Mutations of acetylcholinesterase which confer insecticide resistance in Drosophila melanogaster populations

Comparative toxicity and enzymatic detoxification responses in Spodoptera frugiperda (Lepidoptera: Noctuidae) to two insecticides

The fall armyworm (FAW), Spodoptera frugiperda Smith (Lepidoptera: Noctuidae), poses a significant threat to food security, necessitating effective management strategies. While chemical control remains a primary approach, understanding the toxicity and detoxification mechanisms of different insecticides is crucial. In this study, we conducted leaf-dipping bioassays to assess the toxicity of quinalphos and beta-cypermethrin·emamectin benzoate (β-cyp·EMB) on S. frugiperda larvae. Additionally, we assessed the response of alterations in CarE, GST, MFO, and AChE activities to sublethal concentrations of these insecticides over various treatment durations. Results indicated that β-cyp·EMB exhibited higher toxicity than quinalphos in S. frugiperda. Interestingly, the highest activities of GST, CarE, MFO, and AChE were observed at 6 h exposure to LC10 and LC25 of β-cyp·EMB, surpassing equivalent sublethal concentrations of quinalphos. Subsequently, GST and CarE activities exposure to β-cyp·EMB steadily decreased, while MFO and AChE activities exposure to both insecticides was initially decreased then increased. Conversely, two sublethal concentrations of quinalphos notably enhanced GST activity across all exposure durations, with significantly higher than β-cyp·EMB at 12-48 h. Similarly, CarE activity was also increased at various durations. Our research has exhibited significant alterations in enzyme activities exposure to both concentration and duration. Furthermore, Pearson correlation analysis showed significant correlations among these enzyme activities at different treatment durations. These findings contribute to a better understanding of detoxification mechanisms across different insecticides, providing valuable insights for the rational management of S. frugiperda populations.

Acetylcholine esterase of Drosophila melanogaster: a laboratory model to explore insecticide susceptibility gene drives

BACKGROUND

One of the proposed applications of gene drives has been to revert pesticide resistant mutations back to the ancestral susceptible state. Insecticides that have become ineffective because of the rise of resistance could have reinvigorated utility and be used to suppress pest populations again, perhaps at lower application doses.

RESULTS

We have created a laboratory model for susceptibility gene drives that replaces field-selected resistant variants of the acetylcholine esterase (Ace) locus of Drosophila melanogaster with ancestral susceptible variants. We constructed a CRISPR/Cas9 homing drive and found that homing occurred in many genetic backgrounds with varying efficiencies. While the drive itself could not be homozygous, it converted resistant alleles into susceptible ones and produced recessive lethal alleles that could suppress populations. Our studies provided evidence for two distinct classes of gene drive resistance (GDR): rather than being mediated by the conventional non-homologous end-joining (NHEJ) pathway, one seemed to involve short homologous repair and the other was defined by genetic background. Additionally, we used simulations to explore a distinct application of susceptibility drives; the use of chemicals to prevent the spread of synthetic gene drives into protected areas.

CONCLUSIONS

Insecticide susceptibility gene drives could be useful tools to control pest insects however problems with particularities of target loci and GDR will need to be overcome for them to be effective. Furthermore, realistic patterns of pest dispersal and high insecticide exposure rates would be required if susceptibility were to be useful as a 'safety-switch' to prevent the unwanted spread of gene drives. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Chemical tolerance related to the ABC transporter gene and DNA methylation in cladocera (Daphnia magna)

We performed multigenerational tests to clarify the chemical tolerance mechanisms of a nontarget aquatic organism, Daphnia magna. We continuously exposed D. magna to a carbamate insecticide (pirimicarb) at lethal or sublethal concentrations (0, 3.8, 7.5, and 15 μg/L) for 15 generations (F0-F14). We then determined the 48 h-EC50 values and mRNA expression levels of acetylcholinesterase, glutathione S-transferase, and ATP (Adenosine triphosphate)-binding cassette transporter (ABCt) in neonates (<24 h old) from F0, F4, F9, and F14. To ascertain the effects of DNA methylation on pirimicarb sensitivity, we measured 5-methylcytosine levels (DNA methylation levels) in neonates of parents in the last generation (F14). In addition, we cultured groups exposed to 0 and 7.5 μg/L (the latter of which acquired chemical tolerance to pirimicarb) with or without 5-azacytidine (de-methylating agent) and determined methylation levels and 48 h-EC50 values in neonates (<24 h old) from the treated parents. The EC50 values (30.3-31.6 μg/L) in F14 of the 7.5 and 15 μg/L groups were approximately two times higher than that in the control (16.0 μg/L). A linear mixed model analysis showed that EC50 and ABCt mRNA levels were significantly increased with generational alterations; further analysis showed that the ABCt mRNA level was positively related to the EC50 . Therefore, ABCt may be associated with altered pirimicarb sensitivity. In addition, the EC50 value and DNA methylation levels in pirimicarb-tolerant clones decreased after exposure to 5-azacytidine, suggesting that DNA methylation contributes to chemical tolerance. These findings improved our knowledge regarding the acquisition of chemical tolerance in aquatic organisms.

Frequency and polymorphism of acetylcholinesterase gene involved in the organophosphate resistance of Musca domestica in Guizhou Province, China

Organophosphate (OP) resistance has been prevalent in Musca domestica populations worldwide since 1960s. Previous studies have demonstrated that point mutations of the acetylcholinesterase gene (Ace) are one of the important molecular mechanisms underlying OP resistance. However, few studies have investigated the molecular mechanisms of OP resistance in the past 10 years in China. In this study, we investigated the status of OP resistance and genetic diversity of Ace in the field populations of houseflies in Guizhou Province of China. The bioassays showed that the houseflies had 142-304-fold resistance to dichlorvos (DDVP) and 122-364-fold resistance to temephos, compared to the susceptible houseflies. Five nonsynonymous mutations (Y226F, V260L, G342A/V, F407Y) in Ace were detected among the 7 field populations, with an average frequency of 5.4%, 55%, 68%, 32%, and 94%, respectively, of which the Y226F mutation had not been reported previously. Eleven combinations of triple mutations (at positions 260, 342, and 407) were observed, of which the combination 260L/V+342A/V+407Y was predominant. The ZY and AS populations showed greatest diversity of allelic combination and the other five populations showed different distributions among different regions. These results indicate that the resistance to OPs is prevalent among the housefly populations and target-site insensitivity is the main cause of resistance in Guizhou Province. The difference in distribution and the allelic diversity of Ace in field populations may be due to the complexity and variability of insecticide application. It is necessary to monitor resistance to insecticides and conduct management of houseflies in Guizhou Province.

The complex II resistance mutation H258Y in succinate dehydrogenase subunit B causes fitness penalties associated with mitochondrial respiratory deficiency

BACKGROUND

The acaricides cyflumetofen, cyenopyrafen and pyflubumide inhibit the mitochondrial electron transport chain at complex II [succinate dehydrogenase (SDH) complex]. A target site mutation H258Y was recently discovered in a resistant strain of the spider mite pest Tetranychus urticae. H258Y causes strong cross-resistance between cyenopyrafen and pyflubumide, but not cyflumetofen. In fungal pests, fitness costs associated with substitutions at the corresponding H258 position that confer resistance to fungicidal SDH inhibitors have not been uncovered. Here, we used H258 and Y258 near-isogenic lines of T. urticae to quantify potential pleiotropic fitness effects on mite physiology.

RESULTS

The H258Y mutation was not associated with consistent significant changes of single generation life history traits and fertility life table parameters. In contrast, proportional Sanger sequencing and droplet digital polymerase chain reaction showed that the frequency of the resistant Y258 allele decreased when replicated 50:50 Y258:H258 experimentally evolving populations were maintained in an acaricide-free environment for approximately 12 generations. Using in vitro assays with mitochondrial extracts from resistant (Y258) and susceptible (H258) lines, we identified a significantly reduced SDH activity (48% lower activity) and a slightly enhanced combined complex I and III activity (18% higher activity) in the Y258 lines.

CONCLUSION

Our findings suggest that the H258Y mutation is associated with a high fitness cost in the spider mite T. urticae. Importantly, while it is the most common approach, it is clear that only comparing life history traits and life table fecundity does not allow to reliably estimate fitness costs of target site mutations in natural pest populations. © 2023 Society of Chemical Industry.

The Transcriptomic Response of the Boll Weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curculionidae), following Exposure to the Organophosphate Insecticide Malathion

Insecticide tolerance and resistance have evolved countless times in insect systems. Molecular drivers of resistance include mutations in the insecticide target site and/or gene duplication, and increased gene expression of detoxification enzymes. The boll weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curculionidae), is a pest of commercial cotton and has developed resistance in the field to several insecticides; however, the current organophosphate insecticide, malathion, used by USA eradication programs remains effective despite its long-term use. Here, we present findings from an RNA-seq experiment documenting gene expression post-exposure to field-relevant concentrations of malathion, which was used to provide insight on the boll weevil's continued susceptibility to this insecticide. Additionally, we incorporated a large collection of boll weevil whole-genome resequencing data from nearly 200 individuals collected from three geographically distinct areas to determine SNP allele frequency of the malathion target site, as a proxy for directional selection in response to malathion exposure. No evidence was found in the gene expression data or SNP data consistent with a mechanism of enhanced tolerance or resistance adaptation to malathion in the boll weevil. Although this suggests continued effectiveness of malathion in the field, we identified important temporal and qualitative differences in gene expression between weevils exposed to two different concentrations of malathion. We also identified several tandem isoforms of the detoxifying esterase B1 and glutathione S-transferases, which are putatively associated with organophosphate resistance.

Predicting the insecticide-driven mutations in a crop pest insect: Evidence for multiple polymorphisms of acetylcholinesterase gene with potential relevance for resistance to chemicals

The silverleaf whitefly Bemisia tabaci (Gennadius, 1889) (Homoptera: Aleyrodidae) is a serious invasive herbivorous insect pest worldwide. The excessive use of pesticides has progressively selected B. tabaci specimens, reducing the effectiveness of the treatments, and ultimately ending in the selection of pesticide-resistant strains. The management of this crop pest has thus become challenging owing to the level of resistance to all major classes of recommended insecticides. Here, we used in silico techniques for detecting sequence polymorphisms in ace1 gene from naturally occurring B. tabaci variants, and monitor the presence and frequency of the detected putative mutations from 30 populations of the silverleaf whitefly from Egypt and Pakistan. We found several point mutations in ace1-type acetylcholinesterase (ace1) in the studied B. tabaci variants naturally occurring in the field. By comparing ace1 sequence data from an organophosphate-susceptible and an organophosphate-resistant strains of B. tabaci to ace1 sequence data retrieved from GenBank for that species and to nucleotide polymorphisms from other arthropods, we identified novel mutations that could potentially influence insecticide resistance. Homology modeling and molecular docking analyses were performed to determine if the mutation-induced changes in form 1 acetylcholinesterase (AChE1) structure could confer resistance to carbamate and organophosphate insecticides. Mutations had small effects on binding energy (ΔG_b) interactions between mutant AChE1 and insecticides; they altered the conformation of the peripheral anionic site of AChE1, and modified the enzyme surface, and these changes have potential effects on the target-site sensitivity. Altogether, the results from this study provide information on genic variants of B. tabaci ace1 for future monitoring insecticide resistance development and report a potential case of environmentally driven gene variations.

Enrichment of Hard Sweeps on the X Chromosome in Drosophila melanogaster

The characteristic properties of the X chromosome, such as male hemizygosity and its unique inheritance pattern, expose it to natural selection in a way that can be different from the autosomes. Here, we investigate the differences in the tempo and mode of adaptation on the X chromosome and autosomes in a population of Drosophila melanogaster. Specifically, we test the hypothesis that due to hemizygosity and a lower effective population size on the X, the relative proportion of hard sweeps, which are expected when adaptation is gradual, compared with soft sweeps, which are expected when adaptation is rapid, is greater on the X than on the autosomes. We quantify the incidence of hard versus soft sweeps in North American D. melanogaster population genomic data with haplotype homozygosity statistics and find an enrichment of the proportion of hard versus soft sweeps on the X chromosome compared with the autosomes, confirming predictions we make from simulations. Understanding these differences may enable a deeper understanding of how important phenotypes arise as well as the impact of fundamental evolutionary parameters on adaptation, such as dominance, sex-specific selection, and sex-biased demography.

Resistance to Multiple Insecticide Classes in the Vinegar Fly Drosophila melanogaster (Diptera: Drosophilidae) in Michigan Vineyards

Vinegar flies are vectors of pathogens causing fruit rots of grapes, so control of these insects is important for preventing vineyard yield loss. Recent outbreaks of sour rots may be linked to greater challenges controlling vinegar flies, so we investigated the insecticide susceptibility of populations collected from commercial vineyards across Michigan. We first determined the discriminating concentration for phosmet, malathion, methomyl, and zeta-cypermethrin using a laboratory susceptible (Canton-S) strain of D. melanogaster females. The discriminating concentrations were determined as 252.08, 2.58, 0.96, and 1.68 ppm of the four insecticides, respectively. These concentrations were first tested in 2020 against populations from the two major counties for grape production. In 2021, we expanded monitoring to twenty-three populations collected from vineyards across six counties. All populations had significantly lower sensitivity to all four insecticides compared with Canton-S strain, with up to 98.8% lower mortality for phosmet. The LC50, LC90, and LC99 values of the four insecticides for the two populations tested in 2020 were 7-1,157-fold higher than the Canton-S strain. For the twenty-three populations collected in 2021, mortality ranged from 56.3 to 100% when the flies were screened using a 10x concentration of the discriminating concentration of the insecticides, whereas it ranged from 82.4 to 100% when the flies were screened using a 20x concentration. Our results suggest variable levels of resistance to insecticides from multiple chemical classes in D. melanogaster populations in Michigan vineyards, highlighting the need to implement integrated sour rot management approaches that are less dependent on insecticides for control of this species.

Discovery of malathion resistance QTL in Drosophila melanogaster using a bulked phenotyping approach

Drosophila melanogaster has proved an effective system with which to understand the evolutionary genetics and molecular mechanisms of insecticide resistance. Insecticide use has left signatures of selection in the fly genome, and both functional and quantitative genetic studies in the system have identified genes and variants associated with resistance. Here, we use D. melanogaster and leverage a bulk phenotyping and pooled sequencing "extreme quantitative trait loci" approach to genetically dissect variation in resistance to malathion, an organophosphate insecticide. We resolve 2 quantitative trait loci, one of which implicates allelic variation at the cytochrome P450 gene Cyp6g1, a strong candidate based on previous work. The second shows no overlap with hits from a previous genome-wide association study for malathion resistance, recapitulating other studies showing that different strategies for complex trait dissection in flies can yield apparently different architectures. Notably, we see no genetic signal at the Ace gene. Ace encodes the target of organophosphate insecticide inhibition, and genome-wide association studies have identified strong Ace-linked associations with resistance in flies. The absence of quantitative trait locus implicating Ace here is most likely because our mapping population does not segregate for several of the known functional polymorphisms impacting resistance at Ace, perhaps because our population is derived from flies collected prior to the widespread use of organophosphate insecticides. Our fundamental approach can be an efficient, powerful strategy to dissect genetic variation in resistance traits. Nonetheless, studies seeking to interrogate contemporary insecticide resistance variation may benefit from deriving mapping populations from more recently collected strains.

Mechanisms of protein evolution

How do proteins evolve? How do changes in sequence mediate changes in protein structure, and in turn in function? This question has multiple angles, ranging from biochemistry and biophysics to evolutionary biology. This review provides a brief integrated view of some key mechanistic aspects of protein evolution. First, we explain how protein evolution is primarily driven by randomly acquired genetic mutations and selection for function, and how these mutations can even give rise to completely new folds. Then, we also comment on how phenotypic protein variability, including promiscuity, transcriptional and translational errors, may also accelerate this process, possibly via "plasticity-first" mechanisms. Finally, we highlight open questions in the field of protein evolution, with respect to the emergence of more sophisticated protein systems such as protein complexes, pathways, and the emergence of pre-LUCA enzymes.

Dominance shifts increase the likelihood of soft selective sweeps

Genetic models of adaptation to a new environment have typically assumed that the alleles involved maintain a constant fitness dominance across the old and new environments. However, theories of dominance suggest that this should often not be the case. Instead, the alleles involved should frequently shift from recessive deleterious in the old environment to dominant beneficial in the new environment. Here, we study the consequences of these expected dominance shifts for the genetics of adaptation to a new environment. We find that dominance shifts increase the likelihood that adaptation occurs from standing variation, and that multiple alleles from the standing variation are involved (a soft selective sweep). Furthermore, we find that expected dominance shifts increase the haplotypic diversity of selective sweeps, rendering soft sweeps more detectable in small genomic samples. In cases where an environmental change threatens the viability of the population, we show that expected dominance shifts of newly beneficial alleles increase the likelihood of evolutionary rescue and the number of alleles involved. Finally, we apply our results to a well-studied case of adaptation to a new environment: the evolution of pesticide resistance at the Ace locus in Drosophila melanogaster. We show that, under reasonable demographic assumptions, the expected dominance shift of resistant alleles causes soft sweeps to be the most frequent outcome in this case, with the primary source of these soft sweeps being the standing variation at the onset of pesticide use, rather than recurrent mutation thereafter.

Geographical distribution and origin of acetylcholinesterase mutations conferring acaricide resistance in Tetranychus urticae populations from Turkey

Two-spotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae), is a cosmopolitan pest species that can feed on more than 1000 host plant species. Historically, organophosphate (OP) and carbamate insecticides have been used to control this extremely polyphagous pest. However, its ability to develop acaricide resistance rapidly has led to failure in control. Mutations in acetylcholinesterase gene (ace), the target-site of OP and carbamate insecticides, have been reported to be one of the major mechanisms underlying this developing resistance. In this study, mutations previously associated with resistance (G119S, A201S, T280A, G328A, F331W/Y) in ace have been screened in 37 T. urticae populations collected across Turkey. All mutations were found in various populations, except G119S. Almost all populations had F331W/Y mutation (being fixed in 32 populations), whereas only two populations harboured A201S mutation, but not fixed. On the other hand, more than half of the populations contained T280A and G328A mutations. In addition, the presence of same haplotypes in populations originating from distinct geographic locations and a wide variety of ace haplotypes might indicate multiple origins of F331W and F331Y mutations; however, this needs further investigation. The results of area-wide screening showed that ace mutations are widely distributed among T. urticae populations. Therefore, the use of this group of insecticides should be limited or only rotational use might be regarded as a resistance management tool due to its different mode of action from other main acaricide groups in T. urticae control across Turkey.

Why are Drosophila larvae more sensitive to avermectin than adults?

The insects have different physiological and morphological characteristics in various developmental stages. The difference in the characteristics may be related to the different sensitivity of insects to insecticides. In avermectin resistant strain screening assay, we found that the Drosophila larvae displayed a higher sensitivity to the insecticidal effect of avermectin, compared with adults. In this study, we found that the Drosophila larvae have relatively thicker chitin layer, faster avermectin metabolism and lower P-glycoprotein (P-gp) level, when compared with the adults. Besides, the expression levels of the molecular targets of avermectin, glutamate-gated chloride channel and γ-aminobutyric acid (GABA)-gated chloride channel, are lower in the larval stage than the adult. These results suggested that lower P-gp level in the body especially in brain may be the major reason for the higher sensitivity of Drosophila larvae to the insecticide. In summary, these results shed new light on the concept that different developmental stages of insects display different sensitivity to the same insecticide, which also provided a physiological explanation of the relevant mechanism of the difference of sensitivity of insect at its larval and adult stages to insecticide.

A Population Genomic Assessment of Three Decades of Evolution in a Natural Drosophila Population

Population genetics seeks to illuminate the forces shaping genetic variation, often based on a single snapshot of genomic variation. However, utilizing multiple sampling times to study changes in allele frequencies can help clarify the relative roles of neutral and non-neutral forces on short time scales. This study compares whole-genome sequence variation of recently collected natural population samples of Drosophila melanogaster against a collection made approximately 35 years prior from the same locality—encompassing roughly 500 generations of evolution. The allele frequency changes between these time points would suggest a relatively small local effective population size on the order of 10,000, significantly smaller than the global effective population size of the species. Some loci display stronger allele frequency changes than would be expected anywhere in the genome under neutrality—most notably the tandem paralogs Cyp6a17 and Cyp6a23, which are impacted by structural variation associated with resistance to pyrethroid insecticides. We find a genome-wide excess of outliers for high genetic differentiation between old and new samples, but a larger number of adaptation targets may have affected SNP-level differentiation versus window differentiation. We also find evidence for strengthening latitudinal allele frequency clines: northern-associated alleles have increased in frequency by an average of nearly 2.5% at SNPs previously identified as clinal outliers, but no such pattern is observed at random SNPs. This project underscores the scientific potential of using multiple sampling time points to investigate how evolution operates in natural populations, by quantifying how genetic variation has changed over ecologically relevant timescales.

Biochemical evaluation and molecular docking assessment of Cymbopogon citratus as a natural source of acetylcholine esterase (AChE)- targeting insecticides

Acetylcholinesterase (AChE) has been an effective target for insecticide development which is a very important aspect of the global fight against insect-borne diseases. The drastic reduction in the sensitivity of insects to AChE-targeting insecticides like organophosphates and carbamates have increased the need for insecticides of natural origin. In this study, we used Drosophila melanogaster as a model to investigate the insecticidal and AChE inhibitory potentials of Cymbopogon citratus and its bioactive compounds. Flies were exposed to 100 and 200 mg/mL C. citratus leaf extract for a 3-h survival assay followed by 45 min exposure for negative geotaxis and biochemical assays. Molecular docking analysis of 45 bioactive compounds of the plant was conducted against Drosophila melanogaster AChE (DmAChE). Exposure to C. citratus significantly reduced the survival rate of flies throughout the exposure period and this was accompanied by a significant decrease in percentage negative geotaxis, AChE activity, catalase activity, total thiol level and a significant increase in glutathione-S-transferase (GST) activity. The bioactive compounds of C. citratus showed varying levels of binding affinities for the enzyme. (+)-Cymbodiacetal scored highest (−9.407 kcal/mol) followed by proximadiol (−8.253 kcal/mol), geranylacetone (−8.177 kcal/mol), and rutin (−8.148 kcal/mol). The four compounds occupied the same binding pocket and interacted with important active site amino acid residues as the co-crystallized ligand (1qon). These compounds could be responsible for the insecticidal and AChE inhibitory potentials of C. citratus and they could be further explored in the development of AChE-targeting insecticides.

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Cymbopogon citratus reduced the AChE activity, catalase activity, total thiol level in Drosophilia melanogaster.

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The bioactive compounds of Cymbopogon citratus displayed considerable binding affinities for Drosophila melanogaster AChE and the four top-scoring compounds are (+)-Cymbodiacetal, proximadiol, geranylacetone, and rutin.

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(+)-Cymbodiacetal showed the highest binding affinity to AChE (DmAChE).

Common substitution mutation F348Y of acetylcholinesterase gene contributes to organophosphate and carbamate resistance in Cimex lectularius and C. hemipterus

Bed bug control highly depends on insecticides with a limited number of modes of action, especially since the global prevalence of pyrethroid resistance. De facto insecticide options against bed bugs in Japan are acetylcholinesterase inhibitors (AChEis) that consist of organophosphates and carbamates. However, the status of AChEi resistance and the mechanisms involved have not been ascertained. An amino acid substitution mutation, F348Y (or F331Y in standard numbering), occurring at an acyl-binding site of the paralogous AChE gene (p-Ace), was identified among AChEi-resistant colonies of both common and tropical bed bugs (Cimex lectularius and C. hemipterus, respectively). This mutation was genetically associated with propoxur and fenitrothion resistance in F348Y-segregating colonies of C. hemipterus. Inhibition of heterologously expressed C. lectularius p-Ace with insecticides revealed that the sensitivities of F348Y-carrying AChE decreased by orders of 10- to more than 100-fold for diazoxon, carbaryl, fenitroxon, paraoxon, chlorpyrifos-methyl, malaoxon, azamethiphos, methyl-paraoxon, and propoxur. In contrast, the mutant AChE showed a slightly decreased degree of sensitivity for dichlorvos and almost unchanged sensitivity for metoxadiazone. Further studies are needed to ascertain whether the practical efficacies of dichlorvos and metoxadiazone are ensured against F348Y-carrying bed bugs and whether other resistance mechanisms are involved.

Amplicon sequencing detects mutations associated with pyrethroid resistance in Bemisia tabaci (Hemiptera: Aleyrodidae)

BACKGROUND

Bemisia tabaci (Gennadius) is a major damaging agricultural pest that exhibits high resistance to pyrethroid insecticides. L925I (TTA to ATA) and T929V (ACT to GTT) mutations in the para-type voltage-gated sodium channel (VGSC) are associated with resistance of B. tabaci to pyrethroids. Amplicon sequencing is a reliable and highly efficient method to detect the frequency of mutations linked with insecticide resistance.

RESULTS

Similar frequencies of L925I and T929V mutations were obtained by amplicon sequencing and Sanger sequencing (L925I: 0.3548 vs 0.3619; T929V: 0.6140 vs 0.6381) with overlap of 95% confidence interval in the SX population of B. tabaci. In five populations of B. tabaci from China, the maximum and minimum frequencies of the two mutations were found in the LN (L925I: 0.1126; T929V: 0.8834) and JS (L925I: 0.8776; T929V: 0.1166) populations by amplicon sequencing. However, there was no significant difference in frequencies between the L925I and T929V mutations. The sum frequency of L925I and T929V exceeded 0.9688 in all populations. In addition, a combining mutation, L925 + T929V (L925I and T929V located in same allele), was found in five populations by amplicon sequencing even though its highest frequency was only 0.0157.

CONCLUSION

We established an efficient approach for detecting frequency of mutation by amplicon sequencing. The frequencies of L925I and T929V in VGSC associated with pyrethroid resistance were detected in this study, which could provide foundational data for resistance management of B. tabaci. © 2021 Society of Chemical Industry.

Inferring Adaptive Introgression Using Hidden Markov Models

Adaptive introgression-the flow of adaptive genetic variation between species or populations-has attracted significant interest in recent years and it has been implicated in a number of cases of adaptation, from pesticide resistance and immunity, to local adaptation. Despite this, methods for identification of adaptive introgression from population genomic data are lacking. Here, we present Ancestry_HMM-S, a hidden Markov model-based method for identifying genes undergoing adaptive introgression and quantifying the strength of selection acting on them. Through extensive validation, we show that this method performs well on moderately sized data sets for realistic population and selection parameters. We apply Ancestry_HMM-S to a data set of an admixed Drosophila melanogaster population from South Africa and we identify 17 loci which show signatures of adaptive introgression, four of which have previously been shown to confer resistance to insecticides. Ancestry_HMM-S provides a powerful method for inferring adaptive introgression in data sets that are typically collected when studying admixed populations. This method will enable powerful insights into the genetic consequences of admixture across diverse populations. Ancestry_HMM-S can be downloaded from https://github.com/jesvedberg/Ancestry_HMM-S/.

A Likelihood Approach for Uncovering Selective Sweep Signatures from Haplotype Data

Selective sweeps are frequent and varied signatures in the genomes of natural populations, and detecting them is consequently important in understanding mechanisms of adaptation by natural selection. Following a selective sweep, haplotypic diversity surrounding the site under selection decreases, and this deviation from the background pattern of variation can be applied to identify sweeps. Multiple methods exist to locate selective sweeps in the genome from haplotype data, but none leverages the power of a model-based approach to make their inference. Here, we propose a likelihood ratio test statistic T to probe whole-genome polymorphism data sets for selective sweep signatures. Our framework uses a simple but powerful model of haplotype frequency spectrum distortion to find sweeps and additionally make an inference on the number of presently sweeping haplotypes in a population. We found that the T statistic is suitable for detecting both hard and soft sweeps across a variety of demographic models, selection strengths, and ages of the beneficial allele. Accordingly, we applied the T statistic to variant calls from European and sub-Saharan African human populations, yielding primarily literature-supported candidates, including LCT, RSPH3, and ZNF211 in CEU, SYT1, RGS18, and NNT in YRI, and HLA genes in both populations. We also searched for sweep signatures in Drosophila melanogaster, finding expected candidates at Ace, Uhg1, and Pimet. Finally, we provide open-source software to compute the T statistic and the inferred number of presently sweeping haplotypes from whole-genome data.

Benzo[a]pyrene and Benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide induced locomotor and reproductive senescence and altered biochemical parameters of oxidative damage in Canton-S Drosophila melanogaster

Benzo[a]pyrene (B[a]P) is a polycyclic aromatic hydrocarbon (PAH) commonly found in cigarette smoke, automobile exhaust fumes, grilled meat, and smoked food among others. Exposure to B[a]P is associated with a range of toxic effects including developmental, neurological, oxidative, inflammatory, mutagenic, carcinogenic and mortal. Efficient and more affordable experimental models like Drosophila melanogaster could provide more insight into the mechanism of PAH toxicity and help develop new strategies for prevention, diagnosis and treatment of PAH-related conditions. In this study, we examined the induction of some biochemical changes along with mortality and functional senescence by B[a]P and its metabolite, benzo[a]pyrene- 7,8-dihydrodiol-910-epoxide (BPDE) in the Canton-S strain of Drosophila melanogaster, with the aim to establish an alternative assay medium for B[a]P toxicity in flies. Flies were exposed to 2-200 μM of B[a]P and 1-10 μM of BPDE through diet for a seven-day survival assay followed by a four-day treatment to determine the effects of the compounds on negative geotaxis, fecundity and some biochemical parameters of oxidative damage. BPDE significantly reduced the survival rate of flies along the 7 days of exposure whereas B[a]P did not cause any significant change in the survival rate of flies. B[a]P and BPDE significantly reduced the climbing ability of flies after 4 days of exposure. Rate of emergence of flies significantly reduced at 10-200 μM of B[a]P and 5-10 μM of BPDE. Both compounds caused various levels of alterations in the values of reduced glutathione (GSH), total thiol (T-SH), glutathione-S-transferase (GST), catalase (CAT), hydrogen peroxide (H2O2), nitric oxide (NO) and acetylcholinesterase (AChE) of the flies. The compounds also exhibited high binding affinities and molecular interactions with the active site amino acid residues of Drosophila GST and the inhibitor binding site of Drosophila AChE in an in silico molecular docking analysis, with BPDE forming stable hydrogen bonds with AChE. Hence, the Canton-S strain of Drosophila melanogaster could offer a simple and affordable assay medium to study B[a]P toxicity.

Temperature, rainfall and wind variables underlie environmental adaptation in natural populations of Drosophila melanogaster

While several studies in a diverse set of species have shed light on the genes underlying adaptation, our knowledge on the selective pressures that explain the observed patterns lags behind. Drosophila melanogaster is a valuable organism to study environmental adaptation because this species originated in Southern Africa and has recently expanded worldwide, and also because it has a functionally well-annotated genome. In this study, we aimed to decipher which environmental variables are relevant for adaptation of D. melanogaster natural populations in Europe and North America. We analysed 36 whole-genome pool-seq samples of D. melanogaster natural populations collected in 20 European and 11 North American locations. We used the BayPass software to identify single nucleotide polymorphisms (SNPs) and transposable elements (TEs) showing signature of adaptive differentiation across populations, as well as significant associations with 59 environmental variables related to temperature, rainfall, evaporation, solar radiation, wind, daylight hours, and soil type. We found that in addition to temperature and rainfall, wind related variables are also relevant for D. melanogaster environmental adaptation. Interestingly, 23%-51% of the genes that showed significant associations with environmental variables were not found overly differentiated across populations. In addition to SNPs, we also identified 10 reference transposable element insertions associated with environmental variables. Our results showed that genome-environment association analysis can identify adaptive genetic variants that are undetected by population differentiation analysis while also allowing the identification of candidate environmental drivers of adaptation.

Differences in larval pesticide tolerance and esterase activity across honey bee (Apis mellifera) stocks

Honey bee populations in North America are an amalgamation of diverse progenitor ecotypes experiencing varying levels of artificial selection. Genetic differences between populations can result in variable susceptibility towards environmental stressors, and here we compared pesticide tolerances across breeding stocks using a mixture of seven pesticides frequently found in colonies providing pollination services. We administered the pesticide mixture chronically to in vitro reared larvae at four concentrations of increasing Hazard Quotient (HQ, or cumulative toxicity) and measured mortality during larval development. We found that different stocks had significantly different tolerances to our pesticide mixture as indicated by their median lethal toxicity (HQ₅₀). The intensively selected Pol-Line stock exhibited the greatest pesticide sensitivity while Old World (progenitor) and putatively feral stocks were the most pesticide-tolerant. Furthermore, we found that activity of the detoxification enzyme esterase was positively correlated with pesticide tolerance when measured using two different substrate standards, and confirmed that larvae from the Pol-Line stock had generally lower esterase activity. Consistent with an increased pesticide tolerance, the Old World and putatively feral stocks had higher esterase activities. However, esterases and other detoxification enzymes (CYP450s and GSTs) were found in similar abundances across stocks, suggesting that the differences in enzyme activity we observed might arise from stock-specific single nucleotide polymorphisms or post-translational modifications causing qualitative variation in enzyme activity. These results suggest that selective breeding may inadvertently increase honey bees' sensitivity to pesticides, whereas unselected, putatively feral and Old World stocks have larvae that are more tolerant.

The Neurotransmitters Involved in Drosophila Alcohol-Induced Behaviors

Alcohol is a widely used and abused substance with numerous negative consequences for human health and safety. Historically, alcohol's widespread, non-specific neurobiological effects have made it a challenge to study in humans. Therefore, model organisms are a critical tool for unraveling the mechanisms of alcohol action and subsequent effects on behavior. Drosophila melanogaster is genetically tractable and displays a vast behavioral repertoire, making it a particularly good candidate for examining the neurobiology of alcohol responses. In addition to being experimentally amenable, Drosophila have high face and mechanistic validity: their alcohol-related behaviors are remarkably consistent with humans and other mammalian species, and they share numerous conserved neurotransmitters and signaling pathways. Flies have a long history in alcohol research, which has been enhanced in recent years by the development of tools that allow for manipulating individual Drosophila neurotransmitters. Through advancements such as the GAL4/UAS system and CRISPR/Cas9 mutagenesis, investigation of specific neurotransmitters in small subsets of neurons has become ever more achievable. In this review, we describe recent progress in understanding the contribution of seven neurotransmitters to fly behavior, focusing on their roles in alcohol response: dopamine, octopamine, tyramine, serotonin, glutamate, GABA, and acetylcholine. We chose these small-molecule neurotransmitters due to their conservation in mammals and their importance for behavior. While neurotransmitters like dopamine and octopamine have received significant research emphasis regarding their contributions to behavior, others, like glutamate, GABA, and acetylcholine, remain relatively unexplored. Here, we summarize recent genetic and behavioral findings concerning these seven neurotransmitters and their roles in the behavioral response to alcohol, highlighting the fitness of the fly as a model for human alcohol use.

Fitness effects for Ace insecticide resistance mutations are determined by ambient temperature

BACKGROUND

Insect pest control programs often use periods of insecticide treatment with intermittent breaks, to prevent fixing of mutations conferring insecticide resistance. Such mutations are typically costly in an insecticide-free environment, and their frequency is determined by the balance between insecticide treatment and cost of resistance. Ace, a key gene in neuronal signaling, is a prominent target of many insecticides and across several species, three amino acid replacements (I161V, G265A, and F330Y) provide resistance against several insecticides. Because temperature disturbs neuronal signaling homeostasis, we reasoned that the cost of insecticide resistance could be modulated by ambient temperature.

RESULTS

Experimental evolution of a natural Drosophila simulans population at hot and cold temperature regimes uncovered a surprisingly strong effect of ambient temperature. In the cold temperature regime, the resistance mutations were strongly counter selected (s = - 0.055), but in a hot environment, the fitness costs of resistance mutations were reduced by almost 50% (s = - 0.031). We attribute this unexpected observation to the advantage of the reduced enzymatic activity of resistance mutations in hot environments.

CONCLUSION

We show that fitness costs of insecticide resistance genes are temperature-dependent and suggest that the duration of insecticide-free periods need to be adjusted for different climatic regions to reflect these costs. We suggest that such environment-dependent fitness effects may be more common than previously assumed and pose a major challenge for modeling climate change.

Transcriptome Sequencing of the Striped Cucumber Beetle, Acalymma vittatum (F.), Reveals Numerous Sex-Specific Transcripts and Xenobiotic Detoxification Genes

Acalymma vittatum (F.), the striped cucumber beetle, is an important pest of cucurbit crops in the contintental United States, damaging plants through both direct feeding and vectoring of a bacterial wilt pathogen. Besides providing basic biological knowledge, biosequence data for A. vittatum would be useful towards the development of molecular biopesticides to complement existing population control methods. However, no such datasets currently exist. In this study, three biological replicates apiece of male and female adult insects were sequenced and assembled into a set of 630,139 transcripts (of which 232,899 exhibited hits to one or more sequences in NCBI NR). Quantitative analyses identified 2898 genes differentially expressed across the male–female divide, and qualitative analyses characterized the insect’s resistome, comprising the glutathione S-transferase, carboxylesterase, and cytochrome P450 monooxygenase families of xenobiotic detoxification genes. In summary, these data provide useful insights into genes associated with sex differentiation and this beetle’s innate genetic capacity to develop resistance to synthetic pesticides; furthermore, these genes may serve as useful targets for potential use in molecular-based biocontrol technologies.

Developmental changes in larvae of the oriental latrine fly, Chrysomya megacephala, exposed to deltamethrin

The Chrysomya megacephala (Fabricius, 1794) (Diptera: Calliphoridae) has a worldwide distribution and is considered of medical and veterinary importance. Its synanthropic behavior combined with the visitation of decaying organic matter allows it to mechanically transmit pathogens to human and animals. Pyrethroids are widely used pesticides, effective in low doses against a broad spectrum of insects. Our objective was to evaluate the action of K-Othrine® on the post-embryonic development of C. megacephala. First instar larvae were exposed to different concentrations of K-Othrine® (3.75 × 10^-5 g a.i/mL (low), 7.5 × 10^-5 g a.i/mL (intermediate low), 1.125 × 10^-4 g a.i/mL (intermediate), 1.5 × 10^-4 g a.i/mL (intermediate high), and 2.5 × 10^-4 g a.i/mL (high)) mixed into artificial diets and a control with no pesticide. We measured weight, time of development, sex ratio, larval and pupal mortality, and esterase patterns. The mean weight values at intermediate low and intermediate concentrations were significantly lower compared with the control; additionally, the development time was delayed compared with the control. The larval and pupal mortality differed among the treatments. The larvae had six esterase regions, which altered its relative activity at 48 h and 72 h after insecticide ingestion. Further studies must investigate the effects of different insecticides on the post-embryonic development of C. megacephala.

Voltage-gated chloride channel blocker DIDS as an acaricide for Varroa mites

The Varroa mite is a primary driver behind periodical losses of honey bee colonies. These mites require honey bees for food and reproduction and, in turn, elicit physiological deficiencies and diseases that compromise colony health. Current acaricides for Varroa mite control, such as Apistan® (the pyrethroid tau-fluvalinate), CheckMite⁺® (the organophosphate coumaphos), and Apivar® (the formamidine amitraz) target the nervous system, can have adverse health effects on honey bees, and have limited effectiveness due to reported resistance issues. New target sites are needed to circumvent these obstacles in Varroa mite management, and voltage-gated chloride channels (VGCCs) are promising candidates due to their important role in the maintenance of nerve and muscle excitability in arthropod pests. Toxicological analysis of Varroa mites sensitive to tau-fluvalinate and coumaphos and Varroa mites with reduced sensitivity to these acaricides showed a significant increase in metabolic detoxification enzyme activities for the latter. Acetylcholinesterase activity in the Varroa mites exhibiting reduced mortality to coumaphos was significantly less sensitive to coumaphos-oxon compared to coumaphos-sensitive Varroa mites, which suggests target-site insensitivity to the acaricide. Voltage-gated chloride channel blocker DIDS had significantly greater field efficacy compared to Apistan® and CheckMite⁺® against Varroa mites from honey bee hives where tau-fluvalinate and coumaphos were observed to be ineffective, respectively. These data suggest that DIDS, and potentially other stilbene chemistries, might serve as candidates for continued field efficacy testing of alternative acaricides in apiaries where Apistan®- and CheckMite⁺® efficacy has been. reduced or lost for Varroa mites.

Drosophila melanogaster as a powerful tool for studying insect toxicology

Insecticides are valuable and widely used tools for the control of pest insects. Despite the use of synthetic insecticides for >50 years, we continue to have a limited understanding of the genes that influence the key steps of the poisoning process. Major barriers for improving our understanding of insecticide toxicity have included a narrow range of tools and/or a large number of candidate genes that could be involved in the poisoning process. Herein, we discuss the numerous tools and resources available in Drosophila melanogaster that could be brought to bear to improve our understanding of the processes determining insecticide toxicity. These include unbiased approaches such as forward genetic screens, population genetic methods and candidate gene approaches. Examples are provided to showcase how D. melanogaster has been successfully used for insecticide toxicology studies in the past, and ideas for future studies using this valuable insect are discussed.

A Re-Evaluation of Olive Fruit Fly Organophosphate-Resistant Ace Alleles in Iberia, and Field-Testing Population Effects after in-Practice Dimethoate Use

The management of the olive fruit fly (Bactrocera oleae) is traditionally based upon the use of organophosphate insecticides, mainly dimethoate. In this evolutionary arms race between man and pest, the flies have adapted a pesticide resistance, implying two point-mutations of the Ace gene -I214V and G488S- and a 9bp deletion -Δ3Q. We revisited 11 Iberian locations to evaluate this adaptation of organophosphate (OP)-resistant alleles through amplicon sequencing. Screening for populations where the wild type is prevalent allows an identification of hotspots for targeted mitigation measures; we have hence refined the scale to the region with the lowest OP-resistant alleles frequency 71 locations were sampled and individuals checked using a fast and low-cost allele-specific-primer polymerase chain reaction (ASP-PCR) method]. An increase in Ace gene point-mutations was observed, and the Δ3Q mutation remains undetected. The lowest frequencies of the OP-resistant alleles remain in the west, underlining the hypothesis of an introduction of resistance from eastern Mediterranean areas. A field test was performed by sampling the fly population before and after in-practice dimethoate application. A clear reduction in olive fruit fly numbers was observed, with no relevant changes in the genotypic frequencies of the resistance alleles. The findings are discussed in frame of the type and intensity of the selection pressure that has led to the adaptation to resistance and its consequences from the producer perspective.

Insecticide Resistance in Drosophila melanogaster (Diptera: Drosophilidae) is Associated with Field Control Failure of Sour Rot Disease in a New York Vineyard

Sour rot is a complex disease of grapes caused by an interaction of yeast, acetic acid bacteria, and Drosophila spp. Application of insecticides (most commonly zeta-cypermethrin) targeting Drosophila has previously provided substantial control of sour rot in wine grapes of New York vineyards. In harvest season of 2018, a control failure of sour rot and high populations of Drosophila, mostly Drosophila melanogaster, were observed in a vineyard in the Finger Lakes region, NY, despite repeated applications of zeta-cypermethrin (Mustang Maxx). To determine if resistance was responsible for the control failure, we quantified the toxicity of zeta-cypermethrin and the four other insecticides registered for Drosophila control in NY vineyards. Diagnostic concentrations (susceptible strain LC95, 4 × LC95, and 16 × LC95) were used to evaluate percentage survival of the field flies relative to the susceptible Canton-S strain. Resistance to zeta-cypermethrin, acetamiprid, and malathion, but not to spinosad and spinetoram, was observed in the field-collected flies. This study provides evidence that insecticide resistance of Drosophila is associated with control failure of sour rot in some vineyards, and directly influencing grape production. The implications of these results to insecticide resistance monitoring and management are discussed.

In Silico Study of the Resistance to Organophosphorus Pesticides Associated with Point Mutations in Acetylcholinesterase of Lepidoptera: B. mandarina, B. mori, C. auricilius, C. suppressalis, C. pomonella, H. armígera, P. xylostella, S. frugiperda, and S. litura

An in silico analysis of the interaction between the complex-ligands of nine acetylcholinesterase (AChE) structures of Lepidopteran organisms and 43 organophosphorus (OPs) pesticides with previous resistance reports was carried out. To predict the potential resistance by structural modifications in Lepidoptera insects, due to proposed point mutations in AChE, a broad analysis was performed using computational tools, such as homology modeling and molecular docking. Two relevant findings were revealed: (1) Docking results give a configuration of the most probable spatial orientation of two interacting molecules (AChE enzyme and OP pesticide) and (2) a predicted ΔGb. The mutations evaluated in the form 1 acetylcholinesterase (AChE-1) and form 2 acetylcholinesterase (AChE-2) structures of enzymes do not affect in any way (there is no regularity of change or significant deviations) the values of the binding energy (ΔGb) recorded in the AChE-OPs complexes. However, the mutations analyzed in AChE are associated with a structural modification that causes an inadequate interaction to complete the phosphorylation of the enzyme.

Population genomics of rapid evolution in natural populations: polygenic selection in response to power station thermal effluents

BACKGROUND

Examples of rapid evolution are common in nature but difficult to account for with the standard population genetic model of adaptation. Instead, selection from the standing genetic variation permits rapid adaptation via soft sweeps or polygenic adaptation. Empirical evidence of this process in nature is currently limited but accumulating.

RESULTS

We provide genome-wide analyses of rapid evolution in Fundulus heteroclitus populations subjected to recently elevated temperatures due to coastal power station thermal effluents using 5449 SNPs across two effluent-affected and four reference populations. Bayesian and multivariate analyses of population genomic structure reveal a substantial portion of genetic variation that is most parsimoniously explained by selection at the site of thermal effluents. An FST outlier approach in conjunction with additional conservative requirements identify significant allele frequency differentiation that exceeds neutral expectations among exposed and closely related reference populations. Genomic variation patterns near these candidate loci reveal that individuals living near thermal effluents have rapidly evolved from the standing genetic variation through small allele frequency changes at many loci in a pattern consistent with polygenic selection on the standing genetic variation.

CONCLUSIONS

While the ultimate trajectory of selection in these populations is unknown and we survey only a minority of genomic loci, our findings suggest that polygenic models of adaptation may play important roles in large, natural populations experiencing recent selection due to environmental changes that cause broad physiological impacts.

What can genetic association panels tell us about evolutionary processes in insects?

If we are to fully comprehend the evolution of insect diversity at a genomic level we need to understand how natural selection can alter genetically encoded characters within populations. Genetic association panels have the potential to be standard bearers in this endeavour. They enable the mapping of phenotypes to genotypes at unprecedented resolution while simultaneously providing population genomic samples that can be interrogated for the tell-tale signs of selection. Analyses of these panels promise to elucidate the entanglement of gene ontologies, pathways, developmental processes and evolutionary constraints, and inform how these are shaped by adaptation.

Protein-protein interaction network analysis of insecticide resistance molecular mechanism in Drosophila melanogaster

The problem of resistance has not been solved fundamentally at present, because the development speed of new insecticides can not keep pace with the development speed of resistance, and the lack of understanding of molecular mechanism of resistance. Here we collected seed genes and their interacting proteins involved in insecticide resistance molecular mechanism in Drosophila melanogaster by literature mining and the String database. We identified a total of 528 proteins and 13514 protein-protein interactions. The protein interaction network was constructed by String and Pajek, and we analyzed the topological properties, such as degree centrality and eigenvector centrality. Proteasome complexes and drug metabolism-cytochrome P450 were an enrichment by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. This is the first time to explore the insecticide resistance molecular mechanism of D. melanogaster by the methods and tools of network biology, it can provide the bioinformatic foundation for further understanding the mechanisms of insecticide resistance.

Structural Variants and Selective Sweep Foci Contribute to Insecticide Resistance in the Drosophila Genetic Reference Panel

Patterns of nucleotide polymorphism within populations of Drosophila melanogaster suggest that insecticides have been the selective agents driving the strongest recent bouts of positive selection. However, there is a need to explicitly link selective sweeps to the particular insecticide phenotypes that could plausibly account for the drastic selective responses that are observed in these non-target insects. Here, we screen the Drosophila Genetic Reference Panel with two common insecticides; malathion (an organophosphate) and permethrin (a pyrethroid). Genome-wide association studies map survival on malathion to two of the largest sweeps in the D. melanogaster genome; Ace and Cyp6g1. Malathion survivorship also correlates with lines which have high levels of Cyp12d1, Jheh1 and Jheh2 transcript abundance. Permethrin phenotypes map to the largest cluster of P450 genes in the Drosophila genome, however in contrast to a selective sweep driven by insecticide use, the derived allele seems to be associated with susceptibility. These results underscore previous findings that highlight the importance of structural variation to insecticide phenotypes: Cyp6g1 exhibits copy number variation and transposable element insertions, Cyp12d1 is tandemly duplicated, the Jheh loci are associated with a Bari1 transposable element insertion, and a Cyp6a17 deletion is associated with susceptibility.

Signatures of Insecticide Selection in the Genome of Drosophila melanogaster

Resistance to insecticides has evolved in multiple insect species, leading to increased application rates and even control failures. Understanding the genetic basis of insecticide resistance is fundamental for mitigating its impact on crop production and disease control. We performed a GWAS approach with the Drosophila Genetic Reference Panel (DGRP) to identify the mutations involved in resistance to two widely used classes of insecticides: organophosphates (OPs, parathion) and pyrethroids (deltamethrin). Most variation in parathion resistance was associated with mutations in the target gene Ace, while most variation in deltamethrin resistance was associated with mutations in Cyp6a23, a gene encoding a detoxification enzyme never previously associated with resistance. A "nested GWAS" further revealed the contribution of other loci: Dscam1 and trpl were implicated in resistance to parathion, but only in lines lacking WolbachiaCyp6a17, the paralogous gene of Cyp6a23, and CG7627, an ATP-binding cassette transporter, were implicated in deltamethrin resistance. We observed signatures of recent selective sweeps at all of these resistance loci and confirmed that the soft sweep at Ace is indeed driven by the identified resistance mutations. Analysis of allele frequencies in additional population samples revealed that most resistance mutations are segregating across the globe, but that frequencies can vary substantially among populations. Altogether, our data reveal that the widely used OP and pyrethroid insecticides imposed a strong selection pressure on natural insect populations. However, it remains unclear why, in Drosophila, resistance evolved due to changes in the target site for OPs, but due to a detoxification enzyme for pyrethroids.

Genome-wide patterns of local adaptation in Western European Drosophila melanogaster natural populations

Signatures of spatially varying selection have been investigated both at the genomic and transcriptomic level in several organisms. In Drosophila melanogaster, the majority of these studies have analyzed North American and Australian populations, leading to the identification of several loci and traits under selection. However, several studies based mainly in North American populations showed evidence of admixture that likely contributed to the observed population differentiation patterns. Thus, disentangling demography from selection might be challenging when analyzing these populations. European populations could help identify loci under spatially varying selection provided that no recent admixture from African populations would have occurred. In this work, we individually sequence the genome of 42 European strains collected in populations from contrasting environments: Stockholm (Sweden) and Castellana Grotte (Southern Italy). We found low levels of population structure and no evidence of recent African admixture in these two populations. We thus look for patterns of spatially varying selection affecting individual genes and gene sets. Besides single nucleotide polymorphisms, we also investigated the role of transposable elements in local adaptation. We concluded that European populations are a good dataset to identify candidate loci under spatially varying selection. The analysis of the two populations sequenced in this work in the context of all the available D. melanogaster data allowed us to pinpoint genes and biological processes likely to be relevant for local adaptation. Identifying and analyzing populations with low levels of population structure and admixture should help to disentangle selective from non-selective forces underlying patterns of population differentiation in other species as well.

A Large Panel of Drosophila simulans Reveals an Abundance of Common Variants

The rapidly expanding availability of large NGS data sets provides an opportunity to investigate population genetics at an unprecedented scale. Drosophila simulans is the sister species of the model organism Drosophila melanogaster, and is often presumed to share similar demographic history. However, previous population genetic and ecological work suggests very different signatures of selection and demography. Here, we sequence a new panel of 170 inbred genotypes of a North American population of D. simulans, a valuable complement to the DGRP and other D. melanogaster panels. We find some unexpected signatures of demography, in the form of excess intermediate frequency polymorphisms. Simulations suggest that this is possibly due to a recent population contraction and selection. We examine the outliers in the D. simulans genome determined by a haplotype test to attempt to parse the contribution of demography and selection to the patterns observed in this population. Untangling the relative contribution of demography and selection to genomic patterns of variation is challenging, however, it is clear that although D. melanogaster was thought to share demographic history with D. simulans different forces are at work in shaping genomic variation in this population of D. simulans.

Genetic aberrations of the K-ras proto-oncogene in bladder cancer in relation to pesticide exposure

In Egypt, bladder cancer is one of the most popular cancers, accounting for 31% of all cancer cases. It ranks first in males about 16.2% of male cancer. The incidence in rural areas among males is near 32 per 100,000. The exact etiology of bladder cancer is still unknown; K-ras gene is known as a critical DNA target for chemical carcinogens such as pesticide. Some occupational hazard exposure is thought to be directly genotoxic, while others might enhance the mutagenicity and carcinogenicity of directly acting genotoxic agents. Analysis of the relationship between pesticide exposure and mutation in the K-ras gene in human bladder cancer. One hundred patients were diagnosed with bladder cancer and two hundred controls attended the outpatient clinic; after taking consent and filling a questionnaire for age, sex, occupation and pesticide exposure, surgically resected specimens were collected and the samples were used to determine the k-ras mutation. Blood samples were taken to analyze the level of acetylcholinesterase enzyme and level of P₅₃. The present study indicated that pesticide exposure may play a great role in malignant transformation of the bladder cells through mutation in the K-ras gene; there was a significant correlation between the acetylcholinesterase enzyme level and k-ras mutation (p < 0.001). The results revealed that the level of P₅₃ was significantly high in comparison with the control group (p < 0.001). These findings give an alarm to decrease the amount of pesticides used in our area; also, p₅₃ may be used as an indicator to bladder cancer.

Toxicity, Phytochemical Composition, and Enzyme Inhibitory Activities of Some Indigenous Weed Plant Extracts in Fruit Fly, Drosophila melanogaster

Drosophila melanogaster being used as model organism is considered as pest of homes, restaurants, and fruit markets. The damaged fruits are also reported to serve as a carrier for various diseases. The current study was designed to evaluate the toxicity of petroleum extract of some weed plants, namely, Euphorbia prostrata, Parthenium hysterophorus, Fumaria indica, Chenopodium murale, and Azadirachta indica, against D. melanogaster. Mortality at 10, 20, and 30% concentrations after 24 and 48 hours was found comparatively low. E. prostrata caused high mortality (51.64%) at 30% concentration and was found more toxic (LC₅₀ 27.76; P value 0.00) after 72 hours. A. indica showed high LC₅₀ value (P value 0.15) compared to other weed plants. The combination of E. prostrata and Bti showed highest mortality (100%; LC₅₀ 12.49; P value 0.00) after 72 hours. Similarly, the same combination caused maximum reduction in the activity of AChE, AcP, AkP, α-Carboxyl, and β-Carboxyl enzymes. Phytochemical analysis showed the presence of flavonoids, saponins, tannins, steroids, cardiac glycosides, alkaloids, anthraquinones, and terpenoids. FTIR analysis of E. prostrata showed the presence of phenolic compounds. It is suggested that further studies are needed in order to incorporate weed plant extracts in combination with Bti for the management of fruit flies.

Identification and characterization of ace1-type acetylcholinesterase in insecticide-resistant and -susceptible Propylaea japonica (Thunberg)

Characterization and gene cloning of acetylecholinesterase (AChE) in the insecticide-resistant (R) and -susceptible (S) insects have been reported in the past. However, the studies focused mostly on herbivorous pests, rather than predacious species, such as ladybird beetles. Using R and S Propylaea japonica (thunberg), a full-length cDNA sequence (2928 bp) of the ace1-type AChE gene was determined for the first time. The ace1 encoding a protein of 645 amino acids contained typical conserved motifs, such as FGESAG domains, catalytic triad, acyl pocket, oxyanino hole, choline binding site, peripheral anionic site, omega loop and conserved aromatic residues. R P. japonica displayed 50-times greater resistance to chlorpyrifos or mathamidophos with a significantly lower AChE sensitivity to paraoxon, malaoxon, chlorpyrifos or methamidophos than its S counterpart. Five amino acids in the ace1 of R P. japonica differed from those found in S P. japonica. One of them, F358S, located in the acyl-binding pocket, might play a crucial role in the resistance of the insect to organophosphates (OPs). Whereas, K493E and I538V, which were close to some of the conserved aromatic amino acids (i.e., H509, Y511, and W499) in the gorge, and G571R and T576A near C593 that formed the disulfide bonds with C471, might also involve in the change of insecticide resistance in P. japonica. AChE insensitivity and amino acid replacements, particularly F358S, might be the determining factors in the alteration of OPs-resistance in P. japonica.

Baseline susceptibility of spotted wing Drosophila (Drosophila suzukii) to four key insecticide classes

BACKGROUND

The invasive drosophilid pest, Drosophila suzukii Matsumura, is affecting berry production in most fruit-producing regions of the world. Chemical control is the dominant management approach, creating concern for insecticide resistance in this pest. We compared the insecticide susceptibility of D. suzukii populations collected from conventional, organic or insecticide-free blueberry sites.

RESULTS

The sensitivity of D. suzukii to malathion and spinetoram declined slightly across the 3 years of monitoring, whereas it was more consistent for methomyl and zeta-cypermethrin. The sensitivity of D. suzukii to all four insecticides (LC₅₀ and LC₉₀ values) did not differ significantly among the blueberry fields using different management practices.

CONCLUSIONS

The baseline sensitivity of D. suzukii has been characterized, allowing future comparisons if field failures of chemical control are reported. The concentration achieving high control indicates that effective levels of control can still be achieved with field rates of these four insecticides. However, declining susceptibility of some populations of D. suzukii to some key insecticides highlights the need for resistance monitoring. © 2017 Society of Chemical Industry.

Using Next-Generation Sequencing to Detect Differential Expression Genes in Bradysia odoriphaga after Exposure to Insecticides

Bradysia odoriphaga (Diptera: Sciaridae) is the most important pest of Chinese chive. Insecticides are used widely and frequently to control B. odoriphaga in China. However, the performance of the insecticides chlorpyrifos and clothianidin in controlling the Chinese chive maggot is quite different. Using next generation sequencing technology, different expression unigenes (DEUs) in B. odoriphaga were detected after treatment with chlorpyrifos and clothianidin for 6 and 48 h in comparison with control. The number of DEUs ranged between 703 and 1161 after insecticide treatment. In these DEUs, 370–863 unigenes can be classified into 41–46 categories of gene ontology (GO), and 354–658 DEUs can be mapped into 987–1623 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The expressions of DEUs related to insecticide-metabolism-related genes were analyzed. The cytochrome P450-like unigene group was the largest group in DEUs. Most glutathione S-transferase-like unigenes were down-regulated and most sodium channel-like unigenes were up-regulated after insecticide treatment. Finally, 14 insecticide-metabolism-related unigenes were chosen to confirm the relative expression in each treatment by quantitative Real Time Polymerase Chain Reaction (qRT-PCR). The results of qRT-PCR and RNA Sequencing (RNA-Seq) are fairly well-established. Our results demonstrate that a next-generation sequencing tool facilitates the identification of insecticide-metabolism-related genes and the illustration of the insecticide mechanisms of chlorpyrifos and clothianidin.

Insights into DDT Resistance from the Drosophila melanogaster Genetic Reference Panel

Insecticide resistance is considered a classic model of microevolution, where a strong selective agent is applied to a large natural population, resulting in a change in frequency of alleles that confer resistance. While many insecticide resistance variants have been characterized at the gene level, they are typically single genes of large effect identified in highly resistant pest species. In contrast, multiple variants have been implicated in DDT resistance in Drosophila melanogaster; however, only the Cyp6g1 locus has previously been shown to be relevant to field populations. Here we use genome-wide association studies (GWAS) to identify DDT-associated polygenes and use selective sweep analyses to assess their adaptive significance. We identify and verify two candidate DDT resistance loci. A largely uncharacterized gene, CG10737, has a function in muscles that ameliorates the effects of DDT, while a putative detoxifying P450, Cyp6w1, shows compelling evidence of positive selection.

Inheritance and stability of mevinphos-resistance in Plutella xylostella (L.), with special reference to mutations of acetylcholinesterase 1

Diamondback moth (Plutella xylostella L.) causes enormous damage on cruciferous vegetables and can rapidly develop resistance to all kinds of insecticides. To effectively manage the insecticide resistance of P. xylostella, an understanding of its inheritance and stability is essential. Here we investigated the phenotypic and genotypic basis of mevinphos resistance by crossing two genetically pure lines of P. xylostella, an SH_ggt wild-type strain and an SHM_TCN resistant strain carrying 892T/T, 971C/C, and 1156T/G (TCN) mutations of the acetylcholinesterase 1 gene (Pxace1). Similar median lethal concentrations and degrees of dominance in the reciprocal cross progeny, and no plateau on the log concentration-probit line of F1 backcross and self-cross progeny, suggest that the mevinphos-resistance in P. xylostella is inherited as an autosomal and incomplete dominant trait governed by more than one gene. In the absence of mevinphos exposure, the resistance ratio and Pxace1 mutation frequency declined concomitantly in the SHM_TCN strain. After 20-generation relaxation, the mevinphos resistance decreased from 52- to 6-fold and the Pxace1 mutation frequency of the TCN haplotype pair decreased from 100% to 0%. A good correlation was found between the resistance ratio and TCN frequency within the range of 12.5- to 25-fold resistance. Since there was no TCN haplotype pair detected below a resistance level of 12.5-fold, we speculate that resistance mechanisms other than target site insensitivity may exist. These observations are important for the prediction and management of mevinphos and related organophosphate resistance in field populations of P. xylostella.

Signatures of soft sweeps across the Dt1 locus underlying determinate growth habit in soya bean [Glycine max (L.) Merr.]

Determinate growth habit is an agronomically important trait associated with domestication in soya bean. Previous studies have demonstrated that the emergence of determinacy is correlated with artificial selection on four nonsynonymous mutations in the Dt1 gene. To better understand the signatures of the soft sweeps across the Dt1 locus and track the origins of the determinate alleles, we examined patterns of nucleotide variation in Dt1 and the surrounding genomic region of approximately 800 kb. Four local, asymmetrical hard sweeps on four determinate alleles, sized approximately 660, 120, 220 and 150 kb, were identified, which constitute the soft sweeps for the adaptation. These variable-sized sweeps substantially reflected the strength and timing of selection and indicated that the selection on the alleles had been completed rapidly within half a century. Statistics of EHH, iHS, H12 and H2/H1 based on haplotype data had the power to detect the soft sweeps, revealing distinct signatures of extensive long-range LD and haplotype homozygosity, and multiple frequent adaptive haplotypes. A haplotype network constructed for Dt1 and a phylogenetic tree based on its extended haplotype block implied independent sources of the adaptive alleles through de novo mutations or rare standing variation in quick succession during the selective phase, strongly supporting multiple origins of the determinacy. We propose that the adaptation of soya bean determinacy is guided by a model of soft sweeps and that this model might be indispensable during crop domestication or evolution.