Gene interactions constrain the course of evolution of phosphine resistance in the lesser grain borer, Rhyzopertha dominica

Development, application and evaluation of three novel TaqMan qPCR assays for phosphine resistance monitoring in major stored product pests Tribolium castaneum and Rhyzopertha dominica

BACKROUND

Stored product protection from insect pests relies heavily on the use of phosphine. The most serious drawback of phosphine is the development of resistance in major stored product insects worldwide, including the red flour beetle, Tribolium castaneum (Herbst) and the lesser grain borer, Rhyzopertha dominica (F.). Two genetic loci are responsible for phosphine resistance: the rph1 (S349G mutation in the cyt-b5-r homolog) in T. castaneum and the rph2 (P45/49S mutation in the dihydrolipoamide dehydrogenase (dld) gene) in T. castaneum and R. dominica.

RESULTS

In this study, we have developed and applied high-throughput, practical and specific molecular diagnostics (TaqMan qPCR) for monitoring mutations S349G, P45S and P49S. In our pilot monitoring application, we have included phosphine-resistant and susceptible populations from different parts of the world (USA, Australia, Brazil) and European strains from Greece and Serbia. Our results for the resistant T. castaneum showed a P45S mutant allele frequency (MAF) of 100% and 75.0% in the populations from Serbia and Brazil, respectively. Regarding the susceptible T. castaneum, P45S was detected in Greece (MAF = 62.5%) and was absent in Australia (MAF = 0.0%). Additionally, the S349G mutation was found to be fixed in all resistant populations, while it was also detected in susceptible ones (frequencies: 65.0% and 100.0%). The only case where both mutations were fixed (100%) was a resistant population from Serbia. In R. dominica, the P49S mutation was found only in the two resistant R. dominica populations from Serbia and Greece (50.0% and 100%) and was absent from the susceptible one from Greece; thus, P49S seems to be a satisfactory indicator for monitoring phosphine resistance.

CONCLUSIONS

Our P49S detection assay in R. dominica seems to be a viable option in this direction, yet its utilization needs additional large-scale confirmatory work. The identification of additional resistance markers also should be prioritized. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Amplification refractory mutation system based real-time PCR (ARMS-qPCR) for rapid resistance characterization of Tribolium castaneum to phosphine

Resistance of Tribolium castaneum to phosphine is related to point mutations in DNA code corresponding to amino acid changes associated with a core metabolic enzyme dihydrolipoamide dehydrogenase (DLD), but the mutation patterns vary among different resistant populations. Thus, there is a great need to develop a cost-effective method to detect core mutations in T. castaneum, which would be the key factor to understand the molecular basis of phosphine resistance. Amplification refractory mutation system-based quantitative Real-Time PCR (ARMS-qPCR) is an ideal method that can rapidly detect point mutations. Here, the P45S and G131D mutations existed in the DLD of T. castaneum selected from strong Chinese resistance phenotypes, and the DLD P45S mutation, which represents a strong phosphine resistance allele, was confirmed as the most abundant mutation to determine strong resistance genotypes. Our study found that 85 out of 120 beetles carried the P45S resistance allele, including 51 homozygous and 34 heterozygous individuals. Moreover, there was a strong linear relationship (R² = 0.917) between the resistance ratio and the resistance allele frequency among the strongly resistant populations. Our data showed that the ARMS-qPCR method that we developed could rapidly determine strong resistance phenotypes of T. castaneum to phosphine by detecting the DLD P45S mutation. These results not only provide a detailed example for developing an ARMS-qPCR-based method to characterize pesticide resistance, but also support further elucidation of the molecular basis of phosphine resistance.

A novel biofumigant from Tithonia diversifolia (Hemsl.) A. Gray for control of stored grain insect pests

For the well-being of human health as well as ecological concerns and the development of insect resistance to conventional chemical insecticides, efforts have increased worldwide, to find eco-friendly, effective and safer insect control agents which are of natural origin. A bioactive biofumigant molecule named dihydro-p-coumaric acid was isolated and characterized from the leaves of Tithonia diversifolia Hemsl. A. Gray following laboratory bioassays against the rice weevil, Sitophilus oryzae L (Coleoptera: Curculionidae); the lesser grain borer, Rhyzopertha dominica F (Coleoptera: Bostrichidae) and the rust-red flour beetle, Tribolium castaneum Herbst (Coleoptera: Tenebrionidae). The isolated compound acted as a fumigant, toxic to adults of stored grain insect pests with LC₅₀ values of 17.86, and 11.49 μg/L (S. oryzae), 19.80 and 10.29 μg/L (R. dominica) and 24.41 and 17.80 μg/L air (T. casatneum) respectively. Further, in vivo data reveal that the percentage of inhibition of acetyl cholinesterase (AChE) was dose-dependent and in vitro results showed potent AChE inhibitor. The isolated compound acts as an efficient biofumigant against the stored grain insect pests and has no adverse effect on seed germination. From this study, we assume that the isolated biofumigant molecule has the ability for used in IPM programs for stored-grain pests because of its biofumigant activity.

The Genome of Rhyzopertha dominica (Fab.) (Coleoptera: Bostrichidae): Adaptation for Success

The lesser grain borer, Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae), is a major global pest of cereal grains. Infestations are difficult to control as larvae feed inside grain kernels, and many populations are resistant to both contact insecticides and fumigants. We sequenced the genome of R. dominica to identify genes responsible for important biological functions and develop more targeted and efficacious management strategies. The genome was assembled from long read sequencing and long-range scaffolding technologies. The genome assembly is 479.1 Mb, close to the predicted genome size of 480.4 Mb by flow cytometry. This assembly is among the most contiguous beetle assemblies published to date, with 139 scaffolds, an N₅₀ of 53.6 Mb, and L₅₀ of 4, indicating chromosome-scale scaffolds. Predicted genes from biologically relevant groups were manually annotated using transcriptome data from adults and different larval tissues to guide annotation. The expansion of carbohydrase and serine peptidase genes suggest that they combine to enable efficient digestion of cereal proteins. A reduction in the copy number of several detoxification gene families relative to other coleopterans may reflect the low selective pressure on these genes in an insect that spends most of its life feeding internally. Chemoreceptor genes contain elevated numbers of pseudogenes for odorant receptors that also may be related to the recent ontogenetic shift of R. dominica to a diet consisting primarily of stored grains. Analysis of repetitive sequences will further define the evolution of bostrichid beetles compared to other species. The data overall contribute significantly to coleopteran genetic research.

Immediate and Delayed Mortality of Four Stored-Product Pests on Concrete Surfaces Treated with Chlorantraniliprole

Simple Summary

We examined the mortality caused by the anthranilic diamide, chlorantraniliprole, at four different doses applied on concrete (0.01, 0.05, 0.1, and 0.5 mg a.i./cm²) in Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae) adults and larvae, Rhyzopertha dominica (F.) (Coleoptera: Bostrychidae) adults, Sitophilus oryzae (L.) (Coleoptera: Curculionidae) adults, and Acarus siro L. (Sarcoptiformes: Acaridae) adults and nymphs. Mortality data were recorded after 1, 2, 3, 4, and 5 days to determine the immediate mortality. Furthermore, after the 5-day mortality counts, still living individuals were conveyed for 7 days to untreated concrete surfaces to estimate the delayed mortality. The highest immediate mortality was recorded for the larvae of T. castaneum, reaching 96.7%, followed by the adults of A. siro (92.2%) after 5 days of exposure to 0.5 mg a.i./cm². Complete (100.0%) delayed mortality was noticed for T. castaneum (adults and larvae), S. oryzae, and A. siro (both as adults) at 0.5 mg a.i./cm². Rhyzopertha dominica adults and A. siro nymphs exhibited 98.6% and 96.3% delayed mortality at the same dose, respectively. Overall, our results demonstrate that chlorantraniliprole is effective against all the species tested, causing varying immediate and delayed mortality rates at the developmental stages tested.

Abstract

Chlorantraniliprole is an effective pesticide against a plethora of pests, but its efficacy against stored-product pests is very poorly explored. In this study we treated concrete surfaces with four different doses of chlorantraniliprole (0.01, 0.05, 0.1, and 0.5 mg a.i./cm²) against the red flour beetle, Tribolium castaneum (Herbst) (Coleoptera: Tenebrionidae) adults and larvae, the lesser grain borer, Rhyzopertha dominica (F.) (Coleoptera: Bostrychidae) adults, the rice weevil, Sitophilus oryzae (L.) (Coleoptera: Curculionidae) adults, and the flour mite, Acarus siro L. (Sarcoptiformes: Acaridae) adults and nymphs, to examine the immediate mortalities after 1, 2, 3, 4, and 5 days of exposure. Additionally, the delayed mortality of the individuals that survived the 5-day exposure was also evaluated after a further 7 days on untreated concrete surfaces. We documented high mortality rates for all tested species and their developmental stages. After 5 days of exposure to 0.5 mg a.i./cm², T. castaneum larvae and A. siro adults exhibited the highest immediate mortality levels, reaching 96.7% and 92.2%, respectively. Delayed mortality was also very high for all tested species and their developmental stages. Nymphs of A. siro displayed a 96.3% delayed mortality followed by the adults of R. dominica (98.6%) after exposure to 0.5 mg a.i./cm². All other tested species and their developmental stages reached complete (100.0%) delayed mortality, where even 0.01 mg a.i./cm² caused ≥86.6% delayed mortality in all species and their developmental stages. Taking into consideration the effectiveness of chlorantraniliprole on this wide range of noxious arthropods, coupled with its low toxicity towards beneficial arthropods and mammals, this pesticide could provide an effective management tool for stored-product pests in storage facilities.

Comparative Proteomics Analysis of Phosphine-Resistant and Phosphine-Susceptible Sitophilus oryzae (Coleoptera: Curculionidae)

A proteomic method combining two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and matrix-assisted laser desorption/ionization-time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF) was used to compare the protein expression profiles of phosphine-resistant (PH3-R) and -susceptible (PH3-S) strains of Sitophilus oryzae. Thirty-nine differentially expressed protein spots were identified between the PH3-R and PH3-S strains; 20 protein spots were upregulated, and 19 protein spots were downregulated in the PH3-R strain compared with their expression in the PH3-S strain. In particular, cytochrome oxidase subunit I showed 15-fold higher expression in the PH3-R strain than in the PH3-S strain. Additionally, citrate synthase 2, delta-1-pyrolline-5-carboxylate dehydrogenase, and triose-phosphate isomerase were highly expressed in the PH3-R strain. In summary, our study has improved understanding of the molecular mechanisms of phosphine resistance in the rice weevil.

Variants in the Mitochondrial Genome Sequence of Rhyzopertha dominica (Fabricius) (Coleoptera: Bostrycidae)

Simple Summary

The lesser grain borer damages grains in storage worldwide. The major control method for this beetle is phosphine fumigation, but the increase in resistant populations has led to a loss in phosphine efficacy. Insect mitochondria are the major source of energy, and some phosphine-resistant insects have reduced energy production. Therefore, we want to understand whether changes in the mitochondrial genome may promote phosphine resistance in insects, but we need an accurate mitogenome sequence and annotation. We extracted and sequenced genomic DNA from a laboratory colony of the lesser grain borer and assembled and annotated the mitochondrial genome. The mitochondrial genome sequence was similar in structure to other insect mitochondria and encoded typical mitochondrial genes. We compared our predicted mitochondrial genome sequence to that of another lesser grain borer strain from Jingziguan (China). While there was mostly agreement among the two sequences, the data will be used to determine if key differences may suggest mutations in the two populations related to phosphine control pressure. However, differences also could be the result in different genome sequences and interpretations. The data will be useful as a research tool to examine the expression of mitochondrial genes in phosphine susceptible and -resistant insect populations.

Abstract

The lesser grain borer, Rhyzopertha dominica, is a coleopteran pest of stored grains and is mainly controlled by phosphine fumigation, but the increase in phosphine-resistant populations threatens efficacy. Some phosphine-resistant insects have reduced respiration, and thus studying the mitochondrial genome may provide additional information regarding resistance. Genomic DNA from an inbred laboratory strain of R. dominica was extracted and sequenced with both short (Illumina) and long (Pacific Biosciences) read technologies for whole genome sequence assembly and annotation. Short read sequences were assembled and annotated by open software to identify mitochondrial sequences, and the assembled sequence was manually annotated and verified by long read sequences. The mitochondrial genome sequence for R. dominica had a total length of 15,724 bp and encoded 22 trna genes, 2 rRNA genes, 13 protein coding genes (7 nad subunits, 3 cox, 2 atp, and 1 cytB), flanked by a long control region. We compared our predicted mitochondrial genome to that of another from a R. dominica strain from Jingziguan (China). While there was mostly agreement between the two assemblies, key differences will be further examined to determine if mutations in populations are related to insecticide control pressure, mainly that of phosphine. Differences in sequence data, assembly, and annotation also may result in different genome interpretations.

Unique genetic variants in dihydrolipoamide dehydrogenase (dld) gene confer strong resistance to phosphine in the rusty grain beetle, Cryptolestes ferrugineus (Stephens)

The rusty grain beetle, Cryptolestes ferrugineus, a major pest of stored commodities, has developed very high levels (>1000×) of resistance to the fumigant phosphine. Resistance in this species is remarkably stronger than reported in any other stored product pests demanding the need to understand the molecular basis of this trait. Previous genetic studies in other grain insect pests identified specific variants in two major genes, rph1 and rph2 in conferring the strong resistance trait. However, in C. ferrugineus, although the gene, rph1 was identified as cytochrome-b5-fatty acid desaturase, the rph2 gene has not been reported so far. We tested the candidate gene for rph2, dihydrolipoamide dehydrogenase (dld) using the recently published transcriptome of C. ferrugineus and identified three variants, L73N and A355G + D360H, a haplotype, conferring resistance in this species. Our sequence analysis in resistant strain and phosphine selected resistant survivors indicates that these variants occur either alone as a homozygote or a mixture of heterozygotes (i.e complex heterozygotes) both conferring strong resistance. We also found that one of the three variants, possibly L73N expressing "dominant" trait at low frequency in resistant insects. Comparison of dld sequences between Australian and Chinese resistant strain of this species confirmed that the identified variants are highly conserved. Our fitness analysis indicated that resistant insects may not incur significant biological costs in the absence of phosphine selection for 19 generations. Thus, we propose that the observed high levels of resistance in C. ferrugineus could be primarily due to the characteristics of three unique variants, L73N and A355G + D360H within dld.

Identification and functional analysis of cytochrome P450 CYP346 family genes associated with phosphine resistance in Tribolium castaneum

Resistance to phosphine fumigation has been frequently reported in insect pests of stored products and remains one of the obstacles in controlling these pests, including Tribolium castaneum. In this study, six field populations of T. castaneum were collected from different localities in China. Bioassay data showed that SZ population was strongly resistant to phosphine, followed by moderate-resistance populations WL and SF and three susceptible populations JX, YN, and ML. In addition, synergism assays showed that piperonyl butoxide significantly increased the toxicity of phosphine in resistant population SZ. Furthermore, CYP346B subfamily genes, CYP346B1, CYP346B2, and CYP346B3, were significantly overexpressed in resistant populations. Expression of CYP346B1, CYP346B2, and CYP346B3 were significantly upregulated following exposure to phosphine. RNAi assays showed that depletions on the expression levels of CYP346B1, CYP346B2, and CYP346B3 resulted in an increase of susceptibility to phosphine in T. castaneum, respectively. Our data demonstrated that CYP346B subfamily genes in T. castaneum were associated with the resistance of phosphine. Moreover, the study also increased our understanding of the molecular basis of phosphine resistance in stored pest insects.

Oxygen and Arsenite Synergize Phosphine Toxicity by Distinct Mechanisms

Phosphine is the only fumigant approved globally for general use to control insect pests in stored grain. Due to the emergence of resistance among insect pests and the lack of suitable alternative fumigants, we are investigating ways to synergistically enhance phosphine toxicity, by studying the mechanism of action of known synergists, such as oxygen, temperature, and arsenite. Under normoxia, exposure of the model organism Caenorhabditis elegans for 24 h at 20°C to 70 ppm phosphine resulted in 10% mortality, but nearly 100% mortality if the oxygen concentration was increased to 80%. In wild-type C. elegans, toxicity of phosphine was negatively affected by a decrease in temperature to 15°C and positively affected by an increase in temperature to 25°C. The dld-1(wr4) strain of C. elegans is resistant to phosphine due to a mutation in the dihydrolipoamide dehydrogenase gene. It also exhibits increased mortality that is dependent on hyperoxia, when exposed to 70 ppm phosphine at 20°C. As with the wild-type strain, mortality decreased when exposure was carried out at 15°C. At 25°C, however, the strain was completely resistant to the phosphine exposure at all oxygen concentrations. Arsenite is also a synergist of phosphine toxicity, but only in the dld-1(wr4)-mutant strain. Thus, exposure to 4 mM arsenite resulted in 50% mortality, which increased to 89% mortality when 70 ppm phosphine and 4 mM arsenite were combined. In stark contrast, 70 ppm phosphine rendered 4 mM arsenite nontoxic to wild-type C. elegans. These results reveal two synergists with distinct modes of action, one of which targets individuals that carry a phosphine resistance allele in the dihydrolipoamide dehydrogenase gene.

Resistance to the Fumigant Phosphine and Its Management in Insect Pests of Stored Products: A Global Perspective

Development of resistance in major grain insect pest species to the key fumigant phosphine (hydrogen phosphide) across the globe has put the viability and sustainability of phosphine in jeopardy. The resistance problem has been aggravated over the past two decades, due mostly to the lack of suitable alternatives matching the major attributes of phosphine, including its low price, ease of application, proven effectiveness against a broad pest spectrum, compatibility with most storage conditions, and international acceptance as a residue-free treatment. In this review, we critically analyze the published literature in the area of phosphine resistance with special emphasis on the methods available for detection of resistance, the genetic basis of resistance development, key management strategies, and research gaps that need to be addressed.

A high-throughput system used to determine frequency and distribution of phosphine resistance across large geographical regions

BACKGROUND

Next-generation sequencing can enable genetic surveys of large numbers of individuals. We developed a genotyping-by-sequencing assay for detecting strong phosphine resistance alleles in the dihydrolipoamide dehydrogenase (dld) gene of Rhyzopertha dominica populations. The assay can estimate the distribution and frequency of resistance variants in thousands of individual insects in a single run.

RESULTS

We analysed 1435 individual insects collected over a 1-year period from 59 grain-storage sites including farms (n = 29) and central storages (n = 30) across eastern Australia. Resistance alleles were detected in 49% of samples, 38% of farms and 60% of central storages. Although multiple alleles were detected, only two resistance variants (P49S and K142E) were widespread and each appeared to have a distinct but overlapping geographical distribution.

CONCLUSION

The type of structure in which the grain is stored had a strong effect on resistance allele frequency. We observed higher frequencies of resistance alleles in bunker storages at central sites compared with other storage types. This contributed to the higher frequencies of resistance alleles in bulk-handling facilities relative to farms. The discovery of a storage structure that predisposes insects to resistance highlights the utility of our high-throughput assay system for improvement of phosphine resistance management practices. © 2018 Society of Chemical Industry.

Variant Linkage Analysis Using de Novo Transcriptome Sequencing Identifies a Conserved Phosphine Resistance Gene in Insects

Next-generation sequencing methods enable identification of the genetic basis of traits in species that have no prior genomic information available. The combination of next-generation sequencing, variant analysis, and linkage is a powerful way of identifying candidate genes for a trait of interest. Here, we used a comparative transcriptomics [RNA sequencing (RNAseq)] and genetic linkage analysis approach to identify the rph1 gene. rph1 variants are responsible for resistance to the fumigant phosphine (PH₃) that is used to control insect pests of stored grain. In each of the four major species of pest insect of grain we have investigated, there are two major resistance genes, rph1 and rph2, which interact synergistically to produce strongly phosphine-resistant insects. Using RNAseq and genetic linkage analyses, we identified candidate resistance (rph1) genes in phosphine-resistant strains of three species: Rhyzopertha dominica (129 candidates), Sitophilus oryzae (206 candidates), and Cryptolestes ferrugineus (645 candidates). We then compared these candidate genes to 17 candidate resistance genes previously mapped in Tribolium castaneum and found only one orthologous gene, a cytochrome b5 fatty acid desaturase (Cyt-b5-r), to be associated with the rph1 locus in all four species. This gene had either missense amino acid substitutions and/or insertion/deletions/frameshift variants in each of 18 phosphine-resistant strains that were not observed in the susceptible strains of the four species. We propose a model of phosphine action and resistance in which phosphine induces lipid peroxidation through reactive oxygen species generated by dihydrolipoamide dehydrogenase, whereas disruption of Cyt-b5-r in resistant insects decreases the polyunsaturated fatty acid content of membranes, thereby limiting the potential for lipid peroxidation.

Progression of phosphine resistance in susceptible Tribolium castaneum (Herbst) populations under different immigration regimes and selection pressures

Insecticide resistance is an escalating global issue for a wide variety of agriculturally important pests. The genetic basis and biochemical mechanisms of resistance are well characterized in some systems, but little is known about the ecological aspects of insecticide resistance. We therefore designed a laboratory experiment to quantify the progression of phosphine resistance in Tribolium castaneum populations subject to different immigration regimes and selection pressures. Mated resistant females were added to originally susceptible populations under two distinct migration rates, and in addition, half of the populations in each migration treatment were exposed to selection pressures from phosphine fumigation. The progression of phosphine resistance was assessed by screening beetles for the resistance allele at rph2. Phosphine resistance increased slowly in the low migration treatment and in the absence of selection, as expected. But at the higher migration rate, the increase in frequency of the resistance allele was lower than predicted. These outcomes result from the high levels of polyandry known in T. castaneum females in the laboratory, because most of the Generation 1 offspring (86%) were heterozygous for the rph2 allele, probably because resistant immigrant females mated again on arrival. Phosphine resistance was not fixed by fumigation as predicted, perhaps because susceptible gametes and eggs survived fumigation within resistant females. In terms of phosphine resistance progression in populations exposed to selection, the effect of fumigation negated the difference in migration rates. These results demonstrate how species‐specific traits relating to the mating system may shape the progression of insecticide resistance within populations, and they have broad implications for the management of phosphine resistance in T. castaneum in the field. ​We specify and discuss how these mating system attributes need to be accounted for when developing guidelines for resistance management.

Automated Wormscan

There has been a recent surge of interest in computer-aided rapid data acquisition to increase the potential throughput and reduce the labour costs of large scale Caenorhabditis elegans studies. We present Automated WormScan, a low-cost, high-throughput automated system using commercial photo scanners, which is extremely easy to implement and use, capable of scoring tens of thousands of organisms per hour with minimal operator input, and is scalable. The method does not rely on software training for image recognition, but uses the generation of difference images from sequential scans to identify moving objects. This approach results in robust identification of worms with little computational demand. We demonstrate the utility of the system by conducting toxicity, growth and fecundity assays, which demonstrate the consistency of our automated system, the quality of the data relative to manual scoring methods and congruity with previously published results.

Phosphine Resistance in Adult and Immature Life Stages of Tribolium castaneum (Coleoptera: Tenebrionidae) and Plodia interpunctella (Lepidoptera: Pyralidae) Populations in California

Phosphine resistance in stored-product insects occurs worldwide and is a major challenge to continued effective use of this fumigant. We determined resistance frequencies and levels of resistance in Tribolium castaneum and Plodia interpunctella collected from California almond storage and processing facilities. Discriminating doses of phosphine were established for eggs and larvae of P. interpunctella and eggs of T. castaneum using laboratory susceptible strains of the two species. For T. castaneum and P. interpunctella eggs, discriminating doses were 62.4 and 107.8 ppm, respectively, over a 3-d fumigation period, and for P. interpunctella larvae, discriminating dose was 98.7 ppm over a 20-h fumigation period. Discriminating dose tests on adults and eggs showed that 4 out of 11 T. castaneum populations tested had resistance frequencies that ranged from 42 to 100% for adults and 54 to 100% for eggs. LC99 values for the susceptible and the most resistant adults of T. castaneum were 7.4 and 356.9 ppm over 3 d, respectively. LC99 values for T. castaneum eggs were 51.5 and 653.9 ppm, respectively. Based on adult data, the most resistant T. castaneum beetle population was 49× more resistant than the susceptible strain. Phosphine resistance frequencies in P. interpunctella eggs ranged from 4 to 20%. Results show phosphine resistance is present in both species in California. Future research will investigate phosphine resistance over a wider geographic area. In addition, the history of pest management practices in facilities where insects tested in this study originated will be determined in order to develop phosphine resistance management strategies for California almond storage and processing facilities.

Genetic Conservation of Phosphine Resistance in the Rice Weevil Sitophilus oryzae (L.)

High levels of resistance to phosphine in the rice weevil Sitophilus oryzae have been detected in Asian countries including China and Vietnam, however there is limited knowledge of the genetic mechanism of resistance in these strains. We find that the genetic basis of strong phosphine resistance is conserved between strains of S. oryzae from China, Vietnam, and Australia. Each of 4 strongly resistant strains has an identical amino acid variant in the encoded dihydrolipoamide dehydrogenase (DLD) enzyme that was previously identified as a resistance factor in Rhyzopertha dominica and Tribolium castaneum. The unique amino acid substitution, Asparagine > Threonine (N505T) of all strongly resistant S. oryzae corresponds to the position of an Asparagine > Histidine variant (N506H) that was previously reported in strongly resistant R. dominica. Progeny (F16 and F18) from 2 independent crosses showed absolute linkage of N505T to the strong resistance phenotype, indicating that if N505T was not itself the resistance variant that it resided within 1 or 2 genes of the resistance factor. Non-complementation between the strains confirmed the shared genetic basis of strong resistance, which was supported by the very similar level of resistance between the strains, with LC50 values ranging from 0.20 to 0.36 mg L(-1) for a 48-h exposure at 25 °C. Thus, the mechanism of high-level resistance to phosphine is strongly conserved between R. dominica, T. castaneum and S. oryzae. A fitness cost associated with strongly resistant allele was observed in segregating populations in the absence of selection.

Effectiveness of Sulfuryl Fluoride Fumigation for the Control of Phosphine-Resistant Grain Insects Infesting Stored Wheat

A field experiment was conducted in eight 13.6-MT steel bins containing 6.8 MT each of wheat to assess efficacy of sulfuryl fluoride or SF fumigant to control phosphine-resistant and susceptible Rhyzopertha dominica (F.) and Tribolium castaneum (Herbst). Approximately 400 adults of each type of beetle were added to each bin. Additionally, muslin bags containing immature stages and adults, with their respective diets, were also placed in bins. Four bins were fumigated with SF and others were untreated control bins. The SF dosages in treated bins ranged from 1,196–1,467 mg-h/liter. Mortality of adults in each bag was assessed 5 d postfumigation; diet minus adults was incubated in a jar, and number of adults counted after 8 wk. No significant change occurred in number of insect-damaged kernels in SF-treated bins. In trier samples from SF-treated bins, R. dominica numbers declined from 24 prefumigation to 0 at 3- and 6-wk postfumigation; T. castaneum numbers were unchanged. In WBII traps from SF-treated bins, numbers R. dominica and T. castaneum declined from 25 and 33, respectively, prefumigation to 0 or near 0 at 3- and 6-wk postfumigation. Mortalities of resistant and susceptible adult R. dominica, and adult and large larvae of T. castaneum in SF-treated bags was 100%. For all four types of beetles, adult numbers in jars associated with SF-treated bins were 0 or near 0. Results show SF is effective against all life stages of phosphine-resistant R. dominica and T. castaneum, and can be used for phosphine resistance management.

Resistance of Lasioderma serricorne (Coleoptera: Anobiidae) to Fumigation with Phosphine

Lasioderma serricorne (F.) is a serious pest of stored products that is known to be resistant to the fumigant pesticide gas phosphine. This study investigated resistance in populations from the southeastern United States, and determined if a recommended treatment schedule could kill resistant insects. A laboratory assay for adult insects was developed that used a discriminating concentration of 50 ppm phosphine applied to insects for 20 h at 25°C followed by 7 d of recovery in air. Survivors were classified as resistant. L. serricorne from six different field populations associated with stored tobacco were surveyed with the assay and all had resistant individuals. Four populations had greater than 90% of their insects resistant. Two industry-recommended treatment schedules were evaluated in laboratory fumigations against mixed life stage cultures of the four most resistant populations: the first at 200 ppm for 4 d at 25°C for controlling phosphine-susceptible L. serricorne and the second at 600 ppm for 6 d at 25°C intended to control phosphine-resistant beetles. The four populations with the highest frequency of resistant individuals from the field sampling study were not controlled by the "normal" treatment intended for susceptible insects. The higher concentration treatment greatly reduced beetle progeny from mixed-stage colony jars, but there were substantial numbers of surviving adults from all four highly resistant populations that represented unacceptable levels of control.

Diagnostic molecular markers for phosphine resistance in U.S. populations of Tribolium castaneum and Rhyzopertha dominica

Stored product beetles that are resistant to the fumigant pesticide phosphine (hydrogen phosphide) gas have been reported for more than 40 years in many places worldwide. Traditionally, determination of phosphine resistance in stored product beetles is based on a discriminating dose bioassay that can take up to two weeks to evaluate. We developed a diagnostic cleaved amplified polymorphic sequence method, CAPS, to detect individuals with alleles for strong resistance to phosphine in populations of the red flour beetle, Tribolium castaneum, and the lesser grain borer, Rhyzopertha dominica, according to a single nucleotide mutation in the dihydrolipoamide dehydrogenase (DLD) gene. We initially isolated and sequenced the DLD genes from susceptible and strongly resistant populations of both species. The corresponding amino acid sequences were then deduced. A single amino acid mutation in DLD in populations of T. castaneum and R. dominica with strong resistance was identified as P45S in T. castaneum and P49S in R. dominica, both collected from northern Oklahoma, USA. PCR products containing these mutations were digested by the restriction enzymes MboI and BstNI, which revealed presence or absence, respectively of the resistant (R) allele and allowed inference of genotypes with that allele. Seven populations of T. castaneum from Kansas were subjected to discriminating dose bioassays for the weak and strong resistance phenotypes. Application of CAPS to these seven populations confirmed the R allele was in high frequency in the strongly resistant populations, and was absent or at a lower frequency in populations with weak resistance, which suggests that these populations with a low frequency of the R allele have the potential for selection of the strong resistance phenotype. CAPS markers for strong phosphine resistance will help to detect and confirm resistant beetles and can facilitate resistance management actions against a given pest population.

Constitutive activation of the Nrf2/Keap1 pathway in insecticide-resistant strains of Drosophila

Pesticide resistance poses a major challenge for the control of vector-borne human diseases and agricultural crop protection. Although a number of studies have defined how mutations in specific target proteins can lead to insecticide resistance, much less is known about the mechanisms by which constitutive overexpression of detoxifying enzymes contributes to metabolic pesticide resistance. Here we show that the Nrf2/Keap1 pathway is constitutively active in two laboratory-selected DDT-resistant strains of Drosophila, 91R and RDDTR, leading to the overexpression of multiple detoxifying genes. Disruption of the Drosophila Nrf2 ortholog, CncC, or overexpression of Keap1, is sufficient to block this transcriptional response. In addition, a CncC-responsive reporter is highly active in both DDT-resistant strains and this response is dependent on the presence of an intact CncC binding site in the promoter. Microarray analysis revealed that ∼20% of the genes differentially expressed in the 91R strain are known CncC target genes. Finally, we show that CncC is partially active in these strains, consistent with the fitness cost associated with constitutive activation of the pathway. This study demonstrates that the Nrf2/Keap1 pathway contributes to the widespread overexpression of detoxification genes in insecticide-resistant strains and raises the possibility that inhibitors of this pathway could provide effective synergists for insect population control.

Rapid genome wide mapping of phosphine resistance loci by a simple regional averaging analysis in the red flour beetle, Tribolium castaneum

Background

Next-generation sequencing technology is an important tool for the rapid, genome-wide identification of genetic variations. However, it is difficult to resolve the ‘signal’ of variations of interest and the ‘noise’ of stochastic sequencing and bioinformatic errors in the large datasets that are generated. We report a simple approach to identify regional linkage to a trait that requires only two pools of DNA to be sequenced from progeny of a defined genetic cross (i.e. bulk segregant analysis) at low coverage (<10×) and without parentage assignment of individual SNPs. The analysis relies on regional averaging of pooled SNP frequencies to rapidly scan polymorphisms across the genome for differential regional homozygosity, which is then displayed graphically.

Results

Progeny from defined genetic crosses of Tribolium castaneum (F₄ and F₁₉) segregating for the phosphine resistance trait were exposed to phosphine to select for the resistance trait while the remainders were left unexposed. Next generation sequencing was then carried out on the genomic DNA from each pool of selected and unselected insects from each generation. The reads were mapped against the annotated T. castaneum genome from NCBI (v3.0) and analysed for SNP variations. Since it is difficult to accurately call individual SNP frequencies when the depth of sequence coverage is low, variant frequencies were averaged across larger regions. Results from regional SNP frequency averaging identified two loci, tc_rph1 on chromosome 8 and tc_rph2 on chromosome 9, which together are responsible for high level resistance. Identification of the two loci was possible with only 5-7× average coverage of the genome per dataset. These loci were subsequently confirmed by direct SNP marker analysis and fine-scale mapping. Individually, homozygosity of tc_rph1 or tc_rph2 results in only weak resistance to phosphine (estimated at up to 1.5-2.5× and 3-5× respectively), whereas in combination they interact synergistically to provide a high-level resistance >200×. The tc_rph2 resistance allele resulted in a significant fitness cost relative to the wild type allele in unselected beetles over eighteen generations.

Conclusion

We have validated the technique of linkage mapping by low-coverage sequencing of progeny from a simple genetic cross. The approach relied on regional averaging of SNP frequencies and was used to successfully identify candidate gene loci for phosphine resistance in T. castaneum. This is a relatively simple and rapid approach to identifying genomic regions associated with traits in defined genetic crosses that does not require any specialised statistical analysis.

Dosage consistency is the key factor in avoiding evolution of resistance to phosphine and population increase in stored-grain pests

BACKGROUND

Control of pests in stored grain and the evolution of resistance to pesticides are serious problems worldwide. A stochastic individual-based two-locus model was used to investigate the impact of two important issues, the consistency of pesticide dosage through the storage facility and the immigration rate of the adult pest, on overall population control and avoidance of evolution of resistance to the fumigant phosphine in an important pest of stored grain, the lesser grain borer.

RESULTS

A very consistent dosage maintained good control for all immigration rates, while an inconsistent dosage failed to maintain control in all cases. At intermediate dosage consistency, immigration rate became a critical factor in whether control was maintained or resistance emerged.

CONCLUSION

Achieving a consistent fumigant dosage is a key factor in avoiding evolution of resistance to phosphine and maintaining control of populations of stored-grain pests; when the dosage achieved is very inconsistent, there is likely to be a problem regardless of immigration rate.

Determining changes in the distribution and abundance of a Rhyzopertha dominica phosphine resistance allele in farm grain storages using a DNA marker

BACKGROUND

The lesser grain borer, Rhyzopertha dominica (F.), is a highly destructive pest of stored grain that is strongly resistant to the fumigant phosphine (PH3 ). Phosphine resistance is due to genetic variants at the rph2 locus that alter the function of the dihydrolipoamide dehydrogenase (DLD) gene. This discovery now enables direct detection of resistance variants at the rph2 locus in field populations.

RESULTS

A genotype assay was developed for direct detection of changes in distribution and frequency of a phosphine resistance allele in field populations of R. dominica. Beetles were collected from ten farms in south-east Queensland in 2006 and resampled in 2011. Resistance allele frequency increased in the period from 2006 to 2011 on organic farms with no history of phosphine use, implying that migration of phosphine-resistant R. dominica had occurred from nearby storages.

CONCLUSION

Increasing resistance allele frequencies on organic farms suggest local movement of beetles and dispersal of insects from areas where phosphine has been used. This research also highlighted for the first time the utility of a genetic DNA marker in accurate and rapid determination of the distribution of phosphine-resistant insects in the grain value chain. Extending this research over larger landscapes would help in identifying resistance problems and enable timely pest management decisions.

Shifting focus from the population to the individual as a way forward in understanding, predicting and managing the complexities of evolution of resistance to pesticides

The evolution of resistance to pesticides is often conceptualised and modelled at a population level, but population-based approaches ignore important aspects of variability between individuals within populations that may be essential drivers of resistance. Here it is argued that individual-based modelling has the potential to generate new insights and perspectives, thus deepening our understanding of the complexities of the evolutionary dynamics of resistance to pesticides.

Strong resistance to phosphine in the rusty grain beetle, Cryptolestes ferrugineus (Stephens) (Coleoptera: Laemophloeidae): its characterisation, a rapid assay for diagnosis and its distribution in Australia

BACKGROUND

The recent development of very high resistance to phosphine in rusty grain beetle, Cryptolestes ferrugineus (Stephens), seriously threatens stored-grain biosecurity. The aim was to characterise this resistance, to develop a rapid bioassay for its diagnosis to support pest management and to document the distribution of resistance in Australia in 2007-2011.

RESULTS

Bioassays of purified laboratory reference strains and field-collected samples revealed three phenotypes: susceptible, weakly resistant and strongly resistant. With resistance factors of > 1000 × , resistance to phosphine expressed by the strong resistance phenotype was higher than reported for any stored-product insect species. The new time-to-knockdown assay rapidly and accurately diagnosed each resistance phenotype within 6 h. Although less frequent in western Australia, weak resistance was detected throughout all grain production regions. Strong resistance occurred predominantly in central storages in eastern Australia.

CONCLUSION

Resistance to phosphine in the rusty grain beetle is expressed through two identifiable phenotypes: weak and strong. Strong resistance requires urgent changes to current fumigation dosages. The development of a rapid assay for diagnosis of resistance enables the provision of same-day advice to expedite resistance management decisions.

Phosphine resistance in Tribolium castaneum and Rhyzopertha dominica from stored wheat in Oklahoma

Phosphine gas, or hydrogen phosphide (PH3), is the most common insecticide applied to durable stored products worldwide and is routinely used in the United States for treatment of bulk-stored cereal grains and other durable stored products. Research from the late 1980s revealed low frequencies of resistance to various residual grain protectant insecticides and to phosphine in grain insect species collected in Oklahoma. The present work, which used the same previously established discriminating dose bioassays for phosphine toxicity as in the earlier study, evaluated adults of nine different populations of red flour beetle, Tribolium castaneum (Herbst), and five populations of lesser grain borer, Rhyzopertha dominica (F.) collected from different geographic locations in Oklahoma. One additional population for each species was a laboratory susceptible strain. Discriminating dose assays determined eight out of the nine T. castaneum populations, and all five populations of R. dominica, contained phosphine-resistant individuals, and highest resistance frequencies were 94 and 98%, respectively. Dose-response bioassays and logit analyses determined that LC99 values were approximately 3 ppm for susceptible and 377 ppm for resistant T. castaneum, and approximately 2 ppm for susceptible and 3,430 ppm for resistant R. dominica. The most resistant T. castaneum population was 119-fold more resistant than the susceptible strain and the most resistant R. dominica population was over 1,500-fold more resistant. Results suggest a substantial increase in phosphine resistance in these major stored-wheat pests in the past 21 yr, and these levels of resistance to phosphine approach those reported for other stored-grain pest species in other countries.

The rph2 gene is responsible for high level resistance to phosphine in independent field strains of Rhyzopertha dominica

The lesser grain borer Rhyzopertha dominica (F.) is one of the most destructive insect pests of stored grain. This pest has been controlled successfully by fumigation with phosphine for the last several decades, though strong resistance to phosphine in many countries has raised concern about the long term usefulness of this control method. Previous genetic analysis of strongly resistant (SR) R. dominica from three widely geographically dispersed regions of Australia, Queensland (SR_QLD), New South Wales (SR_NSW) and South Australia (SR_SA), revealed a resistance allele in the rph1 gene in all three strains. The present study confirms that the rph1 gene contributes to resistance in a fourth strongly resistant strain, SR2_QLD, also from Queensland. The previously described rph2 gene, which interacts synergistically with rph1 gene, confers strong resistance on SR_QLD and SR_NSW. We now provide strong circumstantial evidence that weak alleles of rph2, together with rph1, contribute to the strong resistance phenotypes of SR_SA and SR2_QLD. To test the notion that rph1 and rph2 are solely responsible for the strong resistance phenotype of all resistant R. dominica, we created a strain derived by hybridising the four strongly resistant lines. Following repeated selection for survival at extreme rates of phosphine exposure, we found only slightly enhanced resistance. This suggests that a single sequence of genetic changes was responsible for the development of resistance in these insects.

Phosphine resistance in the rust red flour beetle, Tribolium castaneum (Coleoptera: Tenebrionidae): inheritance, gene interactions and fitness costs

The recent emergence of heritable high level resistance to phosphine in stored grain pests is a serious concern among major grain growing countries around the world. Here we describe the genetics of phosphine resistance in the rust red flour beetle Tribolium castaneum (Herbst), a pest of stored grain as well as a genetic model organism. We investigated three field collected strains of T. castaneum viz., susceptible (QTC4), weakly resistant (QTC1012) and strongly resistant (QTC931) to phosphine. The dose-mortality responses of their test- and inter-cross progeny revealed that most resistance was conferred by a single major resistance gene in the weakly (3.2×) resistant strain. This gene was also found in the strongly resistant (431×) strain, together with a second major resistance gene and additional minor factors. The second major gene by itself confers only 12-20× resistance, suggesting that a strong synergistic epistatic interaction between the genes is responsible for the high level of resistance (431×) observed in the strongly resistant strain. Phosphine resistance is not sex linked and is inherited as an incompletely recessive, autosomal trait. The analysis of the phenotypic fitness response of a population derived from a single pair inter-strain cross between the susceptible and strongly resistant strains indicated the changes in the level of response in the strong resistance phenotype; however this effect was not consistent and apparently masked by the genetic background of the weakly resistant strain. The results from this work will inform phosphine resistance management strategies and provide a basis for the identification of the resistance genes.

The rph1 gene is a common contributor to the evolution of phosphine resistance in independent field isolates of Rhyzopertha dominica

Phosphine is the only economically viable fumigant for routine control of insect pests of stored food products, but its continued use is now threatened by the world-wide emergence of high-level resistance in key pest species. Phosphine has a unique mode of action relative to well-characterised contact pesticides. Similarly, the selective pressures that lead to resistance against field sprays differ dramatically from those encountered during fumigation. The consequences of these differences have not been investigated adequately. We determine the genetic basis of phosphine resistance in Rhyzopertha dominica strains collected from New South Wales and South Australia and compare this with resistance in a previously characterised strain from Queensland. The resistance levels range from 225 and 100 times the baseline response of a sensitive reference strain. Moreover, molecular and phenotypic data indicate that high-level resistance was derived independently in each of the three widely separated geographical regions. Despite the independent origins, resistance was due to two interacting genes in each instance. Furthermore, complementation analysis reveals that all three strains contain an incompletely recessive resistance allele of the autosomal rph1 resistance gene. This is particularly noteworthy as a resistance allele at rph1 was previously proposed to be a necessary first step in the evolution of high-level resistance. Despite the capacity of phosphine to disrupt a wide range of enzymes and biological processes, it is remarkable that the initial step in the selection of resistance is so similar in isolated outbreaks.

Mechanisms of phosphine toxicity

Fumigation with phosphine gas is by far the most widely used treatment for the protection of stored grain against insect pests. The development of high-level resistance in insects now threatens its continued use. As there is no suitable chemical to replace phosphine, it is essential to understand the mechanisms of phosphine toxicity to increase the effectiveness of resistance management. Because phosphine is such a simple molecule (PH₃), the chemistry of phosphorus is central to its toxicity. The elements above and below phosphorus in the periodic table are nitrogen (N) and arsenic (As), which also produce toxic hydrides, namely, NH₃ and AsH₃. The three hydrides cause related symptoms and similar changes to cellular and organismal physiology, including disruption of the sympathetic nervous system, suppressed energy metabolism and toxic changes to the redox state of the cell. We propose that these three effects are interdependent contributors to phosphine toxicity.