No Impact of Increased EPSPS Gene Copy Number on Growth and Fecundity of Glyphosate-Resistant Kochia (Bassia scoparia)

AbstractThe level of glyphosate resistance in kochia [Bassia scoparia(L.) A. J. Scott] was reported to be due to an increase in 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene copy number. A field study was conducted near Manhattan, KS, in 2014 and 2015 to evaluate the relationship between EPSPS gene copy number and growth and fecundity variables ofB. scopariaindividuals within suspected glyphosate-resistant (GR) populations from western Kansas. Initial assays of EPSPS gene copy and in vivo shikimate accumulation showed thatB. scopariapopulations from Finney (FN-R), Scott (SC-R), and Thomas (TH-R) counties were segregating for glyphosate resistance, with some individuals still being glyphosate susceptible (GS). A target-neighborhood competition approach was used to evaluate the competitive response of individual target plants with relatively low (classified as GS) and high (classified as GR) EPSPS gene copy number within the populations. There was no relationship observed between EPSPS gene copy number and vegetative or fecundity variables. There was no differential competitive response of target plant biomass to increasing neighbor density between individuals with low and high EPSPS gene copy number within each population. Lack of associated vegetative growth and fecundity cost to the increased EPSPS gene copy in the GRB. scopariaplants suggests that the plants are likely to persist in field populations, except when effective weed management strategies are adopted that would prevent their growth and seed production.

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Fitness Cost Associated With Enhanced EPSPS Gene Copy Number and Glyphosate Resistance in an Amaranthus tuberculatus Population

Frontiers in Plant Science ◽

10.3389/fpls.2021.651381 ◽

2021 ◽

Vol 12 ◽

Author(s):

Helen M. Cockerton ◽

Shiv S. Kaundun ◽

Lieselot Nguyen ◽

Sarah Jane Hutchings ◽

Richard P. Dale ◽

...

Keyword(s):

Interspecific Competition ◽

Gene Amplification ◽

Copy Number ◽

Gene Copy Number ◽

Glyphosate Resistance ◽

Gene Copy ◽

Competitive Response ◽

Trade Off ◽

Epsps Gene ◽

Amaranthus Tuberculatus

The evolution of resistance to pesticides in agricultural systems provides an opportunity to study the fitness costs and benefits of novel adaptive traits. Here, we studied a population of Amaranthus tuberculatus (common waterhemp), which has evolved resistance to glyphosate. The growth and fitness of seed families with contrasting levels of glyphosate resistance was assessed in the absence of glyphosate to determine their ability to compete for resources under intra- and interspecific competition. We identified a positive correlation between the level of glyphosate resistance and gene copy number for the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) glyphosate target, thus identifying gene amplification as the mechanism of resistance within the population. Resistant A. tuberculatus plants were found to have a lower competitive response when compared to the susceptible phenotypes with 2.76 glyphosate resistant plants being required to have an equal competitive effect as a single susceptible plant. A growth trade-off was associated with the gene amplification mechanism under intra-phenotypic competition where 20 extra gene copies were associated with a 26.5 % reduction in dry biomass. Interestingly, this growth trade-off was mitigated when assessed under interspecific competition from maize.

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Prediction of glyphosate resistance level based on EPSPS gene copy number in Kochia scoparia

10.1101/047878 ◽

2016 ◽

Author(s):

Todd A. Gaines ◽

Abigail L. Barker ◽

Eric L. Patterson ◽

Philip Westra ◽

Eric P. Westra ◽

...

Keyword(s):

Gene Duplication ◽

Empirical Model ◽

Copy Number ◽

Gene Copy Number ◽

Glyphosate Resistance ◽

Gene Copy ◽

Kochia Scoparia ◽

Resistance Level ◽

Epsps Gene ◽

Fallow Systems

AbstractGlyphosate-resistant (GR) Kochia scoparia has evolved in dryland chemical fallow systems throughout North America and the mechanism involves 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene duplication. Sugarbeet fields in four states were surveyed for K. scoparia in 2013 and tested for glyphosate-resistance level and EPSPS gene copy number. Glyphosate resistance was confirmed in K. scoparia populations collected from sugarbeet fields in Colorado, Wyoming, and Nebraska. The GR samples all had increased EPSPS gene copy number, with median population values up to 11. An empirical model was developed to estimate the level of glyphosate-resistance in K. scoparia based on EPSPS gene copy number. The results suggested that glyphosate susceptibility can be accurately diagnosed using EPSPS gene copy number, and further increases in EPSPS gene copy number could increase resistance levels up to 8-fold relative to susceptible K. scoparia. These trends suggest that continued glyphosate selection pressure is selecting for higher EPSPS copy number and higher resistance levels in K. scoparia. By including multiple K. scoparia samples lacking EPSPS gene duplication, our empirical model provides a more realistic estimate of fold-resistance due to EPSPS gene copy number compared to methods that do not account for normal variation of herbicide response in susceptible biotypes.

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Confirmation of Glyphosate-Resistant Kochia (Kochia scoparia) from Sugar Beet Fields in Idaho and Oregon

Weed Technology ◽

10.1017/wet.2017.80 ◽

2017 ◽

Vol 32 (1) ◽

pp. 27-33 ◽

Cited By ~ 3

Author(s):

Vipan Kumar ◽

Joel Felix ◽

Don Morishita ◽

Prashant Jha

Keyword(s):

Sugar Beet ◽

Copy Number ◽

Cropping Systems ◽

Gene Copy Number ◽

Glyphosate Resistance ◽

Gene Copy ◽

Resistance Level ◽

Control Programs ◽

Gene Copies

AbstractGlyphosate-resistant (GR) kochia is an increasing management concern in major cropping systems of the northwestern US. In 2014, we investigated four putative GR kochia accessions (designated as ALA, VAL, WIL, DB) collected from sugar beet fields in eastern Oregon and southwestern Idaho to characterize the level of evolved glyphosate resistance and determine the relationship between the 5-enol-pyruvylshikimate-3-phospate synthase (EPSPS) gene copy number and level of glyphosate resistance. TheEPSPSgene copy number was used as a molecular marker to detect GR kochia in subsequent surveys in 2015 and 2016. Based on LD50values from a whole-plant dose-response study, the four putative GR kochia populations were 2.0- to 9.6-fold more resistant to glyphosate than the glyphosate-susceptible (GS) accession. In anin vivoleaf-disk shikimate assay, leaf disks of GS kochia plants treated with 100-μM glyphosate accumulated 2.4- to 4.0-fold higher amounts of shikimate than the GR plants. The four GR accessions had 2.7 to 9.1 relativeEPSPSgene copies compared with the GS accession (<1EPSPSgene copies), and there was a linear relationship betweenEPSPSgene copy number and glyphosate resistance level (LD50values). The 2015 and 2016 GR kochia survey results indicated that about half of the collected populations from sugar beet fields in eastern Oregon had developed resistance to glyphosate whereas only one population from the Idaho collection was confirmed glyphosate resistant. This is the first confirmation of GR kochia in sugar beet fields in eastern Oregon and southwestern Idaho. Diversified weed control programs will be required to prevent further development and spread of GR kochia in sugar beet-based rotations in this region.

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EPSPS Gene Copy Number and Whole-Plant Glyphosate Resistance Level in Kochia scoparia

PLoS ONE ◽

10.1371/journal.pone.0168295 ◽

2016 ◽

Vol 11 (12) ◽

pp. e0168295 ◽

Cited By ~ 18

Author(s):

Todd A. Gaines ◽

Abigail L. Barker ◽

Eric L. Patterson ◽

Philip Westra ◽

Eric P. Westra ◽

...

Keyword(s):

Copy Number ◽

Gene Copy Number ◽

Glyphosate Resistance ◽

Gene Copy ◽

Kochia Scoparia ◽

Resistance Level ◽

Epsps Gene ◽

Whole Plant

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Effect of EPSPS Gene Copy Number and Glyphosate Selection on Fitness of Glyphosate-Resistant Bassia Scoparia in The Field

10.21203/rs.3.rs-155310/v1 ◽

2021 ◽

Author(s):

Charlemagne Ajoc Lim ◽

Prashant Jha ◽

Vipan Kumar ◽

Alan T. Dyer

Keyword(s):

Sugar Beet ◽

Seed Production ◽

Great Plains ◽

Copy Number ◽

Gene Copy Number ◽

Reproductive Traits ◽

Gene Copy ◽

Epsps Gene ◽

Gene Copies

Abstract The widespread evolution of glyphosate-resistant (GR) Bassia scoparia in the U.S. Great Plains poses a serious threat to the long-term sustainability of GR sugar beet. Glyphosate resistance in B. scoparia is due to an increase in the EPSPS (5-enolpyruvyl-shikimate-3-phosphate) gene copy number. The variation in EPSPS gene copies among individuals from within a single GR B. scoparia population indicated a differential response to glyphosate selection. We tested the hypothesis of reduced GR B. scoparia fitness (reproductive traits) to increasing glyphosate rates (applied as single or sequential applications) potentially experienced within a GR sugar beet field. The variation in EPSPS gene copy number and total glyphosate rate (single or sequential applications) did not influence any of the reproductive traits of GR B. scoparia, except seed production. Sequential applications of glyphosate with a total rate of 2,214 g ae ha− 1 or higher prevented seed production in B. scoparia plants with 2–4 (low levels of resistance) and 5–6 (moderate levels of resistance) EPSPS gene copies. Timely sequential applications of glyphosate (full recommended rates) can potentially slow down the evolution of GR B. scoparia with low to moderate levels of resistance (2–6 EPSPS gene copies), but any survivors (highly-resistant individuals with ≥ 8 EPSPS gene copies) need to be mechanically removed before flowering from GR sugar beet fields. This research warrants the need to adopt ecologically based, multi-tactic strategies to reduce exposure of B. scoparia to glyphosate in GR sugar beet.

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Ceftazidime-Avibactam Resistance Associated with Increased blaKPC-3 Gene Copy Number Mediated by pKpQIL Plasmid Derivatives in Sequence Type 258 Klebsiella pneumoniae

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01816-19 ◽

2020 ◽

Vol 64 (4) ◽

Cited By ~ 5

Author(s):

Marco Coppi ◽

Vincenzo Di Pilato ◽

Francesco Monaco ◽

Tommaso Giani ◽

Pier Giulio Conaldi ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Copy Number ◽

Acquired Resistance ◽

Gene Copy Number ◽

Gene Copy ◽

Content Type ◽

Outer Membrane Porins ◽

Long Read ◽

Multiple Copies

ABSTRACT This study reports on the characterization of two ceftazidime-avibactam (CZA)-resistant KPC-producing Klebsiella pneumoniae strains (KP-14159 and KP-8788) sequentially isolated from infections occurred in a patient never treated with CZA. Whole-genome sequencing characterization using a combined short- and long-read sequencing approach showed that both isolates belonged to the same ST258 strain, had altered outer membrane porins (a truncated OmpK35 and an Asp137Thr138 duplication in the L3 loop of OmpK36), and carried novel pKpQIL plasmid derivatives (pIT-14159 and pIT-8788, respectively) harboring two copies of the Tn4401a KPC-3-encoding transposon. Plasmid pIT-8788 was a cointegrate of pIT-14159 with a ColE replicon (that was also present in KP-14159) apparently evolved in vivo during infection. pIT-8788 was maintained at a higher copy number than pIT-14159 and, upon transfer to Escherichia coli DH10B, was able to increase the CZA MIC by 32-fold. The present findings provide novel insights about the mechanisms of acquired resistance to CZA, underscoring the role that the evolution of broadly disseminated pKpQIL plasmid derivatives may have in increasing the blaKPC gene copy number and KPC-3 expression in bacterial hosts. Although not self-transferable, similar elements, with multiple copies of Tn4401 and maintained at a high copy number, could mediate transferable CZA resistance upon mobilization.

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Increased gene copy number of DEFA1/DEFA3 worsens sepsis by inducing endothelial pyroptosis

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1812947116 ◽

2019 ◽

Vol 116 (8) ◽

pp. 3161-3170 ◽

Cited By ~ 10

Author(s):

QiXing Chen ◽

Yang Yang ◽

JinChao Hou ◽

Qiang Shu ◽

YiXuan Yin ◽

...

Keyword(s):

Endothelial Cell ◽

Copy Number ◽

Treatment Options ◽

Gene Copy Number ◽

High Copy Number ◽

Gene Copy ◽

Dependent Manner ◽

Barrier Dysfunction ◽

Specific Expression

Sepsis claims an estimated 30 million episodes and 6 million deaths per year, and treatment options are rather limited. Human neutrophil peptides 1–3 (HNP1–3) are the most abundant neutrophil granule proteins but their neutrophil content varies because of unusually extensive gene copy number polymorphism. A genetic association study found that increased copy number of the HNP-encoding gene DEFA1/DEFA3 is a risk factor for organ dysfunction during sepsis development. However, direct experimental evidence demonstrating that these risk alleles are pathogenic for sepsis is lacking because the genes are present only in some primates and humans. Here, we generate DEFA1/DEFA3 transgenic mice with neutrophil-specific expression of the peptides. We show that mice with high copy number of DEFA1/DEFA3 genes have more severe sepsis-related vital organ damage and mortality than mice with low copy number of DEFA1/DEFA3 or wild-type mice, resulting from more severe endothelial barrier dysfunction and endothelial cell pyroptosis after sepsis challenge. Mechanistically, HNP-1 induces endothelial cell pyroptosis via P2X7 receptor-mediating canonical caspase-1 activation in a NLRP3 inflammasome-dependent manner. Based on these findings, we engineered a monoclonal antibody against HNP-1 to block the interaction with P2X7 and found that the blocking antibody protected mice carrying high copy number of DEFA1/DEFA3 from lethal sepsis. We thus demonstrate that DEFA1/DEFA3 copy number variation strongly modulates sepsis development in vivo and explore a paradigm for the precision treatment of sepsis tailored by individual genetic information.

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Defense by duplication: The relation between phenotypic glyphosate resistance and EPSPS gene copy number variation in Amaranthus palmeri

10.1101/2021.04.13.439524 ◽

2021 ◽

Author(s):

Sarah B Yakimowski ◽

Zachary Teitel ◽

Christina M. Caruso

Keyword(s):

Copy Number Variation ◽

Copy Number ◽

Gene Copy Number ◽

Glyphosate Resistance ◽

Gene Copy ◽

Quantitative Relation ◽

Stabilizing Selection ◽

Amaranthus Palmeri ◽

Gene Copy Number Variation ◽

Number Variation

Gene copy number variation (CNV) has been increasingly associated with organismal responses to environmental stress, but we know little about the quantitative relation between CNV and phenotypic variation. In this study we quantify variation in EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) copy number using digital drop PCR and variation in phenotypic glyphosate resistance in 22 populations of Amaranthus palmeri (Palmer Amaranth), a range-expanding agricultural weed. Overall, we detected a significant positive relation between population mean copy number and mean resistance. The majority of populations exhibited high glyphosate resistance, yet maintained low-resistance individuals resulting in bimodality in many populations. We investigated linear and threshold models for the relation between copy number and resistance, and found evidence for a threshold of ~15 EPSPS copies: there was a steep increase in resistance before the threshold, followed by a much shallower slope. Moreover, as copy number increases, the range of variation in resistance decreases. This suggests a working hypothesis that as EPSPS copies and dosage increases, negative epistatic interactions may be compensated. We detected a quadratic relation between mean resistance and variation (s.d.) in resistance, consistent with the prediction that as phenotypic resistance increases in populations, stabilizing selection decreases variation in the trait. Finally, patterns of variation across the landscape are consistent with less variation among populations in mean copy number / resistance in Georgia where glyphosate resistance was first detected, and wider variation among populations in resistance and copy number in a more northern state where resistance evolution may be at a younger evolutionary state.

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