Perspectives on gene copy number variation and pesticide resistance

Heckel, David G.

doi:10.1002/ps.6631

Cited by 16 publications

(12 citation statements)

References 60 publications

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“…resistant to acetyl-CoA carboxylase inhibitors (Laforest et al 2017). Although seldom identified as a herbicide-resistance mechanism, increase in gene copy number has been reported in several cases of fungicide or insecticide resistance (Anthony et al 1998;Cattel et al 2021;Elmore et al 2015;Heckel 2022;Puinean et al 2010).…”

Section: Glutamine Synthetase Sequencing Relative Copy Number and Exp...mentioning

confidence: 99%

Unraveling the mechanism of resistance in a glufosinate-resistant Palmer amaranth (Amaranthus palmeri) accession

Carvalho-Moore

Norsworthy²,

González-Torralva

et al. 2022

Weed Sci

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Glufosinate resistance in Palmer amaranth (Amaranthus palmeri S. Watson] was recently detected in three accessions from Arkansas. Amaranthus palmeri is the first and only broadleaf weed species resistant to this herbicide, and the resistance mechanism is still unclear. A previous study characterized the glufosinate resistance level in the accessions from Arkansas. A highly glufosinate-resistant accession was further used to investigate the mechanism conferring glufosinate resistance in A. palmeri. Experiments were designed to sequence the herbicide target enzyme cytosolic and chloroplastic glutamine synthetase isoforms (GS1 and GS2, respectively) and quantify copy number and expression. Absorption, translocation, and metabolism of glufosinate using the carbon-14-labeled herbicide were also evaluated in resistant and susceptible accessions. The glufosinate-resistant accession had an increase in copy number and expression of GS2 compared to susceptible plants. All accessions showed only one GS1 copy and no differences in expression. No mutations were identified in GS1 or GS2. Absorption (54 to 60%) and metabolism (13 to 21%) were not different between the glufosinate-resistant and susceptible accessions. Most residues of glufosinate (94 to 98%) were present in the treated leaf. Glufosinate translocation to tissues above the treated leaf and in the roots was not different among accessions. However, glufosinate translocation to tissues below the treated leaf (not including roots) was greater in the resistant A. palmeri (2%) compared to the susceptible (less than 1%) accessions. The findings of this paper strongly indicate that gene amplification and increased expression of the chloroplastic glutamine synthetase enzyme are the mechanisms conferring glufosinate resistance in the A. palmeri accession investigated. Thus far, no additional resistance mechanism was observed, but further investigations are ongoing.

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Section: Glutamine Synthetase Sequencing Relative Copy Number and Exp...mentioning

confidence: 99%

Unraveling the mechanism of resistance in a glufosinate-resistant Palmer amaranth (Amaranthus palmeri) accession

Carvalho-Moore

Norsworthy²,

González-Torralva

et al. 2022

Weed Sci

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“…In light of the potential for rapid adaptation to novel environments to proceed from polygenic adaptation and genetic redundancy, it will be important to revisit the theoretical underpinnings of pest management recommendations as they pertain to the rotation of insecticides, RNAi target screening and the encouragement of biological control. For instance, if the genetic redundancy of insecticide resistance genes is high (e.g., copy number variations; Heckel, 2022), frequent insecticide rotation may have little effect in delaying product failures. With the recent expansion of genomic resources and analytical approaches to detect polygenic adaptation (Pritchard & Di Rienzo, 2010), quantitative genetics and an appreciation for the impact of genetic redundancy can provide new insights into evolutionary conundrums that are difficult to explain in classical population genetics, such as repeated evolution in insecticide resistance (Pélissié et al, 2022), and the phenomenon of host switching in herbivorous insects.…”

Section: Discussionmentioning

confidence: 99%

“…Heckel, 2022), frequent insecticide rotation may have little effect in delaying product failures. With the recent expansion of genomic resources and analytical approaches to detect polygenic adaptation(Pritchard & Di Rienzo, 2010), quantitative genetics and an appreciation for the impact of genetic redundancy can provide new insights into evolutionary conundrums that are difficult to explain in classical population genetics, such as repeated evolution in insecticide resistance(Pélissié et al, 2022), and the phenomenon of host switching in herbivorous insects.…”

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confidence: 99%

Polygenic adaptation contributes to the invasive success of the Colorado potato beetle

et al. 2022

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Invasive species often experience extreme demographic reductions.A common but counterintuitive phenomenon, the so-called "genetic paradox" of invasion, is that many species still successfully adapt to novel conditions despite heavy reductions in standing genetic variation and effective population size (Allendorf & Lundquist, 2003).Numerous empirical standpoints have emerged to explain this paradox, such as genetic admixture from intra- (Errbii et al., 2021;Kolbe et al., 2004) or interspecies populations (Petit et al., 2004;Wang et al., 2020), activation of transposable elements (Schrader et al., 2014;Stapley et al., 2015), and balancing selection which tends to preserve heterozygosity and prevent the loss of minor alleles (Gloag et al., 2017;Stern & Lee, 2020). However, contingencies and counterexamples prevent coalescence into general rules valid across taxa. Indeed, scepticism has been raised regarding the

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“…CNVs have gained interest in recent decades because these are much more extensive than SNPs, altering a higher number of base pairs and impacting a wider proportion of the genome (Freeman et al, 2006). The association of CNVs with pesticide resistance has been described for various genes related to drug response; however, the correct identification of these structural variants depends on the transcriptome and genome sequencing technology applied (Heckel, 2022). Short-read transcriptome assemblies may overlook CNVs in the genomic regions.…”

Section: Introductionmentioning

confidence: 99%

Whole-genome resequencing in the sea louse Caligus rogercresseyi uncovers gene duplications and copy number variants associated with pesticide resistance

et al. 2023

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The sea louse Caligus rogercresseyi is a marine ectoparasite that constitutes one of the major threats to the salmon farming industry, where the primary control strategy is the use of delousing drugs through immersion treatments. The emergence of pharmacological resistance in this copepodid species has previously been described using transcriptome data. However, the molecular mechanisms underlying chromosome rearrangements have not yet been explored. This study aimed to identify structural genomic variations and gene expression in C. rogercresseyi associated with pesticide sensitivity. In this study, genome resequencing was conducted using Oxford Nanopore Technology on lice strains with contrasting sensitivity to azamethiphos to detect genome duplications. Transcriptome profiling of putative gene duplications was performed by Illumina sequencing. Copy Number Variants (CNVs) were identified through comparative coverage, and collinear/tandem gene duplications over all the chromosomal regions by sequence homology. Duplications or CNVs in functional genes were primarily identified in transposable elements and genes related to the drug response, with differential expression values calculated by RNA-seq analyses of the same strains. Notably, differentially duplicated genes were found in coding regions related to cuticle proteins, suggesting that a putative resistance mechanism may be associated with cuticular structure formation and the proteins involved. Collectively, the results revealed that the intensive use of pesticides on sea lice populations increases the frequency of gene duplication, expanding the molecular elements involved in drug response. This study is the first to report an association between genome rearrangements and pharmacological resistance in sea lice populations.

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Perspectives on gene copy number variation and pesticide resistance

Cited by 16 publications

References 60 publications

Unraveling the mechanism of resistance in a glufosinate-resistant Palmer amaranth (Amaranthus palmeri) accession

Unraveling the mechanism of resistance in a glufosinate-resistant Palmer amaranth (Amaranthus palmeri) accession

Polygenic adaptation contributes to the invasive success of the Colorado potato beetle

Whole-genome resequencing in the sea louse Caligus rogercresseyi uncovers gene duplications and copy number variants associated with pesticide resistance

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