Novel genetic basis of resistance to Bt toxin Cry1Ac in Helicoverpa zea

Genetic basis of resistance to Cry1Ac in Rachiplusia nu (Lepidoptera: Noctuidae): inheritance mode, cross-resistance patterns and fitness cost

BACKGROUND

Rachiplusia nu (Guenée) was historically a secondary soybean pest in Brazil, but a key soybean pest in Argentina. From 2021 onwards, injury caused by R. nu has been reported in soybean that expresses the Cry1Ac toxin from Bacillus thuringiensis (Berliner) in both countries. In this study, we selected resistant and susceptible strains of R. nu to Cry1Ac using Cry1Ac-containing leaf tissue and characterized the inheritance of resistance, cross-resistance patterns and fitness cost.

RESULTS

Neonates of the Cry1Ac-resistant strain of R. nu were able to develop on Cry1Ac soybean leaves and emerge as fertile adults, while neonates from the susceptible and heterozygous strains did not survive beyond 10 days. The resistance ratio to Cry1Ac estimated in diet-overlay bioassays in the resistant strain was > 736.92-fold. The inheritance pattern of Cry1Ac resistance in R. nu was characterized as autosomal recessive and monogenic. The Cry1Ac-resistant strain of R. nu also exhibited high resistance to Cry1A.105 (resistance ratio > 159.87-fold), but negligible resistance to Cry2Ab2 (resistance ratio = 1.25-fold). Life history data showed that the resistance to Cry1Ac in R. nu is not associated with a substantial fitness cost.

CONCLUSIONS

The inheritance pattern of Cry1Ac resistance in R. nu is autosomal recessive, monogenic and not associated with obvious fitness costs. Cross-resistance occurred between Cry1Ac and Cry1A.105 in R. nu but not between Cry1Ac and Cry2Ab2, indicating that Cry1A.105/Cry2Ab2/Cry1Ac soybean is a valuable tool to manage Cry1Ac resistance in R. nu. This is the first study reporting the genetic basis of Cry1Ac resistance in R. nu. © 2024 Society of Chemical Industry.

Inheritance of Cry2Ab2 resistance in two Helicoverpa zea (Lepidoptera: Noctuidae) populations resistant to single- and dual-Bacillus thuringiensis proteins

Cry2Ab2 is a Bacillus thuringiensis (Bt) protein that has been pyramided with Cry1A.105 in transgenic maize and Cry1Ac in cotton to control some major lepidopteran pests including the corn earworm/bollworm, Helicoverpa zea (Boddie). However, the widespread occurrence of resistance of this pest to the pyramided Cry1A/Cry2A crops in the southern region of the United State has become a threat to the sustainability of the technology. In this study, multiple genetic crosses and backcrosses were developed to characterize the inheritance of Cry2Ab2 resistance in two H. zea populations resistant to the single protein, Cry2Ab2 (RR2Ab) and the dual proteins in Bt maize, Cry1A.105/Cry2Ab2 (RRVT2P). Diet-overlay bioassays with F1 hybrids from reciprocal crosses between a susceptible and the resistant populations showed that the Cry2Ab2 resistance in both RR2Ab and RRVT2P was inherited autosomally and non-recessively. Segregation tests in F2 and backcrossed generations indicated that the resistance was likely controlled by more than one locus. The effective dominance levels of the resistance estimated at each of three discriminating concentrations were similar between RR2Ab and RRVT2P, ranging from incompletely dominant to incompletely recessive. The similar inheritance observed in RR2Ab and RRVT2P suggests that the Cry2Ab2 resistance is independent from the Cry1A.105 resistance. The non-recessive inheritance of the resistance could be an important factor causing the widespread resistance of this insect to the Cry1A/Cry2A crops in the southern region. Implications of the observed inheritance properties in Bt crop resistance management are discussed.

Polygenic response to selection by transgenic Bt-expressing crops in wild Helicoverpa zea and characterization of a major effect locus

Strong and shifting selective pressures of the Anthropocene are rapidly shaping phenomes and genomes of organisms worldwide. Crops expressing pesticidal proteins from Bacillus thuringiensis (Bt) represent one major selective force on insect genomes. Here we characterize a rapid response to selection by Bt crops in a major crop pest, Helicoverpa zea. We reveal the polygenic architecture of Bt resistance evolution in H. zea and identify multiple genomic regions underlying this trait. In the genomic region of largest effect, we identified a gene amplification event, where resistant individuals showed variation in copy number for multiple genes. Signals of this amplification increased over time, consistent with the history of field-evolved Bt resistance evolution. Modern wild populations from disparate geographical regions are positive for this variant at high, but not fixed, allele frequencies. We also detected selection against single copy variants at this locus in wild H. zea collected from Bt expressing plants, further supporting its role in resistance. Multiple genes were annotated in this genomic region, and all appeared to be significantly upregulated in Bt resistant H. zea. We functionally characterized genes within the copy number variant (CNV), providing insight into their potential roles in resistance evolution. Our findings reveal the nature of rapid genome evolution in a major crop pest following anthropogenic selection and highlight the role that CNVs can have in rapid evolutionary responses.

Mismatch between lab-generated and field-evolved resistance to transgenic Bt crops in Helicoverpa zea

Transgenic crops producing crystalline (Cry) proteins from the bacterium Bacillus thuringiensis (Bt) have been used extensively to control some major crop pests. However, many populations of the noctuid moth Helicoverpa zea, one of the most important crop pests in the United States, have evolved practical resistance to several Cry proteins including Cry1Ac. Although mutations in single genes that confer resistance to Cry proteins have been identified in lab-selected and gene-edited strains of H. zea and other lepidopteran pests, the genetic basis of field-evolved resistance to Cry proteins in H. zea has remained elusive. We used a genomic approach to analyze the genetic basis of field-evolved resistance to Cry1Ac in 937 H. zea derived from 17 sites in seven states of the southern United States. We found evidence for extensive gene flow among all populations studied. Field-evolved resistance was not associated with mutations in 20 single candidate genes previously implicated in resistance or susceptibility to Cry proteins in H. zea or other lepidopterans. Instead, resistance in field samples was associated with increased copy number of a cluster of nine trypsin genes. However, trypsin gene amplification occurred in a susceptible sample and not in all resistant samples, implying that this amplification does not always confer resistance and mutations in other genes also contribute to field-evolved resistance to Cry1Ac in H. zea. The mismatch between lab-generated and field-evolved resistance in H. zea is unlike other cases of Bt resistance and reflects challenges for managing this pest.

Distinct regulatory mechanisms by the nuclear Argonautes HRDE-1 and NRDE-3 in the soma of Caenorhabditis elegans

RNA interference is a conserved silencing mechanism that depends on the generation of small RNA molecules that disrupt synthesis of their corresponding transcripts. Nuclear RNA interference is a unique process that triggers regulation through epigenetic alterations to the genome. This pathway has been extensively characterized in Caenorhabditis elegans and involves the nuclear recruitment of H3K9 histone methyltransferases by the Argonautes HRDE-1 and NRDE-3. The coordinate regulation of genetic targets by H3K9 methylation and the nuclear Argonautes is highly complex and has been mainly described based on the small RNA populations that are involved. Recent studies have also linked the nuclear RNAi pathway to the compaction of the hermaphrodite X chromosomes during dosage compensation, a mechanism that balances genetic differences between the biological sexes by repressing X chromosomes in hermaphrodites. This chromosome-wide process provides an excellent opportunity to further investigate the relationship between H3K9 methylation and the nuclear Argonautes from the perspective of the transcriptome. Our work suggests that the nuclear RNAi and the H3K9 methylation pathways each contribute to the condensation of the X chromosomes during dosage compensation but the consequences on their transcriptional output are minimal. Instead, nuclear RNAi mutants exhibit global transcriptional differences, in which HRDE-1 and NRDE-3 affect expression of their native targets through different modes of regulation and different relationships to H3K9 methylation.

ARTICLE SUMMARY

This study examines the transcriptional consequences during the disruption of the nuclear RNAi silencing mechanism in C. elegans . Through microscopy and bioinformatic work, we demonstrate that although nuclear RNAi mutants exhibit significantly decondensed X chromosomes, chromosome-wide transcriptional de-repression is not detectable. Downstream analyses further explore the global influence of the nuclear RNAi pathway, indicating that the nuclear Argonautes HRDE-1 and NRDE-3 function through two distinct mechanisms.

Rapid Adaptation and Interspecific Introgression in the North American Crop Pest Helicoverpa zea

Insect crop pests threaten global food security. This threat is amplified through the spread of nonnative species and through adaptation of native pests to control measures. Adaptations such as pesticide resistance can result from selection on variation within a population, or through gene flow from another population. We investigate these processes in an economically important noctuid crop pest, Helicoverpa zea, which has evolved resistance to a wide range of pesticides. Its sister species Helicoverpa armigera, first detected as an invasive species in Brazil in 2013, introduced the pyrethroid-resistance gene CYP337B3 to South American H. zea via adaptive introgression. To understand whether this could contribute to pesticide resistance in North America, we sequenced 237 H. zea genomes across 10 sample sites. We report H. armigera introgression into the North American H. zea population. Two individuals sampled in Texas in 2019 carry H. armigera haplotypes in a 4 Mbp region containing CYP337B3. Next, we identify signatures of selection in the panmictic population of nonadmixed H. zea, identifying a selective sweep at a second cytochrome P450 gene: CYP333B3. We estimate that its derived allele conferred a ∼5% fitness advantage and show that this estimate explains independently observed rare nonsynonymous CYP333B3 mutations approaching fixation over a ∼20-year period. We also detect putative signatures of selection at a kinesin gene associated with Bt resistance. Overall, we document two mechanisms of rapid adaptation: the introduction of fitness-enhancing alleles through interspecific introgression, and selection on intraspecific variation.

A chromosome-level genome assembly of the soybean pod borer: insights into larval transcriptional response to transgenic soybean expressing the pesticidal Cry1Ac protein

BACKGROUND

Genetically modified (GM) crop plants with transgenic expression of Bacillus thuringiensis (Bt) pesticidal proteins are used to manage feeding damage by pest insects. The durability of this technology is threatened by the selection for resistance in pest populations. The molecular mechanism(s) involved in insect physiological response or evolution of resistance to Bt is not fully understood.

RESULTS

To investigate the response of a susceptible target insect to Bt, the soybean pod borer, Leguminivora glycinivorella (Lepidoptera: Tortricidae), was exposed to soybean, Glycine max, expressing Cry1Ac pesticidal protein or the non-transgenic parental cultivar. Assessment of larval changes in gene expression was facilitated by a third-generation sequenced and scaffolded chromosome-level assembly of the L. glycinivorella genome (657.4 Mb; 27 autosomes + Z chromosome), and subsequent structural annotation of 18,197 RefSeq gene models encoding 23,735 putative mRNA transcripts. Exposure of L. glycinivorella larvae to transgenic Cry1Ac G. max resulted in prediction of significant differential gene expression for 204 gene models (64 up- and 140 down-regulated) and differential splicing among isoforms for 10 genes compared to unexposed cohorts. Differentially expressed genes (DEGs) included putative peritrophic membrane constituents, orthologs of Bt receptor-encoding genes previously linked or associated with Bt resistance, and those involved in stress responses. Putative functional Gene Ontology (GO) annotations assigned to DEGs were significantly enriched for 36 categories at GO level 2, respectively. Most significantly enriched cellular component (CC), biological process (BP), and molecular function (MF) categories corresponded to vacuolar and microbody, transport and metabolic processes, and binding and reductase activities. The DEGs in enriched GO categories were biased for those that were down-regulated (≥ 0.783), with only MF categories GTPase and iron binding activities were bias for up-regulation genes.

CONCLUSIONS

This study provides insights into pathways and processes involved larval response to Bt intoxication, which may inform future unbiased investigations into mechanisms of resistance that show no evidence of alteration in midgut receptors.

Cross-pollination in seed-blended refuge and selection for Vip3A resistance in a lepidopteran pest as detected by genomic monitoring

The evolution of pest resistance to management tools reduces productivity and results in economic losses in agricultural systems. To slow its emergence and spread, monitoring and prevention practices are implemented in resistance management programs. Recent work suggests that genomic approaches can identify signs of emerging resistance to aid in resistance management. Here, we empirically examined the sensitivity of genomic monitoring for resistance management in transgenic Bt crops, a globally important agricultural innovation. Whole genome resequencing of wild North American Helicoverpa zea collected from non-expressing refuge and plants expressing Cry1Ab confirmed that resistance-associated signatures of selection were detectable after a single generation of exposure. Upon demonstrating its sensitivity, we applied genomic monitoring to wild H. zea that survived Vip3A exposure resulting from cross-pollination of refuge plants in seed-blended plots. Refuge seed interplanted with transgenic seed exposed H. zea to sublethal doses of Vip3A protein in corn ears and was associated with allele frequency divergence across the genome. Some of the greatest allele frequency divergence occurred in genomic regions adjacent to a previously described candidate gene for Vip3A resistance. Our work highlights the power of genomic monitoring to sensitively detect heritable changes associated with field exposure to Bt toxins and suggests that seed-blended refuge will likely hasten the evolution of resistance to Vip3A in lepidopteran pests.

Inheritance and fitness cost of laboratory-selected resistance to Vip3Aa in Helicoverpa zea (Lepidoptera: Noctuidae)

The polyphagous pest Helicoverpa zea (Lepidoptera: Noctuidae) has evolved practical resistance to transgenic corn and cotton producing Cry1 and Cry2 crystal proteins from Bacillus thuringiensis (Bt) in several regions of the United States. However, the Bt vegetative insecticidal protein Vip3Aa produced by Bt corn and cotton remains effective against this pest. To advance knowledge of resistance to Vip3Aa, we selected a strain of H. zea for resistance to Vip3Aa in the laboratory. After 28 generations of continuous selection, the resistance ratio was 267 for the selected strain (GA-R3) relative to a strain not selected with Vip3Aa (GA). Resistance was autosomal and almost completely recessive at a concentration killing all individuals from GA. Declines in resistance in heterogeneous strains containing a mixture of susceptible and resistant individuals reared in the absence of Vip3Aa indicate a fitness cost was associated with resistance. Previously reported cases of laboratory-selected resistance to Vip3Aa in lepidopteran pests often show partially or completely recessive resistance at high concentrations and fitness costs. Abundant refuges of non-Bt host plants can maximize the benefits of such costs for sustaining the efficacy of Vip3Aa against target pests.

Population Genomics of Nonrecessive Resistance to Bt Toxin Cry1Ac in Helicoverpa armigera From Northern China

Transgenic crops that produce insecticidal proteins from Bacillus thuringiensis (Bt) have provided control of some key pests since 1996. However, the evolution of resistance by pests reduces the benefits of Bt crops. Resistance to Bt crops that is not recessively inherited is especially challenging to manage. Here we analyzed nonrecessive resistance to Bt toxin Cry1Ac in eight field populations of Helicoverpa armigera sampled in 2018 from northern China, where this global pest has been exposed to Cry1Ac in Bt cotton since 1997. Bioassays revealed 7.5% of field-derived larvae were resistant to Cry1Ac of which 87% had at least one allele conferring nonrecessive resistance. To analyze this nonrecessive resistance, we developed and applied a variant of a genomic mapping approach called quantitative trait locus (QTL)-seq. This analysis identified a region on chromosome 10 associated with nonrecessive resistance to Cry1Ac in all 21 backcross families derived from field-collected moths. Individual sequencing revealed that all 21 field-collected resistant grandparents of the backcross families had a previously identified dominant point mutation in the tetraspanin gene HaTSPAN1 that occurs in the region of chromosome 10 identified by QTL-seq. QTL-seq also revealed a region on chromosome 26 associated with nonrecessive resistance in at most 14% of the backcross families. Overall, the results imply the point mutation in HaTSPAN1 is the primary genetic basis of nonrecessive resistance to Cry1Ac in field populations of H. armigera from northern China. Moreover, because nonrecessive resistance is predominant, tracking the frequency of this point mutation could facilitate resistance monitoring in the region.

Development of modified Cry1Ac for the control of resistant insect pest of cotton, Pectinophora gossypiella

Cotton has been one of the most important cash crops in Pakistan, but its production is adversely affected by biotic and abiotic stresses. Insect pests such as pink bollworm present a colossal vulnerability to such a financially important commodity. Bt toxins have been widely used to safeguard agricultural plants against notorious insect pests such as cotton bollworm and pink bollworm, and they have proven to be effective in reducing chewing insect pests. However, its efficacy has been challenged due to the development of resistance in insect pests against Bt toxins such as Cry1Ac and this poses a significant risk to the long-term adoption of these Bt crops. Resistance in insect pests against Bt toxin Cry1Ac is developed due to the mutations in the midgut receptors such as cadherin. In this study first 56 amino acids which also includes helix alpha-1 portion from N-terminus of the Cry1Ac were removed and the gene was commercially synthesized following codon optimization. Modified Cry1Ac was used to develop transgenic plants of Nicotiana tabacum and insect bioassays were conducted to check the efficacy of Cry1Ac through leaf bioassays. Cry1Ac, a modified Bt toxin, was produced pET-28a (+), and diet bioassays were performed using purified protein at various doses against Pectinophora gossypiella. Based on the insect mortality and LC₅₀, the Cry1AcM3 form of the modified toxins was shown to be more potent than the other modified versions (Cry1AcM1, Cry1AcM2), with more than 80 % mortality against resistant pink bollworm at 1.25 g/mL and an LC₅₀ of 0.48. The results suggest that modified toxin cry1Ac may be useful in controlling population of pink bollworm resistant against cry1Ac.

A Chromosome-Scale Genome Assembly of a Helicoverpa zea Strain Resistant to Bacillus thuringiensis Cry1Ac Insecticidal Protein

Helicoverpa zea (Lepidoptera: Noctuidae) is an insect pest of major cultivated crops in North and South America. The species has adapted to different host plants and developed resistance to several insecticidal agents, including Bacillus thuringiensis (Bt) insecticidal proteins in transgenic cotton and maize. Helicoverpa zea populations persist year-round in tropical and subtropical regions, but seasonal migrations into temperate zones increase the geographic range of associated crop damage. To better understand the genetic basis of these physiological and ecological characteristics, we generated a high-quality chromosome-level assembly for a single H. zea male from Bt-resistant strain, HzStark_Cry1AcR. Hi-C data were used to scaffold an initial 375.2 Mb contig assembly into 30 autosomes and the Z sex chromosome (scaffold N50 = 12.8 Mb and L50 = 14). The scaffolded assembly was error-corrected with a novel pipeline, polishCLR. The mitochondrial genome was assembled through an improved pipeline and annotated. Assessment of this genome assembly indicated 98.8% of the Lepidopteran Benchmark Universal Single-Copy Ortholog set were complete (98.5% as complete single copy). Repetitive elements comprised approximately 29.5% of the assembly with the plurality (11.2%) classified as retroelements. This chromosome-scale reference assembly for H. zea, ilHelZeax1.1, will facilitate future research to evaluate and enhance sustainable crop production practices.

Comparison of Long-Read Methods for Sequencing and Assembly of Lepidopteran Pest Genomes

Lepidopteran species are mostly pests, causing serious annual economic losses. High-quality genome sequencing and assembly uncover the genetic foundation of pest occurrence and provide guidance for pest control measures. Long-read sequencing technology and assembly algorithm advances have improved the ability to timeously produce high-quality genomes. Lepidoptera includes a wide variety of insects with high genetic diversity and heterozygosity. Therefore, the selection of an appropriate sequencing and assembly strategy to obtain high-quality genomic information is urgently needed. This research used silkworm as a model to test genome sequencing and assembly through high-coverage datasets by de novo assemblies. We report the first nearly complete telomere-to-telomere reference genome of silkworm Bombyx mori (P50T strain) produced by Pacific Biosciences (PacBio) HiFi sequencing, and highly contiguous and complete genome assemblies of two other silkworm strains by Oxford Nanopore Technologies (ONT) or PacBio continuous long-reads (CLR) that were unrepresented in the public database. Assembly quality was evaluated by use of BUSCO, Inspector, and EagleC. It is necessary to choose an appropriate assembler for draft genome construction, especially for low-depth datasets. For PacBio CLR and ONT sequencing, NextDenovo is superior. For PacBio HiFi sequencing, hifiasm is better. Quality assessment is essential for genome assembly and can provide better and more accurate results. For chromosome-level high-quality genome construction, we recommend using 3D-DNA with EagleC evaluation. Our study references how to obtain and evaluate high-quality genome assemblies, and is a resource for biological control, comparative genomics, and evolutionary studies of Lepidopteran pests and related species.

Utility and challenges of using whole-genome resequencing to detect emerging insect and mite resistance in agroecosystems

Arthropods that invade agricultural ecosystems systematically evolve resistance to the control measures used against them, and this remains a significant and ongoing challenge for sustainable food production systems. Early detection of resistance evolution could prompt remedial action to slow the spread of resistance alleles in the landscape. Historical approaches used to detect emerging resistance included phenotypic monitoring of agricultural pest populations, as well as monitoring of allele frequency changes at one or a few candidate pesticide resistance genes. In this article, I discuss the successes and limitations of these traditional monitoring approaches and then consider whether whole-genome scanning could be applied to samples collected from agroecosystems over time for resistance monitoring. I examine the qualities of agroecosystems that could impact application of this approach to pesticide resistance monitoring and describe a recent retrospective analysis where genome scanning successfully detected an oligogenic response to selection by pesticides years prior to pest management failure. I conclude by considering areas of further study that will shed light on the feasibility of applying whole-genome scanning for resistance risk monitoring in agricultural pest species.

Inheritance of Resistance to Cry1A.105 in Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae)

Cry1A.105 is a bioengineered Bacillus thuringiensis (Bt) insecticidal protein consisting of three domains derived from Cry1Ac, Cry1Ab, and Cry1F. It is one of the two pyramided Bt toxins expressed in the MON 89034 event, a commonly planted Bt maize trait in the Americas. Recent studies have documented that field resistance of the corn earworm, Helicoverpa zea (Boddie), to the Cry1A.105 toxin in maize plants has become widespread in the United States. To investigate the inheritance of resistance to Cry1A.105 in H. zea, two independent tests, each with various genetic crosses among susceptible and Cry1A.105-resistant populations, were performed. The responses of these susceptible, resistant, F₁, F₂, and backcrossed insect populations to Cry1A.105 were assayed using a diet overlay method. The bioassays showed that the resistance to Cry1A.105 in H. zea was inherited as a single, autosomal, nonrecessive gene. The nonrecessive nature of the resistance could be an important factor contributing to the widespread resistance of maize hybrids containing Cry1A.105 in the United States. The results indicate that resistance management strategies for Bt crops need to be refined to ensure that they are effective in delaying resistance evolution for nonrecessive resistance (nonhigh dose).