one of the most detrimental weeds in crop fields, especially in rice paddies. Its evolutionary history is similar to that of bread wheat, arising through polyploidization after hybridization between a tetraploid and a diploid species. In this study, we generated and analyzed high-quality genome sequences of diploid (E. haploclada), tetraploid (E. oryzicola), and hexaploid (E. crus-galli) Echinochloa species. Gene family analysis showed a significant loss of disease-resistance genes such as those encoding NB-ARC domain-containing proteins during Echinochloa polyploidization, contrary to their significant expansionduring wheat polyploidization, suggesting that natural selection might favor reduced investment in resistance in this weed to maximize its growth and reproduction. In contrast to the asymmetric patterns of genome evolution observed in wheat and other crops, no significant differences in selection pressure were detected between the subgenomes in E. oryzicola and E. crus-galli. In addition, distinctive differences in subgenome transcriptome dynamics during hexaploidization were observed between E. crus-galli and bread wheat. Collectively, our study documents genomic mechanisms underlying the adaptation of a major agricultural weed during polyploidization. The genomic and transcriptomic resources of three Echinochloa species and new insights into the polyploidization-driven adaptive evolution would be useful for future breeding cereal crops.

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Section: Symmetric Selection On Subgenomes During Echinochloa Polyploidizationsupporting

confidence: 62%

Section: Gene Family Identificationmentioning

confidence: 99%

The Genomes of the Allohexaploid Echinochloa crus-galli and Its Progenitors Provide Insights into Polyploidization-Driven Adaptation

Mao

et al. 2020

Molecular Plant

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“…Such weeding stresses, in turn, act as unintentional selection pressures driving the evolution of weed populations. While multiple evolved traits related to weed adaptation in agricultural ecosystems have been documented, such as flowering phenology, mimicry morphology, seed shattering, seed dormancy, and competitiveness (Fukano, Guo, Uchida, Tachiki, & Cornelissen, 2020; Waselkov, Regenold, Lum, & Olsen, 2020; Wedger & Olsen, 2018; Ye et al, 2019), herbicide resistance remains among the best studied and characterised trait (Powles & Yu, 2010). Evolved herbicide resistance has been documented worldwide in as many as 263 weed species (Heap, 2021), posing a great threat to the current global food security.…”

Section: Introductionmentioning

confidence: 99%

Gene expression shapes the patterns of parallel evolution of herbicide resistance in the agricultural weed Monochoria vaginalis

Tanigaki

Uchino

Okawa

et al. 2021

Preprint

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The evolution of herbicide resistance in weeds is an example of parallel evolution, through which genes encoding herbicide target proteins are repeatedly represented as evolutionary loci. The number of herbicide target-site genes differs among species, and little is known regarding the effects of duplicate gene copies on the evolution of herbicide resistance.　We investigated the evolution of herbicide resistance in Monochoria vaginalis, which carries five copies of sulfonylurea target-site acetolactate synthase (ALS) genes. Suspected resistant populations collected across Japan were investigated for herbicide sensitivity and ALS gene sequences, followed by functional characterisation and ALS gene expression analysis.　We identified over 60 resistant populations, all of which carried resistance-conferring amino acid substitutions exclusively in MvALS1 or MvALS3. All MvALS4 alleles carried a loss-of-function mutation. Although the enzymatic properties of ALS encoded by these genes were not markedly different, the expression of MvALS1 and MvALS3 was prominently higher among all ALS genes.　The higher expression of MvALS1 and MvALS3 is the driving force of the biased representation of genes during the evolution of herbicide resistance in M. vaginalis. Our findings highlight that gene expression is a key factor in creating evolutionary hotspots.

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“…Crop plants often possess traits that are rare or absent in wild populations (e.g., salinity tolerance and herbicide resistance) which can improve crop-wild hybrid survival and reproduction in stressful environments (Gasser and Fraley, 1989;Ellstrand and Hoffman, 1990;Bagavathiannan and Van Acker, 2008). Crop-wild hybrid offspring often share morphological features with their crop progenitors and avoid eradication by farmers in the field (Ye et al, 2019); thereby enhancing their survival in agricultural fields. Furthermore, crop-derived traits such as early emergence and high seed production can contribute to crop-wild hybrid success when competing with wild populations in natural environments (Snow and Campbell, 2005;Kost et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Hybridization Slows Rate of Evolution in Crop-Wild Compared to Wild Populations of Weedy Raphanus Across a Moisture Gradient

et al. 2020

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Hybrid offspring of crops and their wild relatives commonly possess non-adaptive phenotypes and diminished fitness. Regularly, diminished success in early-generation hybrid populations is interpreted to suggest reduced biosafety risk regarding the unintended escape of novel traits from crop populations. Yet hybrid populations have been known to evolve to recover fitness relative to wild progenitors and can do so more rapidly than wild populations, although rates of evolution (for both hybrid populations and their wild progenitors) are sensitive to environmental context. In this research, we asked whether hybrid populations evolved more rapidly than wild populations in the context of soil moisture. We estimated evolutionary rates for 40 Raphanus populations that varied in their history of hybridization and environmental context (imposed by an experimental moisture cline) in two common gardens. After five generations of growing wild and crop-wild hybrid populations across a soil-moisture gradient, hybrid populations exhibited increased seedling emergence frequencies (~6% more), earlier emergence (~1 day), later flowering (~3 days), and larger body size (15–35%)—traits correlated with fitness—relative to wild populations. Hybrid populations, however, exhibited slower evolutionary rates than wild populations. Moreover, the rate of evolution in hybrid populations was consistent across evolutionary watering environments, but varied across watering environments in wild populations. These consistent evolutionary rates exhibited in hybrid populations suggests the evolution of robust traits that perform equally across soil moisture environments—a survival strategy characterized as “jack of all trades.” Although, diverse integrated weed management practices must be applied to wild and hybrid genotypes to diversify selection on these populations, evaluating the evolutionary rates of weeds in diverse environments will support the development of multi-faceted weed control strategies and effective integrated weed management policies.

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Genomic evidence of human selection on Vavilovian mimicry

Cited by 38 publications

References 66 publications

The Genomes of the Allohexaploid Echinochloa crus-galli and Its Progenitors Provide Insights into Polyploidization-Driven Adaptation

The Genomes of the Allohexaploid Echinochloa crus-galli and Its Progenitors Provide Insights into Polyploidization-Driven Adaptation

Gene expression shapes the patterns of parallel evolution of herbicide resistance in the agricultural weed Monochoria vaginalis

Hybridization Slows Rate of Evolution in Crop-Wild Compared to Wild Populations of Weedy Raphanus Across a Moisture Gradient

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