Gene amplification confers glyphosate resistance in Amaranthus palmeri

In agriculture, various chemicals are used to control the weeds. Out of which, glyphosate is an important herbicide invariably used in the cultivation of glyphosate-resistant crops to control weeds. Overuse of glyphosate results in the evolution of glyphosate-resistant weeds. Evolution of glyphosate resistance (GR) in Amaranthus palmeri (AP) is a serious concern in the USA. Investigation of the mechanism of GR in AP identified different resistance mechanisms of which 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene amplification is predominant. Molecular analysis of GR AP identified the presence of a 5- to >160-fold increase in copies of the EPSPS gene than in a glyphosate-susceptible (GS) population. This increased copy number of the EPSPS gene increased the genome size ranging from 3.5 to 11.8%, depending on the copy number compared to the genome size of GS AP. FISH analysis using a 399-kb EPSPS cassette derived from bacterial artificial chromosomes (BACs) as probes identified that amplified EPSPS copies in GR AP exist in extrachromosomal circular DNA (eccDNA) in addition to the native copy in the chromosome. The EPSPS gene-containing eccDNA having a size of ∼400 kb is termed EPSPS-eccDNA and showed somatic mosacism in size and copy number. EPSPS-eccDNA has a genetic mechanism to tether randomly to mitotic or meiotic chromosomes during cell division or gamete formation and is inherited to daughter cells or progeny generating copy number variation. These eccDNAs are stable genetic elements that can replicate and exist independently. The genomic characterization of the EPSPS locus, along with the flanking regions, identified the presence of a complex array of repeats and mobile genetic elements. The cytogenomics approach in understanding the biology of EPSPS-eccDNA sheds light on various characteristics of EPSPS-eccDNA that favor GR in AP.

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Glyphosate Resistance and Gene Amplification in Selected Daucus carota Suspension Cultures

Progress in Plant Cellular and Molecular Biology - Current Plant Science and Biotechnology in Agriculture ◽

10.1007/978-94-009-2103-0_21 ◽

1990 ◽

pp. 148-152 ◽

Cited By ~ 7

Author(s):

Y. Y. Shyr ◽

J. M. Widholm

Keyword(s):

Gene Amplification ◽

Daucus Carota ◽

Glyphosate Resistance ◽

Suspension Cultures

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Distribution and validation of genotypic and phenotypic glyphosate and PPO-nhibitor resistance in Palmer amaranth (Amaranthus palmeri) from southwestern Nebraska

Weed Technology ◽

10.1017/wet.2020.74 ◽

2020 ◽

pp. 1-12 ◽

Cited By ~ 1

Author(s):

Maxwel C Oliveira ◽

Darci A Giacomini ◽

Nikola Arsenijevic ◽

Gustavo Vieira ◽

Patrick J Tranel ◽

...

Keyword(s):

Cluster Analysis ◽

Gene Amplification ◽

Cropping Systems ◽

Resistance Mechanism ◽

Geographic Area ◽

Glyphosate Resistance ◽

Resistance Mechanisms ◽

Palmer Amaranth ◽

Resistance Evolution ◽

Inhibitor Resistance

Abstract Failure to control Palmer amaranth with glyphosate and protoporphyrinogen IX oxidase (PPO)-inhibitor herbicides was reported across southwestern Nebraska in 2017. The objectives of this study were to 1) confirm and 2) validate glyphosate and PPO-inhibitor (fomesafen and lactofen) resistance in 51 Palmer amaranth accessions from southwestern Nebraska using genotypic and whole-plant phenotypic assay correlations and cluster analysis, and 3) determine which agronomic practices might be influencing glyphosate resistance in Palmer amaranth accessions in that location. Based on genotypic assay, 88% of 51 accessions contained at least one individual with amplification (>2 copies) of the 5-enolypyruvyl-shikimate-3-phosphate synthase (EPSPS) gene, which confers glyphosate resistance; and/or a mutation in the PPX2 gene, either ΔG210 or R128G, which endows PPO-inhibitor resistance in Palmer amaranth. Cluster analysis and high correlation (0.83) between genotypic and phenotypic assays demonstrated that EPSPS gene amplification is the main glyphosate resistance mechanism in Palmer amaranth accessions from southwestern Nebraska. In contrast, there was poor association between genotypic and phenotypic responses for PPO-inhibitor resistance, which was attributed to segregation for PPO-inhibitor resistance within these accessions and/or the methodology that was adopted herein. Genotypic assays can expedite the process of confirming known glyphosate and PPO-inhibitor resistance mechanisms in Palmer amaranth from southwestern Nebraska and other locations. Phenotypic assays are also a robust method for confirming glyphosate resistance but not necessarily PPO-inhibitor resistance in Palmer amaranth. Moreover, random forest analysis of glyphosate resistance in Palmer amaranth indicated that EPSPS gene amplification, county, and current and previous crops are the main factors influencing glyphosate resistance within that geographic area. Most glyphosate-susceptible Palmer amaranth accessions were found in a few counties in areas with high crop diversity. Results presented here confirm the spread of glyphosate resistance and PPO-inhibitor resistance in Palmer amaranth accessions from southwestern Nebraska and demonstrate that less diverse cropping systems are an important driver of herbicide resistance evolution in Palmer amaranth.

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Confirmation of herbicide resistance mutations Trp574Leu, ΔG210, and EPSPS gene amplification and control of multiple herbicide-resistant Palmer amaranth (Amaranthus palmeri) with chlorimuron-ethyl, fomesafen, and glyphosate

PLoS ONE ◽

10.1371/journal.pone.0214458 ◽

2019 ◽

Vol 14 (3) ◽

pp. e0214458 ◽

Cited By ~ 3

Author(s):

Douglas J. Spaunhorst ◽

Haozhen Nie ◽

James R. Todd ◽

Julie M. Young ◽

Bryan G. Young ◽

...

Keyword(s):

Gene Amplification ◽

Herbicide Resistance ◽

Palmer Amaranth ◽

Amaranthus Palmeri ◽

Resistance Mutations ◽

Herbicide Resistant ◽

Epsps Gene ◽

Chlorimuron Ethyl ◽

And Control

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Interference of Selected Palmer Amaranth (Amaranthus palmeri) Biotypes in Soybean (Glycine max)

International Journal of Agronomy ◽

10.1155/2012/168267 ◽

2012 ◽

Vol 2012 ◽

pp. 1-7 ◽

Cited By ~ 3

Author(s):

Aman Chandi ◽

David L. Jordan ◽

Alan C. York ◽

Susana R. Milla-Lewis ◽

James D. Burton ◽

...

Keyword(s):

Glycine Max ◽

Acetolactate Synthase ◽

Dry Weight ◽

Glyphosate Resistance ◽

Palmer Amaranth ◽

Amaranthus Palmeri ◽

Fresh Weight ◽

Row Crops ◽

Soybean Yield ◽

Competitive Disadvantage

Palmer amaranth (Amaranthus palmeriS. Wats.) has become difficult to control in row crops due to selection for biotypes that are no longer controlled by acetolactate synthase inhibiting herbicides and/or glyphosate. Early season interference in soybean [Glycine max(L.) Merr.] for 40 days after emergence by three glyphosate-resistant (GR) and three glyphosate-susceptible (GS) Palmer amaranth biotypes from Georgia and North Carolina was compared in the greenhouse. A field experiment over 2 years compared season-long interference of these biotypes in soybean. The six Palmer amaranth biotypes reduced soybean height similarly in the greenhouse but did not affect soybean height in the field. Reduction in soybean fresh weight and dry weight in the greenhouse; and soybean yield in the field varied by Palmer amaranth biotypes. Soybean yield was reduced 21% by Palmer amaranth at the established field density of 0.37 plant m−2. When Palmer amaranth biotypes were grouped by response to glyphosate, the GS group reduced fresh weight, dry weight, and yield of soybean more than the GR group. The results indicate a possible small competitive disadvantage associated with glyphosate resistance, but observed differences among biotypes might also be associated with characteristics within and among biotypes other than glyphosate resistance.

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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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Evolution of Target-Site Resistance to Glyphosate in an Amaranthus palmeri Population from Argentina and Its Expression at Different Plant Growth Temperatures

Plants ◽

10.3390/plants8110512 ◽

2019 ◽

Vol 8 (11) ◽

pp. 512 ◽

Cited By ~ 4

Author(s):

Kaundun ◽

Jackson ◽

Hutchings ◽

Galloway ◽

Marchegiani ◽

...

Keyword(s):

Fold Increase ◽

Glyphosate Resistance ◽

Target Site ◽

Amaranthus Palmeri ◽

Site Mutation ◽

Medium Temperature ◽

Soybean Field ◽

Over Expression ◽

Target Site Resistance ◽

The Difference

The mechanism and expression of resistance to glyphosate at different plant growing temperatures was investigated in an Amaranthus palmeri population (VM1) from a soybean field in Vicuña Mackenna, Cordoba, Argentina. Resistance was not due to reduced glyphosate translocation to the meristem or to EPSPS duplication, as reported for most US samples. In contrast, a proline 106 to serine target-site mutation acting additively with EPSPS over-expression (1.8-fold increase) was respectively a major and minor contributor to glyphosate resistance in VM1. Resistance indices based on LD50 values generated using progenies from a cross between 52 PS106 VM1 individuals were estimated at 7.1 for homozygous SS106 and 4.3 for heterozygous PS106 compared with homozygous wild PP106 plants grown at a medium temperature of 24 °C day/18 °C night. A larger proportion of wild and mutant progenies survived a single commonly employed glyphosate rate when maintained at 30 °C day/26 °C night compared with 20 °C day/16 night in a subsequent experiment. Interestingly, the P106S mutation was not identified in any of the 920 plants analysed from 115 US populations, thereby potentially reflecting the difference in A. palmeri control practices in Argentina and USA.

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