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

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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Target-Site Resistance to Glyphosate in Chloris Virgata Biotypes and Alternative Herbicide Options for its Control

Agronomy ◽

10.3390/agronomy10091266 ◽

2020 ◽

Vol 10 (9) ◽

pp. 1266

Author(s):

Het Samir Desai ◽

Michael Thompson ◽

Bhagirath Singh Chauhan

Keyword(s):

Glyphosate Resistance ◽

Target Site ◽

Site Mutation ◽

Glufosinate Ammonium ◽

Epsps Gene ◽

First Case ◽

Target Site Resistance ◽

Chloris Virgata ◽

Moderately Resistant ◽

Dose Response Study

Due to the overdependence on glyphosate to manage weeds in fallow conditions, glyphosate resistance has developed in various biotypes of several grass weeds, including Chloris virgata Sw. The first case of glyphosate resistance in C. virgata was found in 2015 in Australia, and since then several cases have been confirmed in several biotypes across Australia. Pot studies were conducted with 10 biotypes of C. virgata to determine glyphosate resistance levels. The biotypes were identified as either susceptible, moderately resistant or highly resistant based on the glyphosate dose required to kill 50% of plants. Two glyphosate-susceptible (GS) and two glyphosate-resistant (GR) biotypes were identified by the dose-response study and analyzed for the presence of target-site mutation in the 5–enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene. Performance of alternative herbicides to glyphosate as well as the double-knock herbicide approach was evaluated on the two GS (Ch and SGM2) and two GR (SGW2 and CP2) biotypes. Three herbicides, clethodim, haloxyfop and paraquat, were found to be effective (100% control) against all four biotypes when applied at the 4–5 leaf stage. All the sequential herbicide treatments, such as glyphosate followed by paraquat and glufosinate-ammonium followed by paraquat, provided 100% control of all four biotypes of C. virgata. This study identified effective herbicide options for the control of GR C. virgata and showed that target-site mutations were involved in the resistance of two biotypes to glyphosate (SGW2 and CP2). Results could aid farmers in selecting herbicides to manage C. virgata in their fields.

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Deciphering the Mechanism of Glyphosate Resistance in Amaranthus palmeri by Cytogenomics

Cytogenetic and Genome Research ◽

10.1159/000521409 ◽

2022 ◽

pp. 1-7

Author(s):

Dal-Hoe Koo ◽

Rajendran Sathishraj ◽

Bernd Friebe ◽

Bikram S. Gill

Keyword(s):

Genome Size ◽

Copy Number ◽

Fold Increase ◽

Glyphosate Resistance ◽

Resistance Mechanisms ◽

Fish Analysis ◽

Amaranthus Palmeri ◽

Artificial Chromosomes ◽

Genetic Elements ◽

Meiotic Chromosomes

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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Transcriptomic analysis of insecticide resistance in the lymphatic filariasis vectorCulex quinquefasciatus

10.1101/589028 ◽

2019 ◽

Author(s):

Walter Fabricio Silva Martins ◽

Craig Stephen Wilding ◽

Alison Taylor Isaacs ◽

Emily Joy Rippon ◽

Karine Megy ◽

...

Keyword(s):

Insecticide Resistance ◽

Lymphatic Filariasis ◽

Fold Increase ◽

Target Site ◽

Detoxification Enzymes ◽

Site Mutation ◽

Public Health Importance ◽

Metabolic Resistance ◽

Vector Borne Diseases ◽

Bendiocarb Resistance

ABSTRACTCulex quinquefasciatusplays an important role in transmission of vector-borne diseases of public health importance, including lymphatic filariasis (LF), as well as many arboviral diseases. Currently, efforts to tackleC. quinquefasciatusvectored diseases are based on either mass drug administration (MDA) for LF, or insecticide-based interventions. Widespread and intensive insecticide usage has resulted in increased resistance in mosquito vectors, includingC. quinquefasciatus. Herein, the transcriptome profile of Ugandan bendiocarb-resistantC. quinquefasciatuswas explored to identify candidate genes associated with insecticide resistance. Resistance to bendiocarb in exposed mosquitoes was marked, with 2.04% mortality following 1h exposure and 58.02% after 4h. Genotyping of the G119SAce-1target site mutation detected a highly significant association (p<0.0001; OR=25) between resistance andAce1-119S. However, synergist assays using the P450 inhibitor PBO or the esterase inhibitor TPP resulted in markedly increased mortality (to ≈80%), suggesting a role of metabolic resistance in the resistance phenotype. Using a novel, custom 60K whole-transcriptome microarray 16 genes significantly overexpressed in resistant mosquitoes were detected, with the P450Cyp6z18showing the highest differential gene expression (>8-fold increase vs unexposed controls). These results provide evidence that bendiocarb-resistance in UgandanC. quinquefasciatusis mediated by both target-site mechanisms and over-expression of detoxification enzymes.

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Functional Genomics Analysis of Horseweed (Conyza canadensis) with Special Reference to the Evolution of Non–Target-Site Glyphosate Resistance

Weed Science ◽

10.1614/ws-d-09-00037.1 ◽

2010 ◽

Vol 58 (2) ◽

pp. 109-117 ◽

Cited By ~ 48

Author(s):

Joshua S. Yuan ◽

Laura L. G. Abercrombie ◽

Yongwei Cao ◽

Matthew D. Halfhill ◽

Xin Zhou ◽

...

Keyword(s):

Functional Genomics ◽

Molecular Mechanisms ◽

Glyphosate Resistance ◽

Resistance Mechanisms ◽

Target Site ◽

Environmentally Benign ◽

Conyza Canadensis ◽

Target Site Resistance ◽

Weedy Species ◽

Heterologous Microarray

The evolution of glyphosate resistance in weedy species places an environmentally benign herbicide in peril. The first report of a dicot plant with evolved glyphosate resistance was horseweed, which occurred in 2001. Since then, several species have evolved glyphosate resistance and genomic information about nontarget resistance mechanisms in any of them ranges from none to little. Here, we report a study combining iGentifier transcriptome analysis, cDNA sequencing, and a heterologous microarray analysis to explore potential molecular and transcriptomic mechanisms of nontarget glyphosate resistance of horseweed. The results indicate that similar molecular mechanisms might exist for nontarget herbicide resistance across multiple resistant plants from different locations, even though resistance among these resistant plants likely evolved independently and available evidence suggests resistance has evolved at least four separate times. In addition, both the microarray and sequence analyses identified non–target-site resistance candidate genes for follow-on functional genomics analysis.

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Glyphosate resistance inAmbrosia trifida:Part 2. Rapid response physiology and non-target-site resistance

Pest Management Science ◽

10.1002/ps.4569 ◽

2017 ◽

Vol 74 (5) ◽

pp. 1079-1088 ◽

Cited By ~ 23

Author(s):

Marcelo L Moretti ◽

Christopher R Van Horn ◽

Renae Robertson ◽

Kabelo Segobye ◽

Stephen C Weller ◽

...

Keyword(s):

Glyphosate Resistance ◽

Rapid Response ◽

Target Site ◽

Target Site Resistance

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Resistance to ACCase inhibitors in Eleusine indica from Brazil involves a target site mutation

Planta Daninha ◽

10.1590/s0100-83582012000300025 ◽

2012 ◽

Vol 30 (3) ◽

pp. 675-681 ◽

Cited By ~ 11

Author(s):

M.D. Osuna ◽

I.C.G.R. Goulart ◽

R.A. Vidal ◽

A. Kalsing ◽

J.P. Ruiz Santaella ◽

...

Keyword(s):

Amino Acid Position ◽

Target Site ◽

In Vitro Assays ◽

Site Mutation ◽

Eleusine Indica ◽

Herbicide Resistant ◽

Frequent Use ◽

Target Site Resistance ◽

Grass Weed

Eleusine indica (goosegrass) is a diploid grass weed which has developed resistance to ACCase inhibitors during the last ten years due to the intensive and frequent use of sethoxydim to control grass weeds in soybean crops in Brazil. Plant dose-response assays confirmed the resistant behaviour of one biotype obtaining high resistance factor values: 143 (fenoxaprop), 126 (haloxyfop), 84 (sethoxydim) to 58 (fluazifop). ACCase in vitro assays indicated a target site resistance as the main cause of reduced susceptibility to ACCase inhibitors. PCR-generated fragments of the ACCase CT domain of the resistant and sensitive reference biotype were sequenced and compared. A point mutation was detected within the triplet of aspartate at the amino acid position 2078 (referred to EMBL accession no. AJ310767) and resulted in the triplet of glycine. These results constitute the first report on a target site mutation for a Brazilian herbicide resistant grass weed.

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Confirmation and Characterization of Non–target site Resistance to Fomesafen in Palmer amaranth (Amaranthus palmeri)

Weed Science ◽

10.1017/wsc.2018.60 ◽

2018 ◽

Vol 66 (6) ◽

pp. 702-709 ◽

Cited By ~ 23

Author(s):

Vijay K. Varanasi ◽

Chad Brabham ◽

Jason K. Norsworthy

Keyword(s):

Cytochrome P450 ◽

Cropping Systems ◽

Palmer Amaranth ◽

Target Site ◽

Amaranthus Palmeri ◽

Allelic Discrimination Assay ◽

Allelic Discrimination ◽

First Case ◽

Target Site Resistance ◽

Novel Target

AbstractPalmer amaranth (Amaranthus palmeri S. Watson), a dioecious summer annual species, is one of the most troublesome weeds in U.S. cropping systems. The evolution of resistance to protoporphyrinogen oxidase inhibitors in A. palmeri biotypes is a major cause of concern to soybean [Glycine max (L.) Merr.] and cotton (Gossypium hirsutum L.) growers in the midsouthern United States. The objective of this study was to confirm and characterize the non–target site mechanism in a fomesafen-resistant accession from Randolph County, AR (RCA). A dose–response assay was conducted to assess the level of fomesafen resistance, and based on the GR50 values, the RCA accession was 18-fold more resistant to fomesafen than a susceptible (S) biotype. A TaqMan allelic discrimination assay and sequencing of the target-site genes PPX2 and PPX1 revealed no known or novel target-site mutations. An SYBR Green assay indicated no difference in PPX2 gene expression between the RCA and S biotypes. To test whether fomesafen resistance is metabolic in nature, the RCA and the S biotypes were treated with different cytochrome P450 (amitrole, piperonyl butoxide [PBO], malathion) and glutathione S-transferase (GST) (4-chloro-7-nitrobenzofurazan [NBD-Cl]) inhibitors, either alone or in combination with fomesafen. Malathion followed by (fb) fomesafen in RCA showed the greatest reduction in survival (67%) and biomass (86%) compared with fomesafen alone (45% and 66%, respectively) at 2 wk after treatment. Interestingly, NBD-Cl fb fomesafen also resulted in low survival (35%) compared with the fomesafen-only treatment (55%). Applications of malathion or NBD-Cl preceding fomesafen treatment resulted in reversal of fomesafen resistance, indicating the existence of cytochrome P450– and GST-based non–target site mechanisms in the RCA accession. This study confirms the first case of non–target site resistance to fomesafen in A. palmeri.

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Target-Site Point Mutation Conferring Resistance to Trifluralin in Rigid Ryegrass (Lolium rigidum)

Weed Science ◽

10.1017/wsc.2017.67 ◽

2017 ◽

Vol 66 (2) ◽

pp. 246-253 ◽

Cited By ~ 8

Author(s):

Benjamin Fleet ◽

Jenna Malone ◽

Christopher Preston ◽

Gurjeet Gill

Keyword(s):

Amino Acid ◽

Amino Acid Substitution ◽

Target Site ◽

Shoot Biomass ◽

Site Mutation ◽

Susceptible Population ◽

Resistant Population ◽

Target Site Resistance ◽

Different Populations ◽

Rigid Ryegrass

Populations of rigid ryegrass suspected of resistance to trifluralin due to control failures exhibited varying levels of susceptibility to trifluralin, with 15 out of 17 populations deemed resistant (>20% plant survival). Detailed dose–response studies were conducted on one highly resistant field-evolved population (SLR74), one known multiply resistant population (SLR31), and one susceptible population (VLR1). On the basis of the dose required to kill 50% of treated plants (LD50), SLR74 had 15-fold greater resistance than VLR1, whereas, the multiply resistant SLR31 had 10-fold greater resistance than VLR1. Similarly, on the basis of dose required to reduce shoot biomass by 50% (GR50), SLR74 had 17-fold greater resistance than VLR1, and SLR31 had 8-fold greater resistance than VLR1. Sequencing of the α-tubulin gene from resistant plants of different populations confirmed the presence of a previously known goosegrass mutation causing an amino acid substitution at position 239 from threonine to isoleucine in resistant population SLR74. This mutation was also found in 4 out of 5 individuals in another highly resistant population TR2 and in 3 out of 5 individuals of TR4. An amino acid substitution from valine to phenylalanine at position 202 was also observed in TR4 (3 out of 5 plants) and TR2 (1 out of 5 plants). There was no target-site mutation identified in SLR31. This study documents the first known case of field-evolved target-site resistance to dinitroaniline herbicides in a population of rigid ryegrass.

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First confirmation and characterization of target and non-target site resistance to glyphosate in Palmer amaranth ( Amaranthus palmeri ) from Mexico

Plant Physiology and Biochemistry ◽

10.1016/j.plaphy.2017.03.022 ◽

2017 ◽

Vol 115 ◽

pp. 212-218 ◽

Cited By ~ 15

Author(s):

Jose Alfredo Dominguez-Valenzuela ◽

Javid Gherekhloo ◽

Pablo Tomás Fernández-Moreno ◽

Hugo Enrique Cruz-Hipolito ◽

Ricardo Alcántara-de la Cruz ◽

...

Keyword(s):

Palmer Amaranth ◽

Target Site ◽

Amaranthus Palmeri ◽

Target Site Resistance

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The genetic architecture and genomic context of glyphosate resistance

10.1101/2020.08.19.257972 ◽

2020 ◽

Author(s):

J.M. Kreiner ◽

P.J. Tranel ◽

D. Weigel ◽

J.R. Stinchcombe ◽

S.I. Wright

Keyword(s):

Herbicide Resistance ◽

Genetic Architecture ◽

Genetic Basis ◽

Glyphosate Resistance ◽

Target Site ◽

Plant Performance ◽

Comparable Amount ◽

Standing Variation ◽

Genome Wide ◽

Target Site Resistance

AbstractAlthough much of what we know about the genetic basis of herbicide resistance has come from detailed investigations of monogenic adaptation at known target-sites, the importance of polygenic resistance has been increasingly recognized. Despite this, little work has been done to characterize the genomic basis of herbicide resistance, including the number and distribution of involved genes, their effect sizes, allele frequencies, and signatures of selection. Here we implement genome-wide association (GWA) and population genomic approaches to examine the genetic architecture of glyphosate resistance in the problematic agricultural weed, Amaranthus tuberculatus. GWA correctly identifies the gene targeted by glyphosate, and additionally finds more than 100 genes across all 16 chromosomes associated with resistance. The encoded proteins have relevant non-target-site resistance and stress-related functions, with potential for pleiotropic roles in resistance to other herbicides and diverse life history traits. Resistance-related alleles are enriched for large effects and intermediate frequencies, implying that strong selection has shaped the genetic architecture of resistance despite potential pleiotropic costs. The range of common and rare allele involvement implies a partially shared genetic basis of non-target-site resistance across populations, complemented by population-specific alleles. Resistance-related alleles show evidence of balancing selection, and suggest a long-term maintenance of standing variation at stress-response loci that have implications for plant performance under herbicide pressure. By our estimates, genome-wide SNPs explain a comparable amount of the total variation in glyphosate resistance to monogenic mechanisms, indicating the potential for an underappreciated polygenic contribution to the evolution of herbicide resistance in weed populations.

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