Insecticide resistance mediated by an exon skipping event

Identification and expression patterns of voltage-gated sodium channel genes with intron retentions in different strains of Bactrocera dorsalis

Pyrethroid are the primary insecticides used for controlling of Bactricera dorsalis, a highly destructive and invasive fruit pest. Field populations have developed serious resistance, especially to β-cypermethrin. While mutations in the voltage-gated sodium channel (Vgsc) are a common mechanism of pyrethroid resistance, variations in BdVgsc associated with β-cypermethrin resistance remain unclear. Here, we reported the resistance levels of five field populations from China, with resistance ratio ranging from 1.54 to 21.34-fold. Cloning the full length of BdVgsc revealed no specific or known amino acid mutations between the most resistant population and the susceptible strain. However, three types of partial intron retention (IRE4-5, IRE19-f and IREL-24) were identified in BdVgsc transcripts, with these intron retentions containing stop codons. The expression of IRE4-5 transcripts and total BdVgsc showed different trends across developmental stages and tissues. Exposure to β-cypermethrin led to increased expression of IRE4-5. Comparison of genomic and transcriptional sequences reveled that IRE4-5 transcripts had two types (IRE4-5.5 T and IRE4-5.6 T) caused by genomic variations. Both field and congenic strains indicated that homozygotes for IRE4-5.5 T had lower IRE4-5 transcript levels than homozygotes for IRE4-5.6 T. However, congenic and field strains exhibited inconsistent results about the association of expression levels of IRE4-5 transcripts with sensitivity to β-cypermethrin. In summary, this study is the first to identify intron retention transcripts in the Vgsc gene from B. dorsalis and to examine their expression patterns across different developmental stages, tissues, and strains with varying sensitivities to β-cypermethrin. The potential role of the intron retentions of BdVgsc in insecticide toxicity is also discussed.

Transcriptome analysis of Drosophila suzukii reveals molecular mechanisms conferring pyrethroid and spinosad resistance

Drosophila suzukii lay eggs in soft-skinned, ripening fruits, making this insect a serious threat to berry production. Since its 2008 introduction into North America, growers have used insecticides, such as pyrethroids and spinosads, as the primary approach for D. suzukii management, resulting in development of insecticide resistance in this pest. This study sought to identify the molecular mechanisms conferring insecticide resistance in these populations. We sequenced the transcriptomes of two pyrethroid- and two spinosad-resistant isofemale lines. In both pyrethroid-resistant lines and one spinosad-resistant line, we identified overexpression of metabolic genes that are implicated in resistance in other insect pests. In the other spinosad-resistant line, we observed an overexpression of cuticular genes that have been linked to resistance. Our findings enabled the development of molecular diagnostics that we used to confirm persistence of insecticide resistance in California, U.S.A. To validate these findings, we leveraged D. melanogaster mutants with reduced expression of metabolic or cuticular genes that were found to be upregulated in resistant D. suzukii to demonstrate that these genes are involved in promoting resistance. This study is the first to characterize the molecular mechanisms of insecticide resistance in D. suzukii and provides insights into how current management practices can be optimized.

Alternative Splicing and Nonsense-Mediated Decay of a Zebrafish GABA Receptor Subunit Transcript

The superfamily of Cys-loop ionotropic neurotransmitter receptors includes those that detect GABA, glutamate, glycine, and acetylcholine. There is ample evidence that many Cys-loop receptor subunit genes include alternatively spliced exons. In this study, we report a novel example of alternative splicing (AS): we show that the 68-bp exon 3 in the zebrafish gabrr2b gene-which codes for the ρ2b GABAAR subunit-is an alternative cassette exon. Skipping of gabrr2b exon 3 results in a downstream frame shift and a premature termination codon (PTC). We provide evidence in larval zebrafish that transcripts containing the PTC are subject to degradation through nonsense-mediated decay. We also compile reports of AS of homologous exons in other Cys-loop receptor genes in multiple species. Our data add to a large body of research demonstrating that exon 3 in Cys-loop receptor genes is a conserved site for AS, the effects of which can vary from novel splice-isoform generation to downregulation of gene expression through transcript degradation.

Aberrant splicing of a nicotinic acetylcholine receptor alpha 6 subunit is associated with spinosad tolerance in the thrips predator Orius laevigatus

Susceptibility to insecticides is one of the limiting factors preventing wider adoption of natural enemies to control insect pest populations. Identification and selective breeding of insecticide tolerant strains of commercially used biological control agents (BCAs) is one of the approaches to overcome this constraint. Although a number of beneficial insects have been selected for increased tolerance to insecticides the molecular mechanisms underpinning these shifts in tolerance are not well characterised. Here we investigated the molecular mechanisms of enhanced tolerance of a lab selected strain of Orius laevigatus (Fieber) to the commonly used biopesticide spinosad. Transcriptomic analysis showed that spinosad tolerance is not a result of overexpressed detoxification genes. Molecular analysis of the target site for spinosyns, the nicotinic acetylcholine receptor (nAChR), revealed increased expression of truncated transcripts of the nAChR α6 subunit in the spinosad selected strain, a mechanism of resistance which was described previously in insect pest species. Collectively, our results demonstrate the mechanisms by which some beneficial biological control agents can evolve insecticide tolerance and will inform the development and deployment of insecticide-tolerant natural enemies in integrated pest management strategies.

Indoxacarb resistance in Iranian populations of Tuta absoluta (Lepidoptera: Gelechiidae): Cross-resistance, biochemical and molecular mechanisms

Tuta absoluta (Meyrick) is an invasive tomato pest that occurs worldwide, including Iran. This study investigates the occurrence of resistance to indoxacarb, an oxadiazine insecticide, and the underlying mechanisms in Iranian populations of T. absoluta. Bioassays were performed on second-instar larvae using indoxacarb alone and in combination with three synergists: Piperonyl butoxide (PBO), diethyl maleate (DEM), and triphenyl phosphate (TPP). The activities of the main detoxification enzymes, including glutathione S-transferases (GST), general carboxylesterases (CarEs), and P450 monooxygenases (P450s), were evaluated. In addition, the presence of known amino acid substitutions in the IV segment 6 domain of the T. absoluta sodium channel was investigated. The results showed that resistance rates to indoxacarb in Iranian populations ranged from 2.37- to 14.45-fold. However, pretreatment with synergists did not significantly increase the toxicity of indoxacarb. Enzyme assays showed that Ardabil (Ar) and Kerman (Kr) populations had the highest CarEs activity, while Ar population showed the highest P450 activity. However, the observed increases in enzyme activities were <2-fold. Two indoxacarb resistance mutations, F1845Y and V1848I, were detected. Apart from a significant and positive correlation between LC50 values of indoxacarb and thiocyclam hydrogen oxalate, no cross-resistance between indoxacarb and other insecticides was detected. Overall, these results suggest that populations of T. absoluta in Iran have developed resistance to indoxacarb, primarily through changes at the target site.

Overexpression of the UDP-glycosyltransferase UGT34A23 confers resistance to the diamide insecticide chlorantraniliprole in the tomato leafminer, Tuta absoluta

The tomato leafminer, Tuta absoluta, is an invasive crop pest that has evolved resistance to many of the insecticides used for its control. To facilitate the investigation of the underpinning mechanisms of resistance in this species we generated a contiguous genome assembly using long-read sequencing data. We leveraged this genomic resource to investigate the genetic basis of resistance to the diamide insecticide chlorantraniliprole in Spanish strains of T. absoluta that exhibit high levels of resistance to this insecticide. Transcriptomic analyses revealed that, in these strains, resistance is not associated with previously reported target-site mutations in the diamide target-site, the ryanodine receptor, but rather is associated with the marked overexpression (20- to >100-fold) of a gene encoding a UDP-glycosyltransferase (UGT). Functional expression of this UGT, UGT34A23, via ectopic expression in Drosophila melanogaster demonstrated that it confers strong and significant resistance in vivo. The genomic resources generated in this study provide a powerful resource for further research on T. absoluta. Our findings on the mechanisms underpinning resistance to chlorantraniliprole will inform the development of sustainable management strategies for this important pest.

Transposable elements and xenobiotic resistance

Transposable elements or TEs are well known drivers of adaptive change in plants and animals but their role in insecticide resistance remains poorly documented. This review examines the potential role of transposons in resistance and identifies key areas where our understanding remains unclear. Despite well-known model systems such as upregulation of Drosophila Cyp6g1, many putative examples lack functional validation. The potential types of transposon-associated changes that could lead to resistance are reviewed, including changes in up-regulation, message stability, loss of function and alternative splicing. Where potential mechanisms appear absent from the resistance literature examples are drawn from other areas of biology. Finally, ways are suggested in which transgenic expression could be used to validate the biological significance of TE insertion. In the absence of such functional expression studies many examples of the association of TEs and resistance genes therefore remain as correlations.

Multigenerational DNA methylation responses to copper exposure in Daphnia: Potential targets for epigenetic biomarkers?

Epigenetic mechanisms are moving to the forefront of environmental sciences, as environmentally induced epigenetic changes shape biological responses to chemical contamination. This work focused on Daphnia as a representative of potentially threatened freshwater biota, aiming to gain an insight into the involvement of epigenetic mechanisms in their response and eventual adaptation to metal contamination. Copper-induced DNA methylation changes, their potential transgenerational inheritance, and life-history traits were assessed. Organisms with different histories of past exposure to copper were exposed to toxic levels of the element for one generation (F0) and then monitored for three subsequent unexposed generations (F1, F2, and F3). Overall, methylation changes targeted important genes for counteracting the effects of metals and oxidative stress, including dynein light chain, ribosomal kinase and nuclear fragile X mental retardation-interacting protein. Also, contrasting overall and gene-specific methylation responses were observed in organisms differing in their history of exposure to copper, with different transgenerational methylation responses being also identified among the two groups, without apparent life-history costs. Taken together, these results demonstrate the capacity of copper to promote epigenetic transgenerational inheritance in a manner related explicitly to history of exposure, thereby supporting the development and incorporation of epigenetic biomarkers in risk assessment frameworks.

CRISPR-mediated knockout of nicotinic acetylcholine receptor (nAChR) α6 subunit confers high levels of resistance to spinosyns in Spodoptera frugiperda

Spinosyn insecticides (spinosad and spinetoram) have been widely used to control a number of agricultural pests including the fall armyworm, Spodoptera frugiperda. Mutations of the nicotinic acetylcholine receptor α6 subunit (nAChRα6) have been reported to confer high levels of resistance to spinosyns in several insect pests. Here we used CRISPR-mediated gene knockout to determine the involvement of S. frugiperda nAChRα6 (Sfα6) in spinosyns susceptibility. A Sfα6 knockout strain of S. frugiperda (Sfα6-KO) was established using dual single guide RNA (sgRNA) directed large fragment deletion with the CRISPR/Cas9 system. Sfα6-KO showed high levels of resistance to spinosad (307-fold) and spinetoram (517-fold) compared with the progenitor strain YJ-19, while no resistance was observed to emamectin benzoate, indoxacarb, chlorfenapyr, chlorantraniliprole and broflanilide. Genetic analyses confirmed that spinosad resistance in Sfα6-KO was autosomal, incompletely recessive and tightly linked to the edited deletion mutation of Sfα6. Our results provided in vivo functional evidence for Sfα6 as the major target of spinosyns against S. frugiperda, and demonstrated that disruption of Sfα6 causes high level resistance to spinosyns. Although no mutations of Sfα6 have yet been reported in any field populations of S. frugiperda, it is critical to develop F₁ screens and/or DNA-based methods to detect and monitor the mutant allele frequencies of Sfα6 across global populations of S. frugiperda.

Effects of nicotinic acetylcholine receptor subunit deletion mutants on insecticide susceptibility and fitness in Drosophila melanogaster

BACKGROUND

Nicotinic acetylcholine receptors (nAChRs) are major excitatory neurotransmitter receptors in insects and also the target site for many insecticides. Unfortunately, the effectiveness of these insecticides is diminishing as a consequence of the evolution of insecticide resistance. Further exploration of insecticide targets is important to sustainable pest management.

RESULTS

In order to validate the role of nAChR subunits in insecticide susceptibility and test whether the subunit's absence imposes the fitness cost on insects, we determined the susceptibility of eight nAChR subunit deletion mutants of Drosophila melanogaster to nine insecticides. These findings highlighted the specific resistance of the Dα6 deletion mutant to spinosyns. Although triflumezopyrim, dinotefuran and imidacloprid are competitive modulators of nAChRs, differences in susceptibility of the insect with different deletion mutants suggested that the target sites of these three insecticides do not overlap completely. Mutants showed decreased susceptibility to insecticides, accompanied by a reduction in fitness. The number of eggs produced by Dα1^attP , Dα2^attP , Dβ2^attP and Dβ3^attP females was significantly lesser than that of the vas-Cas9 strain as the control. In addition, adults of Dα2^attP , Dα3^attP and Dα7^attP strains showed lower climbing performance. Meanwhile, males of Dα3^attP , Dα5^attP , Dβ2^attP and Dβ3^attP , and females of Dβ2^attP showed significantly shorter longevity than those of the vas-Cas9 strain.

CONCLUSION

This study provides new insights into the interactions of different insecticides with different nAChRs subunit in D. melanogaster as a research model, it could help better understand such interaction in agricultural pests whose genetic manipulations for toxicological research are often challenging. © 2022 Society of Chemical Industry.

Knockin of the G275E mutation of the nicotinic acetylcholine receptor (nAChR) α6 confers high levels of resistance to spinosyns in Spodoptera exigua

Spinosyns, including spinosad and spinetoram, act on the insect central nervous system, gradually paralyzing or destroying the target insect. Spinosad resistance is associated with loss-of-function mutations in the nicotinic acetylcholine receptor (nAChR) α6 subunit in a number of agricultural pests. Using gene editing, nAChR α6 has been verified as a target for spinosyns in five insect species. Recently, a point mutation (G275E) in exon 9 of nAChR α6 was identified in spinosad-resistant strains of Thrips palmi and Tuta absoluta. To date, no in vivo functional evidence has been obtained to support that this mutation is involved in spinosyn resistance in lepidopteran pests. In this study, the G275E mutation was introduced into the nAChR of Spodoptera exigua using clustered regularly interspaced short palindromic repeats (CRISPR) / CRISPR-associated protein 9 (Cas9) gene-editing technology. Reverse transcriptase-polymerase chain reaction and sequencing confirmed that this mutation was present in exon 9 of the nAChR transcripts in the edited 275E strain. The results of bioassays showed that the 275E strain was highly resistant to spinosad (230-fold) and spinetoram (792-fold) compared to the unedited background strain, directly confirming that the G275E mutation of the nAChR α6 subunit confers high levels of spinosyn resistance in S. exigua. Inheritance analysis showed that the resistance trait is autosomal and incompletely recessive. This study employs a reverse genetics approach to validate the functional role played by the G275E mutation in nAChR α6 of S. exigua in spinosyns resistance and provides another example of the use of CRISPR/Cas9 gene-editing technology to confirm the role played by candidate target site mutations in insecticide resistance.

RNAseq-based gene expression profiling of the Anopheles funestus pyrethroid-resistant strain FUMOZ highlights the predominant role of the duplicated CYP6P9a/b cytochrome P450s

Insecticide-based interventions, notably long-lasting insecticidal nets, against mosquito vectors of malaria are currently threatened by pyrethroid resistance. Here, we contrasted RNAseq-based gene expression profiling of laboratory-resistant (FUMOZ) and susceptible (FANG) strains of the major malaria vector Anopheles funestus. Cytochrome P450 genes were the predominant over-expressed detoxification genes in FUMOZ, with high expression of the duplicated CYP6P9a (fold-change of 82.23 vs FANG) and CYP6P9b (FC 11.15). Other over-expressed P450s belonged to the same cluster of P450s corresponding to the resistance to pyrethroid 1 (rp1) quantitative trait loci (QTL) on chromosome 2R. Several Epsilon class glutathione S-transferases were also over-expressed in FUMOZ, as was the ATP-binding cassette transporter AFUN019220 (ABCA) which also exhibited between-strain alternative splicing events at exon 7. Significant differences in single-nucleotide polymorphism frequencies between strains occurred in resistance QTLs rp1 (CYP6P9a/b and CYP6AA1), rp2 on chromosome 2L (CYP6Z1, CYP6M7, and CYP6Z3), and rp3 on chromosome 3R (CYP9J5, CYP9J4, and CYP9J3). Differences were also detected in CYP4G17 and CYP4G16 genes on the X chromosome, both of which are associated with cuticular resistance in Anopheles gambiae. A close analysis of nonsynonymous diversity at the CYP6P9a/b loci revealed a drastic loss of diversity in FUMOZ with only a single polymorphism and 2 haplotypes vs 18 substitutions and 8 haplotypes in FANG. By contrast, a lowly expressed cytochrome P450 (CYP4C36) did not exhibit diversity differences between strains. We also detected the known pyrethroid resistance conferring amino acid change N384S in CYP6P9b. This study further elucidates the molecular bases of resistance in An. funestus, informing strategies to better manage widespread resistance across Africa.

Population structure and insecticide resistance status of Tuta absoluta populations from Turkey

BACKGROUND

Tuta absoluta is a devastating pest in tomato production areas worldwide. After its first introduction to Turkey in 2009, it quickly became the major pest of tomato-growing areas. Although some biocontrol agents have been used, especially in greenhouses, the main control of T. absoluta relies heavily on chemical insecticides. However, failure in chemical control has often been reported due to resistance development. In this study, we investigated (i) the population structure of 22 T. absoluta populations across Turkey by analysing haplotypes, based on the cytochrome oxidase subunit I gene; (ii) the efficacy of three registered insecticides from different classes (metaflumizone, chlorantraniliprole and spinosad) in real field-greenhouse conditions; and (iii) the geographic distribution of target-site mutations associated with insecticide resistance.

RESULTS

The efficacy of spinosad was higher than that of chlorantraniliprole and metaflumizone in the greenhouse trials, as documented by the mortality rates obtained, up to 14 days post application. Known resistance mutations in ryanodine receptors (RyR) (i.e. the I4790M/K and G4946E), nicotinic acetylcholine receptors (G275E), acetylcholinesterases (A201S) and voltage-gated sodium channels (F1845Y and V1848I) were found at various frequencies across the populations genotyped. The I4790K diamide resistance mutation in the RyR has been reported for the first time in T. absoluta populations. Although a total of eight haplotypes were found, the overall mean genetic distance was lower than 0.001, indicating the high genetic homogeneity among Turkish T. absoluta populations.

CONCLUSION

The results will contribute to design area-wide resistance management programs in T. absoluta control in Turkey. However, more monitoring studies are needed to implement evidence-based insecticide resistance management strategies in the frame of integrated pest management. © 2021 Society of Chemical Industry.

Transposon-mediated insertional mutagenesis unmasks recessive insecticide resistance in the aphid Myzus persicae

The evolution of resistance to insecticides threatens the sustainable control of many of the world's most damaging insect crop pests and disease vectors. To effectively combat resistance, it is important to understand its underlying genetic architecture, including the type and number of genetic variants affecting resistance and their interactions with each other and the environment. While significant progress has been made in characterizing the individual genes or mutations leading to resistance, our understanding of how genetic variants interact to influence its phenotypic expression remains poor. Here, we uncover a mechanism of insecticide resistance resulting from transposon-mediated insertional mutagenesis of a genetically dominant but insecticide-susceptible allele that enables the adaptive potential of a previously unavailable recessive resistance allele to be unlocked. Specifically, we identify clones of the aphid pest Myzus persicae that carry a resistant allele of the essential voltage-gated sodium channel (VGSC) gene with the recessive M918T and L1014F resistance mutations, in combination with an allele lacking these mutations but carrying a Mutator-like element transposon insertion that disrupts the coding sequence of the VGSC. This results in the down-regulation of the dominant susceptible allele and monoallelic expression of the recessive resistant allele, rendering the clones resistant to the insecticide bifenthrin. These findings are a powerful example of how transposable elements can provide a source of evolutionary potential that can be revealed by environmental and genetic perturbation, with applied implications for the control of highly damaging insect pests.

Insecticide exposure affects intergenerational patterns of DNA methylation in the Colorado potato beetle, Leptinotarsa decemlineata

Insecticide use is pervasive as a selective force in modern agroecosystems. Insect herbivores exposed to these insecticides have been able to rapidly evolve resistance to them, but how they are able to do so is poorly understood. One possible but largely unexplored explanation is that exposure to sublethal doses of insecticides may alter epigenetic patterns that are heritable. For instance, epigenetic mechanisms, such as DNA methylation that modifies gene expression without changing the underlying genetic code, may facilitate the emergence of resistant phenotypes in complex ways. We assessed the effects of sublethal insecticide exposure, with the neonicotinoid imidacloprid, on DNA methylation in the Colorado potato beetle, Leptinotarsa decemlineata, examining both global changes in DNA methylation and specific changes found within genes and transposable elements. We found that exposure to insecticide led to decreases in global DNA methylation for parent and F2 generations and that many of the sites of changes in methylation are found within genes associated with insecticide resistance, such as cytochrome P450s, or within transposable elements. Exposure to sublethal doses of insecticide caused heritable changes in DNA methylation in an agricultural insect herbivore. Therefore, epigenetics may play a role in insecticide resistance, highlighting a fundamental mechanism of evolution while informing how we might better coexist with insect species in agroecosystems.

Soil Surface-Trapping of Tomato Leaf-Miner Flies Emerging from Underground Pupae with a Simple Electrostatic Cover of Seedbeds in a Greenhouse

Simple Summary

Frequent infestation caused by tomato leaf miner flies (Liriomyza sativae) is a serious problem in the pesticide-independent cultivation of greenhouse tomatoes. This problem is caused by the persistent settlement of the flies in the greenhouse through larval movement between the phylloplane and rhizosphere soil of the host plants. The present work was conducted to develop a new physical control method to disrupt this developmental relationship. A simple electrostatic cover (EC) was constructed to trap adult flies emerging from underground pupae. The EC consisted of insulated iron rods linked to a voltage generator, which supplied a negative charge to the insulated iron rods, and non-insulated iron rods linked to a grounded line. The electric field formed in the space between the negatively charged and grounded iron rods generated an attractive force that could trap the target insects entering the electric field. A practical assay to demonstrate the functionality of the EC in a greenhouse revealed that the EC was able to capture all adult flies emerging from pupae. The simple structure of the EC makes it easy to fabricate for farmers who wish to integrate it into their pest management strategy. Thus, the present work provides an experimental basis for an electric field-based method for the control of tomato leaf miner flies.

Abstract

In the present study, an electrostatic apparatus for trapping adult tomato leaf miner flies (Liriomyza sativae) emerging from underground pupae at the surface of a seedbed in an organic greenhouse was developed. The apparatus consisted of insulated iron rods arranged in parallel at set intervals and linked to a voltage generator, which supplied a negative charge to the rods, as well as non-insulated grounded iron rods with the same configuration. The two layers of insulated and non-insulated iron rods were arrayed in parallel to form a static electric field between the layers. The electric field created a strong attractive force capable of capturing flies that entered the field. In a greenhouse assay, the apparatus was placed horizontally above a seedbed in a greenhouse and surveyed for its ability to capture adult flies emerging from pupae that were introduced onto the seedbed beneath the apparatus. The results revealed that the apparatus effectively trapped all adult flies that emerged from the pupae and that it functioned stably while continuously operated during the entire period of the experiment. Thus, our novel apparatus is a promising tool for the physical control of adult tomato leaf miners in the insecticide-independent cultivation of greenhouse tomatoes.

Variable resistance to spinetoram in populations of Thrips palmi across a small area unconnected to genetic similarity

The melon thrips, Thrips palmi, is an increasingly important pest of vegetables in northern China. Some populations have developed resistance in the field to the insecticide spinetoram. Understanding the origin and dispersal of insecticide-resistant populations can shed light on resistance management strategies. In this study, we tested susceptibility of seven greenhouse populations of T. palmi to spinetoram collected from a small area of about 300 km2 in Shandong Province and examined population genetic structure across the area based on a segment of mitochondrial cox1 gene and 22 microsatellite loci to infer the possible origin and dispersal of insecticide resistance. Levels of resistance to spinetoram differed among seven populations, which included one population with high resistance (LC50 = 759.34 mg/L), three populations with medium resistance (LC50 ranged from 28.69 to 34.79 mg/L), and three populations with low resistance (LC50 ranged from 7.61 to 8.97 mg/L). The populations were genetically differentiated into two groups unrelated to both levels of resistance and geographic distance. The molecular data indicated high levels of gene flow between populations with different levels of resistance to spinetoram and low gene flow among populations with the same level of resistance, pointing to a likely separate history of resistance evolution. Resistance levels of two tested populations to spinetoram decreased 23 and 4.6 times after five generations without any exposure to the pesticide. We therefore suspect that resistance of T. palmi most likely evolved in response to local applications of the insecticide. Our study suggests that the development of resistance could be avoided or resistance even reversed by reducing usage of spinetoram.

Functional validation of DvABCB1 as a receptor of Cry3 toxins in western corn rootworm, Diabrotica virgifera virgifera

Western corn rootworm (WCR), Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae), is a serious insect pest in the major corn growing areas of North America and in parts of Europe. WCR populations with resistance to Bacillus thuringiensis (Bt) toxins utilized in commercial transgenic traits have been reported, raising concerns over their continued efficacy in WCR management. Understanding the modes of action of Bt toxins is important for WCR control and resistance management. Although different classes of proteins have been identified as Bt receptors for lepidopteran insects, identification of receptors in WCR has been limited with no reports of functional validation. Our results demonstrate that heterologous expression of DvABCB1 in Sf9 and HEK293 cells conferred sensitivity to the cytotoxic effects of Cry3A toxins. The result was further validated using knockdown of DvABCB1 by RNAi which rendered WCR larvae insensitive to a Cry3A toxin. However, silencing of DvABCB2 which is highly homologous to DvABCB1 at the amino acid level, did not reduce the sensitivity of WCR larvae to a Cry3A toxin. Furthermore, our functional studies corroborate different mode-of-actions for other insecticidal proteins including Cry34Ab1/35Ab1, Cry6Aa1, and IPD072Aa against WCR. Finally, reduced expression and alternatively spliced transcripts of DvABCB1 were identified in a mCry3A-resistant strain of WCR. Our results provide the first clear demonstration of a functional receptor in the molecular mechanism of Cry3A toxicity in WCR and confirmed its role in the mechanism of resistance in a mCry3A resistant strain of WCR.

Highly dynamic transcriptional reprogramming and shorter isoform shifts under acute stresses during biological invasions

Phenotypic plasticity has been increasingly recognized for its importance in adaptation to novel environments, and initial rapid plastic response to acute stresses usually serves as the stepping stone for future adaptation. Differential gene expression and alternative splicing have been proposed as two underlying mechanisms for rapid plastic response to environmental stresses. Here, we used an invasive model species, Ciona savignyi, to investigate the temporary plastic changes under temperature stresses on gene expression and alternative splicing. Our results revealed rapid and highly dynamic gene expression reprogramming and alternative splicing switch under acute stresses. Distinct transcriptional response profiles were triggered by two types of temperature stresses, showing resilience recovery and increasing divergence under heat and cold challenges, respectively. Interestingly, alternative exons were more inclined to be skipped under both heat and cold stresses, leading to shorter isoforms but with maintained Open Reading Frames (ORFs). Although similar response patterns were observed between differential gene expression and alternative splicing, low overlap between Differentially Expressed Genes (DEGs) and Differentially Alternative Spliced Genes (DASGs) suggests that distinct gene sets and associated functions should be involved in temperature challenges. Thus, alternative splicing should offer an additional layer of plastic response to environmental challenges. Finally, we identified key plastic genes involved in both gene expression regulation and alternative splicing. The results obtained here shed light on adaptation and accommodation mechanisms during biological invasions, particularly for acute environmental changes at early stages of biological invasions such as transport and introduction.

Functional validation of nicotinic acetylcholine receptor (nAChR) α6 as a target of spinosyns in Spodoptera exigua utilizing the CRISPR/Cas9 system

BACKGROUND

The beet armyworm, Spodoptera exigua, is a serious agricultural pest that is primarily controlled using chemical insecticides. Recently, resistance to the insecticide spinosad has been described in S. exigua field populations. To date, there has been no functional evidence proving the involvement of the nicotinic acetylcholine receptor (nAChR) α6 mutation in spinosad resistance in S. exigua.

RESULTS

In this study, using the CRISPR/Cas9 genome-editing system, a homozygous strain (Seα6-KO) with approximately 1760-bp deletion within Seα6 in S. exigua causing a premature truncation of Seα6 was successfully constructed. Insecticide bioassays showed that Seα6-KO exhibited 373-fold higher resistance to spinosad and 850-fold higher resistance to spinetoram compared to WH-S strain with the same genetic background but showed no significant change in susceptibility to emamectin benzoate and chlorantraniliprole. Genetic analysis revealed that Seα6-KO is inherited as an incompletely recessive trait.

CONCLUSION

The results clearly demonstrated the functional role of Seα6 in resistance to spinosyn insecticides and provide an example of using genome editing to verify a target premature truncation associated with resistance.

Evolutionary trade-offs of insecticide resistance - The fitness costs associated with target-site mutations in the nAChR of Drosophila melanogaster

The evolution of resistance to drugs and pesticides poses a major threat to human health and food security. Neonicotinoids are highly effective insecticides used to control agricultural pests. They target the insect nicotinic acetylcholine receptor and mutations of the receptor that confer resistance have been slow to develop, with only one field‐evolved mutation being reported to date. This is an arginine‐to‐threonine substitution at position 81 of the nAChR_β1 subunit in neonicotinoid‐resistant aphids. To validate the role of R81T in neonicotinoid resistance and to test whether it may confer any significant fitness costs to insects, CRISPR/Cas9 was used to introduce an analogous mutation in the genome of Drosophila melanogaster. Flies carrying R81T showed an increased tolerance (resistance) to neonicotinoid insecticides, accompanied by a significant reduction in fitness. In comparison, flies carrying a deletion of the whole nAChR_α6 subunit, the target site of spinosyns, showed an increased tolerance to this class of insecticides but presented almost no fitness deficits.

Disruption of nicotinic acetylcholine receptor α6 mediated by CRISPR/Cas9 confers resistance to spinosyns in Plutella xylostella

BACKGROUND

The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system provides some advantages over other reverse genetic techniques to investigate the causal relationship between insecticide resistance phenotype and candidate gene. Several studies published to date point to the nicotinic acetylcholine receptor (nAChR) α6 subunit strongly associated with spinosyns resistance in insects, including Plutella xylostella. However, reverse genetic verification of the P. xylostella nAChRα6 has not yet been achieved via an in vivo approach.

RESULTS

Here, we successfully constructed a homozygous strain (Pxα6-KO) with a 2-nt deletion mutation of nAChRα6 by CRISPR/Cas9 coupled with non-homologous end joining approach in P. xylostella. The manipulated mutation results in a frame shift in the open reading frame of transcripts, which produces a predicted protein truncated in the TM3-TM4 loop region. When compared to the background strain IPP-S, the knockout strain Pxα6-KO exhibited 229- and 1462-fold resistance to spinosad and spinetoram, respectively, but no or limited (resistance ratios <3-fold) effects on the toxicities of imidacloprid, abamectin, β-cypermethrin, indoxacarb, metaflumizone and chlorantraniliprole. Furthermore, the mode of inheritance of the acquired spinetoram resistance was autosomal recessive and significantly linked with the 2-nt deletion mutation of nAChRα6 in the Pxα6-KO strain.

CONCLUSION

In vivo functional investigation demonstrates the causality of the Pxα6 truncating mutation with high levels of resistance to spinosyns in P. xylostella. Our results suggest the Pxα6-KO strain underlies an autosomal, recessive mode of inheritance for spinetoram resistance, and reinforces the association of this gene to the mode of action of spinosyns. © 2019 Society of Chemical Industry.

Alternative splicing and insect ryanodine receptor

Phylogenetic tree of the ryanodine receptor (RyR) family based on maximum likelihood estimation.

The evolution of multiple-insecticide resistance in UK populations of tomato leafminer, Tuta absoluta

BACKGROUND

The tomato leafminer, Tuta absoluta, is an economically important pest of tomatoes in Europe, Africa, Asia and South America. In the UK this species is controlled using an integrated pest management (IPM) programme which incorporates the insecticides spinosad and chlorantraniliprole. In response to UK grower concerns of loss of efficacy of these compounds at certain sites, insecticide bioassays were performed on five populations collected from four commercial glasshouses and potential mechanisms of resistance investigated.

RESULTS

We observed high levels of resistance to spinosad in four of the strains, and in two of these tolerance to chlorantraniliprole. Selection of one of these strains with chlorantraniliprole rapidly resulted in a line exhibiting potent resistance to this compound. Sequencing of messenger RNA encoding the nicotinic acetylcholine receptor (nAChR) α6 subunit, target of spinosad, revealed Taα6 transcripts in the spinosad-resistant strains that lack exon 4 and encode a highly truncated protein, or contain a triplet deletion in the predicted first transmembrane domain resulting in the loss of a highly conserved amino acid. Sequencing of the ryanodine receptor gene, encoding the target of diamide insecticides, of the chlorantraniliprole-selected line revealed an amino acid substitution (G4903V) that has been previously linked to diamide resistance in populations of T. absoluta in the Mediterranean and South America.

CONCLUSION

Taken together our results reveal emerging resistance in UK populations of T. absoluta to two of the most important insecticides used as part of IPM, with significant implications for the control of this species in the UK. © 2019 Society of Chemical Industry.

Chemical Modulation of Alternative Splicing for Molecular-Target Identification by Potential Genetic Control in Agrochemical Research

Alternative splicing (AS), the process of removing introns from pre-mRNA and the rearrangement of exons to produce several types of mature transcripts, is a remarkable step preceding protein synthesis. In particular, it has now been conclusively shown that up to ∼95% of genes are alternatively spliced to generate a complex and diverse proteome in eukaryotic organisms. Consequently, AS is one of the determinants of the functional repertoire of cells. Many studies have revealed that AS in plants can be regulated by cell type, developmental stage, environmental stress, and the circadian clock. Moreover, increasing amounts of evidence reveal that chemical compounds can affect various steps during splicing to induce major effects on plant physiology. Hence, the chemical modulation of AS can serve as a good strategy for molecular-target identification in attempts to potentially control plant genetics. However, the kind of mechanisms involved in the chemical modulation of AS that can be used in agrochemical research remain largely unknown. This review introduces recent studies describing the specific roles AS plays in plant adaptation to environmental stressors and in the regulation of development. We also discuss recent advances in small molecules that induce alterations of AS and the possibility of using this strategy in agrochemical-target identification, giving a new direction for potential genetic control in agrochemical research.

Identification and risk assessment of spinosad resistance in a California population of Drosophila suzukii

BACKGROUND

The bioinsecticide spinosad is among the most widely used insecticides for managing spotted-wing drosophila, Drosophila suzukii (Matsumura), and is critical for preventing fruit infestation in organic berry production. Recent reports, however, have raised concerns that the efficacy of this material is declining in fields near Watsonville, CA, a major hub of commercial berry production in the USA and the first location where D. suzukii was reported in North America.

RESULTS

In this study, we performed dose-response analyses on D. suzukii from commercial raspberry plantings near Watsonville as well as a second untreated site in California using a widely implemented bioassay protocol. We found that Watsonville flies exhibited spinosad LC₅₀ values 4.3-7.7 times higher than those from the untreated location and 11.6-22.4 times higher than previously reported susceptible baselines. Additionally, tolerance to spinosad continued to increase after additional selection for five generations, though this result was only statistically significant after prolonged exposure to residues.

CONCLUSIONS

These findings confirm that spinosad resistance is emerging in the Watsonville area and document the first known occurrence in the USA, presenting an urgent need for the development of alternative management strategies to control this pest. Additional work is needed to resolve the underlying molecular mechanism(s) that confers spinosad resistance in D. suzukii and assess the potential for this trait to spread into new populations. © 2018 Society of Chemical Industry.

Sex Chromosome Turnover in Moths of the Diverse Superfamily Gelechioidea

Sex chromosomes play a central role in genetics of speciation and their turnover was suggested to promote divergence. In vertebrates, sex chromosome-autosome fusions resulting in neo-sex chromosomes occur frequently in male heterogametic taxa (XX/XY), but are rare in groups with female heterogamety (WZ/ZZ). We examined sex chromosomes of seven pests of the diverse lepidopteran superfamily Gelechioidea and confirmed the presence of neo-sex chromosomes in their karyotypes. Two synteny blocks, which correspond to autosomes 7 (LG7) and 27 (LG27) in the ancestral lepidopteran karyotype exemplified by the linkage map of Biston betularia (Geometridae), were identified as sex-linked in the tomato leafminer, Tuta absoluta (Gelechiidae). Testing for sex-linkage performed in other species revealed that while LG7 fused to sex chromosomes in a common ancestor of all Gelechioidea, the second fusion between the resulting neo-sex chromosome and the other autosome is confined to the tribe Gnoreschemini (Gelechiinae). Our data accentuate an emerging pattern of high incidence of neo-sex chromosomes in Lepidoptera, the largest clade with WZ/ZZ sex chromosome system, which suggest that the paucity of neo-sex chromosomes is not an intrinsic feature of female heterogamety. Furthermore, LG7 contains one of the major clusters of UDP-glucosyltransferases, which are involved in the detoxification of plant secondary metabolites. Sex chromosome evolution in Gelechioidea thus supports an earlier hypothesis postulating that lepidopteran sex chromosome-autosome fusions can be driven by selection for association of Z-linked preference or host-independent isolation genes with larval performance and thus can contribute to ecological specialization and speciation of moths.

Multiple mutations in the nicotinic acetylcholine receptor Ccα6 gene associated with resistance to spinosad in medfly

Spinosad is an insecticide widely used for the control of insect pest species, including Mediterranean fruit fly, Ceratitis capitata. Its target site is the α6 subunit of the nicotinic acetylcholine receptors, and different mutations in this subunit confer resistance to spinosad in diverse insect species. The insect α6 gene contains 12 exons, with mutually exclusive versions of exons 3 (3a, 3b) and 8 (8a, 8b, 8c). We report here the selection of a medfly strain highly resistant to spinosad, JW-100 s, and we identify three recessive Ccα6 mutant alleles in the JW-100 s population: (i) Ccα63aQ68* containing a point mutation that generates a premature stop codon on exon 3a (3aQ68*); (ii) Ccα63aAG>AT containing a point mutation in the 5' splicing site of exon 3a (3aAG > AT); and (iii) Ccα63aQ68*-K352* that contains the mutation 3aQ68* and another point mutation on exon 10 (K352*). Though our analysis of the susceptibility to spinosad in field populations indicates that resistance has not yet evolved, a better understanding of the mechanism of action of spinosad is essential to implement sustainable management practices to avoid the development of resistance in field populations.

Spinosad resistance affects biological parameters of Musca domestica Linnaeus

Musca domestica is one of the major cosmopolitan insect pests of public health importance. Spinosad is considered an eco-friendly insecticide used for the management of M. domestica and other pests of significant concern. Cases of resistance against spinosad in M. domestica have been reported from some parts of the world; however, there are no reports of any negative effects of spinosad resistance on the fitness/biological parameters of M. domestica. To investigate fitness costs, a near isogenic M. domestica resistant strain (Spin-R) was constructed using Spin-UNSEL-susceptible and Spin-SEL-resistant strains sharing a close genetic background. We found significantly reduced rates of adult eclosion, fecundity, egg hatching, survival, and lengthened developmental time in the Spin-R strain. Moreover, the values of different fitness parameters like biotic potential, mean relative growth rate, intrinsic rate of natural increase, and net reproductive rate, were also significantly reduced in the Spin-R strain, which reflect fitness costs most probably linked with spinosad resistance. The presence of fitness costs suggests likely instability of resistance to spinosad in M. domestica, which can be reverted by relaxing spinosad selection pressure and rotation with alternate insecticides. The wise use of insecticides will ultimately help to manage resistance in this pest and minimize environmental pollution.

An analysis of variability in genome organisation of intracellular calcium release channels across insect orders

Using publicly available genomic data, combined with RT-PCR validation, we explore structural genomic variation for two major ion channels across insect classes. We have manually curated ryanodine receptor (RyR) and inositol 1,4,5-trisphosphate receptor (IP₃R) ORFs and their corresponding genomic structures from 26 different insects covering major insect orders. We found that, despite high protein identity for both RyRs (>75%) and IP₃Rs (~67%), the overall complexity of the gene structure varies greatly between different insect orders with the simplest genes (fewest introns) found in Diptera and the most complex in Lepidoptera. Analysis of intron conservation patterns indicated that the majority of conserved introns are found close to the 5' end of the channels and in RyR around the highly conserved mutually exclusive splice site. Of the two channels the IP₃Rs appear to have a less well conserved organisation with a greater overall number of unique introns seen between insect orders. We experimentally validated two of the manually curated ORFs for IP₃Rs and confirmed an atypical (3799aa) IP₃R receptor in Myzus persicae, which is approximately 1000 amino acids larger than previously reported for IP₃Rs.

Differentially expressed microRNAs associated with changes of transcript levels in detoxification pathways and DDT-resistance in the Drosophila melanogaster strain 91-R

Dichloro-diphenyl-trichloroethane (DDT) resistance among arthropod species is a model for understanding the molecular adaptations in response to insecticide exposures. Previous studies reported that DDT resistance may involve one or multiple detoxification genes, such as cytochrome P450 monooxygenases (P450s), glutathione S-transferases (GSTs), esterases, and ATP binding cassette (ABC) transporters, or changes in the voltage-sensitive sodium channel. However, the possible involvement of microRNAs (miRNAs) in the post-transcriptional regulation of genes associated with DDT resistance in the Drosophila melanogaster strain 91-R remains poorly understood. In this study, the majority of the resulting miRNAs discovered in small RNA libraries from 91-R and the susceptible control strain, 91-C, ranged from 16-25 nt, and contained 163 precursors and 256 mature forms of previously-known miRNAs along with 17 putative novel miRNAs. Quantitative analyses predicted the differential expression of ten miRNAs between 91-R and 91-C, and, based on Gene Ontology and pathway analysis, these ten miRNAs putatively target transcripts encoding proteins involved in detoxification mechanisms. RT-qPCR validated an inverse correlation between levels of differentially-expressed miRNAs and their putatively targeted transcripts, which implies a role of these miRNAs in the differential regulation of detoxification pathways in 91-R compared to 91-C. This study provides evidence associating the differential expression of miRNAs in response to multigenerational DDT selection in Drosophila melanogaster and provides important clues for understanding the possible roles of miRNAs in mediating insecticide resistance traits.

Does resistance really carry a fitness cost?

Insecticide resistance mutations are widely assumed to carry fitness costs. However studies to measure such costs are rarely performed on genetically related strains and are often only done in the laboratory. Theory also suggests that once evolved the cost of resistance can be offset by the evolution of fitness modifiers. But for insecticide resistance only one such example is well documented. Here we critically examine the literature on fitness costs in the absence of pesticide and ask if our knowledge of molecular biology has helped us predict the costs associated with different resistance mechanisms. We find that resistance alleles can arise from pre-existing polymorphisms and resistance associated variation can also be maintained by sexual antagonism. We describe novel mechanisms whereby both resistant and susceptible alleles can be maintained in permanent heterozygosis and discuss the likely consequences for fitness both in the presence and absence of pesticide. Taken together these findings suggest that we cannot assume that resistance always appears de novo and that our assumptions about the associated fitness costs need to be informed by a deeper understanding of the underlying molecular biology.