Optimizing RNA‐seq studies to investigate herbicide resistance

Giacomini, Darci A.; Gaines, Todd A.; Beffa, Roland; Tranel, Patrick J.

doi:10.1002/ps.4822

Cited by 32 publications

(43 citation statements)

References 31 publications

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“…Of these omics approaches, transcriptomics have provided the most insights thus far. It is generally thought that NTSR is often mediated by increased expression of one or more genes (e.g., a gene encoding a P450 or an ABC transporter) and, consequently, a transcriptomics approach is ideally suited to identify such genes (155). One of the downfalls of a transcriptomic approach, however, is that it usually yields several "false positives," requiring significant downstream research to validate candidate genes.…”

Section: Importance Of Genomics and Transcriptomics In Understanding mentioning

confidence: 99%

Mechanisms of evolved herbicide resistance

Gaines

Duke

Morran

et al. 2020

Journal of Biological Chemistry

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428

493

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The widely successful use of synthetic herbicides over the past 70 years has imposed strong and widespread selection pressure, leading to the evolution of herbicide resistance in hundreds of weed species. Both target-site resistance (TSR) and non-target-site resistance (NTSR) mechanisms have evolved to most herbicide classes. TSR often involves mutations in genes encoding the protein targets of herbicides, affecting the binding of the herbicide either at or near catalytic domains or in regions affecting access to them. Most of these mutations are non-synonymous single-nucleotide polymorphisms, but polymorphisms in more than one codon or entire codon deletions have also evolved. Some herbicides bind multiple proteins, making TSR mechanisms more difficult to evolve. Increased amounts of protein target, by increased gene expression or by gene duplication, is an important, albeit less common, TSR mechanism. NTSR mechanisms include reduced absorption or translocation and increased sequestration or metabolic degradation. The mechanisms that can contribute to NTSR are complex and often involve genes that are members of large gene families. For example, enzymes involved in herbicide metabolism–based resistances include cytochromes P450, glutathione-S-transferases, glucosyl and other transferases, aryl acylamidase, and others. Both TSR and NTSR mechanisms can combine at the individual level to produce higher resistance levels. The vast array of herbicide-resistance mechanisms for generalist (NTSR) and specialist (TSR and some NTSR) adaptations that have evolved over a few decades illustrate the evolutionary resilience of weed populations to extreme selection pressures. These evolutionary processes drive herbicide and herbicide-resistant crop development and resistance management strategies.

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Section: Importance Of Genomics and Transcriptomics In Understanding mentioning

confidence: 99%

Mechanisms of evolved herbicide resistance

Gaines

Duke

Morran

et al. 2020

Journal of Biological Chemistry

Self Cite

428

493

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“…The mechanism of glyphosate resistance remains to be characterized fully in other NRR A. trifida biotypes as noted above, in several RR A. trifida accessions, and in other species . Future research objectives are to investigate cellular uptake and subcellular distribution of glyphosate and transcriptome profiling in Wisconsin A. trifida R and S phenotypes.…”

Section: Resultsmentioning

confidence: 99%

Physiological and molecular analysis of glyphosate resistance in non‐rapid response Ambrosia trifida from Wisconsin

Wilson

Takano

Horn

et al. 2019

Pest Management Science

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BACKGROUND We previously identified a glyphosate‐resistant A. trifida phenotype from Wisconsin USA that showed a non‐rapid response to glyphosate. The mechanism of glyphosate resistance in this phenotype has yet to be elucidated. We conducted experiments to investigate non‐target‐site resistance and target‐site resistance mechanisms. The roles of glyphosate absorption, translocation, and metabolism in resistance of this phenotype have not been reported previously, nor have EPSPS protein abundance or mutations to the full‐length sequence of EPSPS. RESULTS Whole‐plant dose–response results confirmed a 6.5‐level of glyphosate resistance for the resistant (R) phenotype compared to a susceptible (S) phenotype. Absorption and translocation of 14C‐glyphosate were similar between R and S phenotypes over 72 h. Glyphosate and AMPA concentrations in leaf tissue did not differ between R and S phenotypes over 96 h. In vivo shikimate leaf disc assays confirmed that glyphosate EC50 values were 4.6‐ to 5.4‐fold greater for the R than S phenotype. Shikimate accumulation was similar between phenotypes at high glyphosate concentrations (>1000 μM), suggesting that glyphosate entered chloroplasts and inhibited EPSPS. This finding was supported by results showing that EPSPS copy number and EPSPS protein abundance did not differ between R and S phenotypes, nor did EPSPS sequence at Gly101, Thr102, and Pro106 positions. Comparison of full‐length EPSPS sequences found five nonsynonymous polymorphisms that differed between R and S phenotypes. However, their locations were distant from the glyphosate target site and, therefore, not likely to affect enzyme‐glyphosate interaction. CONCLUSION The results suggest that a novel mechanism confers glyphosate resistance in this A. trifida phenotype. © 2019 Society of Chemical Industry

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“…Despite the increasing ease with which long‐read sequence data can be generated and assembled, the genomes of few economically important weed species have been fully sequenced. By contrast, numerous de novo transcriptomes have been completed for investigation of herbicide resistance, and weed biology and evolution . Weed genome assemblies have been published for Conyza canadensis (horseweed), Echinochloa crus‐galli (barnyardgrass), Thlaspi arvense (field pennycress), and Raphanus raphanistrum (wild radish) .…”

Section: The State Of the Art In Genomics And Weed Genomicsmentioning

confidence: 99%

The power and potential of genomics in weed biology and management

Ravet

Patterson

Krähmer

et al. 2018

Pest Management Science

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There have been previous calls for, and efforts focused on, realizing the power and potential of weed genomics for better understanding of weeds. Sustained advances in genome sequencing and assembly technologies now make it possible for individual research groups to generate reference genomes for multiple weed species at reasonable costs. Here, we present the outcomes from several meetings, discussions, and workshops focused on establishing an International Weed Genomics Consortium (IWGC) for a coordinated international effort in weed genomics. We review the 'state of the art' in genomics and weed genomics, including technologies, applications, and on-going weed genome projects. We also report the outcomes from a workshop and a global survey of the weed science community to identify priority species, key biological questions, and weed management applications that can be addressed through greater availability of, and access to, genomic resources. Major focus areas include the evolution of herbicide resistance and weedy traits, the development of molecular diagnostics, and the identification of novel targets and approaches for weed management. There is increasing interest in, and need for, weed genomics, and the establishment of the IWGC will provide the necessary global platform for communication and coordination of weed genomics research. © 2018 Society of Chemical Industry.

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Optimizing RNA‐seq studies to investigate herbicide resistance

Cited by 32 publications

References 31 publications

Mechanisms of evolved herbicide resistance

Mechanisms of evolved herbicide resistance

Physiological and molecular analysis of glyphosate resistance in non‐rapid response Ambrosia trifida from Wisconsin

The power and potential of genomics in weed biology and management

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