Selection and Evaluation of Reference Genes for qRT-PCR in Spodoptera frugiperda (Lepidoptera: Noctuidae)

Selection and Validation of Stable Reference Genes for RT-qPCR in Scotogramma trifolii (Lepidoptera: Noctuidae)

The clover cutworm, Scotogramma trifolii Rottemberg (Lepidoptera: Noctuidae), is a globally distributed polyphagous pest causing significant economic losses to agricultural crops. RT-qPCR is a gold-standard technique for gene expression analysis, yet its accuracy depends critically on stable reference genes for data normalization. To address the lack of validated reference genes in S. trifolii, we evaluated six candidate genes (β-actin, RPL9, GAPDH, RPL10, EF1-α, and TUB) across four developmental stages (egg, larva, pupa, and adult) and six adult tissues (head, thorax, abdomen, wings, legs, and antennae) using geNorm, NormFinder, BestKeeper, and RefFinder algorithms. Stability analysis identified β-actin, RPL9, and GAPDH as the most reliable reference genes for developmental stage normalization, while RPL10, GAPDH, and TUB were validated for adult tissues. Functional validation using the odorant receptor gene StriOR20 revealed significant discrepancies in relative expression levels when normalized with unstable reference genes (TUB and RPL9), emphasizing the necessity of rigorous reference gene selection. This study establishes the first comprehensive reference gene panel for S. trifolii, providing a robust foundation for gene expression studies in this agriculturally important pest.

Function of SfDNAJA1 and SfHSP68 in Temperature Stress Response and Apoptosis in Fall Armyworm (Spodoptera frugiperda)

The fall armyworm (Spodoptera frugiperda) is a major invasive pest. To explore its adaptive mechanisms under temperature stress, we conducted transcriptome analysis across six developmental stages and both sexes at 0, 26, and 46 °C. High-temperature stress induced more differentially expressed genes (DEGs, 8,703) than low-temperature stress (5,426), with fourth instar larvae showing the most DEGs at low temperatures. Sex-specific responses were also evident. Sixteen heat shock protein (HSP) genes and 31 apoptosis-related genes were identified as key stress-responsive factors. RNAi knockdown of SfDNAJA1 and SfHSP68 reduced survival under temperature stress, increased ROS and Cyt c levels, and upregulated apoptosis-related genes, while ATP levels decreased. Elevated caspase-3, G6PD, and GST activities further indicated oxidative and apoptotic responses. These results underscore the essential role of HSPs in maintaining cellular homeostasis and regulating apoptosis during thermal stress, offering insights into pest adaptation and potential control strategies.

Hairy and Krüppel homolog 1 Comediate the Action of Juvenile Hormone/Methoprene-Tolerant Signaling Pathway in Vitellogenesis of Spodoptera frugiperda (J.E. Smith)

Spodoptera frugiperda is a major migratory invasive pest and is of global concern. Vitellogenesis, a crucial process for population multiplication in oviparous insects, is regulated by endocrine hormones. In this study, three primary responders to JH signaling, the JH receptor gene Met, and the downstream transcription factor Kr-h1 and Hairy, were first cloned and identified. RNA interference results showed that silencing SfMet significantly down-regulated the transcription levels of SfKr-h1 and SfHairy, as well as the key reproductive genes Vitellogenin (SfVg) and Vitellogenin receptor (SfVgR). Similarly, silencing SfKr-h1 and SfHairy also inhibited the transcription of SfVg and SfVgR. Silencing of SfMet, SfKr-h1, and SfHairy genes resulted in blocked ovarian development and a significant decrease in reproduction. These findings confirm that Hairy and Kr-h1 comediate the action of the JH-Met signaling pathway in vitellogenesis of S. frugiperda, providing new targets and insights for pest control.

Characterization of sulfakinin and its role in larval feeding and molting in Spodoptera frugiperda

Feeding and molting are particularly important physiological processes for insects, and it has been reported that neuropeptides are involved in the nervous regulation of these 2 processes. Sulfakinin (SK) is an important neuropeptide that is widely distributed among insects and plays a pivotal role in regulating feeding, courtship, aggression, and locomotion. In this study, we investigated the involvement of SK in feeding and molting on a highly notorious pest insect, the fall armyworm, Spodoptera frugiperda. SK transcript levels were found in all larval stages and there was a predominant expression of SK in the brain of 5th instar larvae. By immunostaining, SK was detected in 2 pairs of cells in the median protocerebrum. But during prolonged periods of starvation, there was a significant reduction in SK messenger RNA levels; however, subsequent refeeding led to a notable increase. To investigate the role of SK in feeding and molting, SK was silenced in S. frugiperda larvae through RNA interference. This resulted in a significant increase in food intake, weight gain, and the molting process happened more rapidly in the double-stranded SK-treated larvae compared to the controls. Conversely, injection of sulfated SK peptide (sSK) caused opposite effects. Interestingly, SK-knockdown in larvae resulted in increased levels of 20-hydroxyecdysone and also of the expression of some of it signaling pathway genes. Altogether, this study highlights the important role played by SK in regulating feeding and molting in S. frugiperda.

Disrupting shadow in the prothoracic gland induced larval development arrest in the fall armyworm Spodoptera frugiperda

Introduction

The juvenile hormone (JH) and 20-hydroxyecdysone (20E) are the central regulating hormones of insect development. The timing of their secretion usually leads to developmental transitions.

Methods

The developmental transitions were evaluated via the starvation treatment and the expressions of two key metamorphosis inducing factor in Spodoptera frugiperda. Then, the main endocrine organs, including the brain-corpora cardiacum-corpora allatum and prothoracic gland, were sampled from L4-24 h and L6-24 h larvae for the RNA-seq analysis. Additionally, the critical rate-limiting enzyme of 20E synthesis, shadow, was knocked down to mimic the downregulation of 20E synthesis in the late larval instar.

Results

The critical weight (CW), when JH titer declines for metamorphosis, was determined be approximately L6-24 h in S. frugiperda. However, the expression of the pupal specifier Broad-Complex and the potential "metamorphosis initiation factor" Myoglianin showed a stepwise increase between L4-24 h and L6-24 h, suggesting that the developmental transitions may occur earlier. The RNA-seq analysis revealed that both 20E and JH synthesis enzymes were downregulated at the CW. In addition, strong tendencies in the expression pattern were detected among the lists of transcripts. Further knockdown of shadow induced larval development arrest and subsequent mortality, indicating that disrupting 20E synthesis before the CW is lethal. Besides, JH synthesis enzyme was down-regulated.

Conclusion

The downregulation of 20E synthesis enzymes at the CW may represent a carefully regulated event, suggesting a deceleration of larval growth and the initiation of some underlying physiological changes to set the stage for metamorphosis.

Screening and Validation of Stable Reference Genes for qRT-PCR Analysis in Epicauta gorhami (Coleoptera: Meloidae)

Epicauta gorhami is a hypermetamorphic insect that mainly forage soybeans during the adult stage. However, the lack of appropriate references hinders our studying of the gene function in E. gorhami. In this study, referring to five computational tools (Ct value, geNorm, NormFinder, BestKeeper and RefFinder), the stability of 10 housekeeping genes (GAPDH, ACT, RPL4, RPL27, α-TUB, RPS18, EF1α, RPS28, RPL13 and SOD) was assessed by qRT-PCR under three different conditions (adult ages, tissues/organs and temperatures). The findings suggested that SOD and RPS18 were the most ideal references for examine gene transcripts among diverse adult ages and at various temperatures; a pair of RPS18 and RPS28 was the most reliable genes to assess gene expressions in diverse adult tissues. Finally, the relative expression levels of EgUAP were computed after normalization RPS18 and RPS28 with across diverse adult tissues. As expected, EgUAP expression was abundant in the foregut, trachea and antenna and scarce in the midgut, hindgut and epidermis. These findings will lay a solid foundation for analyzing the gene expression of E. gorhami.

Multi-omics analysis reveal the fall armyworm Spodoptera frugiperda tolerate high temperature by mediating chitin-related genes

Climate change facilitates the rapid invasion of agricultural pests, threatening global food security. The fall armyworm Spodoptera frugiperda is a highly polyphagous migratory pest tolerant to high temperatures, allowing its proliferation in harsh thermal environments. We aimed to demonstrate mechanisms of its high-temperature tolerance, particularly transcriptional and metabolic regulation, which are poorly understood. To achieve the aim, we examined the impact and mechanism of heat events on S. frugiperda by using multiple approaches: ecological measurements, transcriptomics, metabolomics, RNAi, and CRISPR/Cas9 technology. We observed that several physiological indices (larval survival rate, larval period, pupation rate, pupal weight, eclosion rate, and average fecundity) decreased as the temperature increased, with the 32 °C treatment displaying a significant difference from the control group at 26 °C. Significantly upregulated expression of genes encoding endochitinase and chitin deacetylase was observed in the chitin-binding, extracellular region, and carbohydrate metabolic process GO terms of hemolymph, fat body, and brain, exhibiting a tissue-specific pattern. Significantly enriched pathways (e.g., cutin, suberin, and wax biosynthesis; oxidative phosphorylation and cofactor biosynthesis; diverse amino acid biosynthesis and degradation; carbon metabolism; and energy metabolism), all of which are essential for S. frugiperda larvae to tolerate temperature, were found in metabolites that were expressed differently. Successful RNA interference targeting of the three chitin-related genes reduced gene expression levels and larval survival rate. Knockout of the endochitinase gene by using the CRISPR/Cas9 system significantly reduced the relative gene expression and increased sensitivity to high-temperature exposure. On the basis of our findings, theoretical foundations for understanding the high-temperature tolerance of S. frugiperda populations and latent genetic control strategies were established.

Omics Analysis of Odorant-Binding Proteins and Cuticle-Enriched SfruOBP18 Confers Multi-Insecticide Tolerance in Spodoptera frugiperda

Spodoptera frugiperda is a notorious pest that develops a high resistance to many insecticides. Recently, insect odorant-binding proteins (OBPs) have been proven to participate in insecticide resistance. However, the functional evidence supporting the cross-link between OBPs and insecticide resistance remains unexplored. Here, we identified 50 SfruOBPs from the larval transcriptome and genome. Notably, SfruOBP18 was highly expressed in the larval cuticle and could be induced to upregulate its expression by multi-insecticides. Ligand-binding assays revealed that SfruOBP18 bound strongly with four insecticides; RNAi and insecticide bioassay demonstrated that the knockdown of SfruOBP18 did not affect larval survival and development. However, it can significantly increase the larval susceptibility to multi-insecticides, suggesting an uncommon role of SfruOBP18 in multi-insecticide susceptibility. Our study provides a comprehensive understanding of SfruOBPs and furthermore proves that a larval cuticle-enriched OBP can bind with and confer larval tolerance to multi-insecticides. SfruOBP18 could be a new insecticidal target for controlling Lepidoptera pests.

Evaluation and Validation of Reference Genes for Gene Expression Analysis Using qRT-PCR in the Sugarcane Stem Borer Chilo sacchariphagus (Lepidoptera: Pyralidae)

Chilo sacchariphagus (Lepidoptera: Pyralidae) is an economically important sugarcane pest. Although numerous studies were conducted on the physiological responses in C. sacchariphagus, little is known regarding the genes regulating these physiological processes. Gene expression analysis by qRT-PCR can offer a significant indication for functional gene studies. To our knowledge, the reference genes of C. sacchariphagus have not been screened or evaluated, which hinders the functional gene study. In the present study, the stability of seven reference genes (β-ACT, GAPDH, BTF3, 28S, RPL7, EF1α, and SDHA) was evaluated in C. sacchariphagus under different experimental conditions, including tissues (antenna, head, thorax, abdomen, leg, and wing), temperatures (4 °C, 25 °C, and 37 °C) and sexes (male and female), through RefFinder, which integrates four algorithms (Normfinder, BestKeeper, ΔCt method, and geNorm). The findings suggested that the combination of β-ACT and RPL7 is ideal to analyze gene expressions in different tissues and at distinct temperatures, and EF1α and SDHA were suitable reference genes for comparing gene expressions between sexes. Finally, the expression profiles of CsacPBP1 gene were evaluated, and the outcomes further confirm the importance of selecting fitting reference genes for normalization of qRT-PCR data. This study represents the first kind in screening out suitable reference genes for gene expression analysis in C. sacchariphagus. Information from this study is poised to galvanize future inquiry into the gene expression of C. sacchariphagus, an economically important pest of sugarcane.

Neuropeptide natalisin regulates reproductive behaviors in Spodoptera frugiperda

Natalisin (NTL) is a conserved neuropeptide, only present in insects, that has been reported to regulate their sexual activity. In this study, we investigated the involvement of NTL in the reproductive behaviors of a major invasive pest, Spodoptera frugiperda. We identified NTL precursor-encoded transcripts, and evaluated their transcript levels in different stages and tissues of S. frugiperda. The results showed that the NTL transcript level was expressed in both male and female pupae and both male and female adults in the later stage. It was highly expressed in male pupae, 3-day-old male and female adults, and 5-day-old male adults. In different tissues, the expression level is higher in the male and female adult brain and male testis. Immunohistochemical staining of the brain of S. frugiperda female and male adults revealed that three pairs of brain neurons of S. frugiperda adults of both sexes secreted and expressed NTL. To study the role of NTL in reproductive behaviors, NTL was silenced in S. frugiperda male and female adults by RNA interference (RNAi) technology, the results showed that silencing NTL could significantly affect the sexual activity behavior of the adults, reducing the calling rate of females, the courtship rate of males, and the mating rate. In summary, this study emphasizes the important role of NTL in regulating the mating behavior and sexual activity of S. frugiperda in both male and female adults, potentially laying a foundation to employ NTL as a new insect-specific target to control populations of pest insects.

Evaluation of reference genes for quantitative expression analysis in Mylabris sibirica (Coleoptera, Meloidae)

Mylabris sibirica is a hypermetamorphic insect whose adults feed on oilseed rape. However, due to a shortage of effective and appropriate endogenous references, studies on molecular functional genes in Mylabris sibirica, have been tremendously limited. In this study, ten internal reference genes (ACT, ARF1, AK, EF1α, GAPDH, α-TUB, RPL6, RPL13, RPS3 and RPS18) were tested and assessed under four selected treatments including adult ages, adult tissues, temperatures, and sex by RT-qPCR based on five methods (Ct value, geNorm, NormFinder, BestKeeper and RefFinder). Our findings showed that RPL6 and RPL13 were the most optimal internal reference gene combination for gene expression during various adult ages and under diverse temperatures; The combination of RPL6 and RPS18 was recommended to test gene transcription levels under different adult tissues. AK and RPL6 were the best reference genes in male and female adults. RPL6 and RPL13 were the most appropriate reference gene pair to estimate gene expression levels under four different tested backgrounds. The relative transcript levels of a uridine diphosphate (UDP)-N-acetylglucosamine-pyrophosphorylase (MsUAP), varied greatly according to normalization with the two most- and least-suited reference genes. This study will lay the basis for further molecular physiology and biochemistry studies in M. sibirica, such as development, reproduction, sex differentiation, cold and heat resistance.

Evaluation of Reference Genes for Quantitative Real-Time PCR Analysis in the Bean Bug, Riptortus pedestris (Hemiptera: Alydidae)

Quantitative real-time PCR (qRT-PCR) is widely accepted as a precise and convenient method for quantitatively analyzing the expression of functional genes. The data normalization strongly depends upon stable reference genes. The bean bug, Riptortus pedestris (Hemiptera: Alydidae), is a significant pest of leguminous crops and broadly distributed across Southeast Asia. In this study, a total of 16 candidate reference genes (RPL32, RPS23, SDHA, UBQ, UCCR, GST, TATA-box, HSP70, GAPDH, RPL7A, SOD, RPS3, Actin, α-tubulin, AK, and EF1) were carefully chosen in R. pedestris, and their expression levels were assessed across various conditions, including different developmental stages, diverse tissues, temperature treatments, adult age, molting time, and mating status. Following this, the stability of these reference genes was evaluated using four algorithms (ΔCt, GeNorm, NormFinder, and BestKeeper). Ultimately, the comprehensive rankings were determined using the online tool RefFinder. Our results demonstrate that the reference gene for qRT-PCR analysis in R. pedestris is contingent upon the specific experimental conditions. RPL7A and EF1 are optimal reference genes for developmental stages. Furthermore, α-tubulin and EF1 exhibit the most stable expression across various adult tissues. RPL32 and RPL7A exhibit the most stable expression for adult age. For nymph age, RPL32 and SOD display the most stable expression. For temperature conditions, RPS23 and RPL7A were identified as the most suitable for monitoring gene expression. Lastly, we verified the practicability of evaluating expression levels of odorant-binding protein 37 (RpedOBP37) and cytochrome P450 6a2 (RpedCYP6) throughout developmental stages, tissues, and temperature conditions. These findings are a significant addition to the qRT-PCR analysis studies on R. pedestris, serving as a fundamental groundwork for future investigations on stable reference genes in R. pedestris as well as other organisms.

Azadirachtin Inhibits Nuclear Receptor HR3 in the Prothoracic Gland to Block Larval Ecdysis in the Fall Armyworm, Spodoptera frugiperda

Azadirachtin has been used to control agricultural pests for a long time; however, the molecular mechanism of azadirachtin on lepidopterans is still not clear. In this study, the fourth instar larvae of fall armyworm were fed with azadirachtin, and then the ecdysis was blocked in the fourth instar larval stage (L4). The prothoracic glands (PGs) of the treated larvae were dissected for RNA sequencing to determine the effect of azadirachtin on ecdysis inhibition. Interestingly, one of the PG-enriched genes, the nuclear hormone receptor 3 (HR3), was decreased after azadirachtin treatment, which plays a critical role in the 20-hydroxyecdysone action during ecdysis. To deepen the understanding of azadirachtin on ecdysis, the HR3 was knocked out by using the CRISPR/Cas9 system, while the HR3 mutants displayed embryonic lethal phenotype; thus, the stage-specific function of HR3 during larval molting was not enabled to unfold. Hence, the siRNA was injected into the 24 h L4 larvae to knock down HR3. After 96 h, the injected larvae were blocked in the old cuticle during ecdysis which is consistent with the azadirachtin-treated larvae. Taken together, we envisioned that the inhibition of ecdysis in the fall armyworm after the azadirachtin treatment is due to an interference with the expression of HR3 in PG, resulting in larval mortality. The results in this study specified the understanding of azadirachtin on insect ecdysis and the function of HR3 in lepidopteran in vivo.

Evaluation of suitable reference genes for expression analysis using quantitative real-time polymerase chain reaction in the parasitoid Exorista sorbillans (Diptera: Tachinidae)

The parasitoid Exorista sorbillans (Diptera: Tachinidae) is a larval endoparasitoid of the silkworm Bombyx mori, causing severe damage to silkworm cocoon industry. It is also an important natural enemy resource of insect pests in agriculture and forestry. Despite their roles in biocontrol and pest status on sericulture, there has been limited research on the functional studies of dipteran parasitoids. Quantitative real-time polymerase chain reaction (qRT-PCR) is the most commonly used to address gene functions. Using qRT-PCR, stably expressed reference genes under different experimental conditions are required to normalize the expression of target genes. However, no information regarding suitable qRT-PCR reference genes in dipteran parasitoids has been reported. In this study, we evaluate the expression stability of nine commonly used reference genes in insects including eukaryotic translation elongation factor 1δ (eEF1δ), elongation factor 2, 18S ribosomal RNA (18S rRNA), tubulin 3, actin87, ribosomal protein 49 (RP49), ribosomal protein S15, glyceraldehyde-3-phosphate dehydrogenase, and TATA-box binding protein (TBP) in E. sorbillans under different treatments, including tissues, developmental stages, genders, feeding density and pesticide stress, using ∆C_t , BestKeeper, geNorm, Normfinder and RefFinder, respectively. The results showed that the genes RP49, eEF1δ and 18S rRNA were recommended as the most suitable reference genes in E. sorbillans across all experimental conditions. This finding provides the necessary foundation for future functional studies in E. sorbillans and its effective use in both sericulture and pest control.

Effects of lufenuron treatments on the growth and development of Spodoptera frugiperda (Lepidoptera: Noctuidae)

Lufenuron is an effective benzoylurea insecticide that inhibits the synthesis of chitin and regulates the growth of insects. However, little is known about the effects of lufenuron treatment on the development of Spodoptera frugiperda (J. E. Smith). In this study, we assessed the toxicity of lufenuron on S. frugiperda and evaluated the effects of lufenuron treatment on the growth and development of S. frugiperda. The results showed that lufenuron exhibits high insecticidal activity against S. frugiperda, with the LC₅₀ value of 0.99 mg L^-1. Lufenuron treatments can significantly prolong the larval developmental duration and reduce the rates of pupation and emergence. To further explore the underlying mechanism of this observation, the expression profiles of the chitin synthase gene (SfCHS) and chitinase gene (SfCHT), two key enzyme genes involved in the molting of S. frugiperda, were determined after exposure to lufenuron for 96 h. The results of qRT-PCR demonstrated that lufenuron treatments can significantly reduce the expression of SfCHT, while the expression of SfCHS remained relatively stable. Furthermore, we found that lufenuron strongly interacted with chitinase (SfCHT) (-10.8 kcal/mol) and chitin synthase (SfCHS) (R1: -9.7 kcal/mol; R2: -10.2 kcal/mol). Our results indicated that lufenuron has significant effects on the development of S. frugiperda that might be attributed to the differential expression of SfCHT and SfCHS.

Molecular Characterization of Vitellogenin and Its Receptor in Spodoptera frugiperda (J. E. Smith, 1797), and Their Function in Reproduction of Female

The fall armyworm Spodoptera frugiperda is a highly polyphagous invasive pest. The strong reproductive capacity is an important factor in the rapid colonization and expansion of S. frugiperda. Vitellogenin (Vg) and vitellogenin receptor (VgR) play important roles in insect reproduction. As the precursor of vitellin (Vn), Vg provides essential nutrition for embryonic development, and VgR mediates the uptake of Vg by oocytes. In this context, we cloned and characterized these two genes of S. frugiperda (SfVg and SfVgR) and evaluated their expression profiles in different developmental stages and tissues. The RNA interference experiment was used to investigate their function in vitellogenesis. The ORF values of SfVg and SfVgR were 5250 and 5445 bp, encoding 1749 and 1815 amino acid residues, respectively. The qRT-PCR results revealed that both SfVg and SfVgR were highly expressed in female adults; SfVg was specifically expressed in the fat body, whereas SfVgR was highly expressed in the ovary. In addition, the depletion of either SfVg or SfVgR hindered oocyte maturation and ovarian development, leading to a significant decrease in fecundity. The present study reveals the importance of SfVg and SfVgR in the vitellogenesis of S. frugiperda, laying a theoretical foundation for the development of pollution-free pest control strategies with SfVg and SfVgR as new targets.

Reference Genes for Expression Analyses by qRT-PCR in Phthorimaea operculella (Lepidoptera: Gelechiidae)

Due to a lack of effective internal references, studies on functional genes in Phthorimaea operculella, a serious Lepidopteran pest attacking potatoes worldwide, have been greatly limited. To select suitable endogenous controls, ten housekeeping genes of actin (ACT), α-tubulin (α-TUB), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), elongation factor 1α (EF1α), 18S and 28S ribosomal RNA (18S, 28S), ribosomal protein genes RPL4, RPL13 and RPL27 and superoxide dismutase (SOD) were tested. Their expression levels were determined under three different experimental conditions (developmental stages, tissues/organs and temperatures) using qRT-PCR technology. The stability was evaluated with five methods (Ct value, geNorm, NormFinder, BestKeeper and RefFinder). The results clarified that RPL13, EF1α and RPL27 are ranked as the best reference gene combination for measuring gene expression levels among different developing stages and under various temperatures; EF1α and RPL13 are recommended to normalize the gene expression levels among diverse tissues. EF1α and RPL13 are the best reference genes in all the experimental conditions. To validate the utility of the selected reference pair, EF1α and RPL13, we estimated the tissue-biased expression level of chitin synthase A gene (PoChSA). As expected, PoChSA was abundantly expressed in ectodermally derived epidermal cells, and lowly transcribed in the midgut. These findings will lay the foundation for future research on the molecular physiology and biochemistry of P. operculella.