The quest for the best target genes for RNAi-mediated pest control

Silencing PsASH2 affects embryo development in the cotton mealybug

Mealybugs are highly aggressive pests that infest various plants and cause substantial economic losses. Histone lysine methyltransferases (KMT) are evolutionarily conserved and proposed to be essential in early embryo development in animals. However, few KMTs have been reported in mealybugs. Here, we identified a novel KMT gene, PsASH2, in the cotton mealybug, Phenacoccus solenopsis Tinsley. This gene was highly expressed in the ovary of female adults. Through RNA interference (RNAi) of PsASH2 by dsRNA microinjection, we found a reduction in the number of male embryos and total embryos in the ovaries of pregnant females. Continuous downregulation of PsASH2 in mated females until their death resulted in few changes in sex ratio but significant decreases in the number of both male and female offspring. Therefore, we believe that PsASH2 plays essential roles in embryo survival for both sexes of the cotton mealybug which may provide a potential target gene for the management of cotton mealybug by disrupting embryo development.

Stage-specific transcriptomic analysis reveals insights into the development, reproduction and biological function of allergens in the European house dust mite Dermatophagoides pteronyssinus

BACKGROUND

House dust mites (HDMs) such as Dermatophagoides pteronyssinus are major allergy elicitors worldwide, yet their gene expression across developmental stages remains underexplored. Herein, we report a comprehensive RNAseq analysis of larvae, nymphs, and adult males and females, mapped to a recently published high-quality genome with extended functional annotations.

RESULTS

Analysis of differentially expressed genes (DEG) revealed that female-biased expression was the most prevalent profile (16% of genes), while males exhibited the highest fold-change differences. DEG data, combined with network clustering and functional enrichment analysis, highlighted distinct genes and biological processes for each stage and sex: females showed upregulation of genes related to cell division and oogenesis, with vitellogenins among the most abundant transcripts; males exhibited increased expression of genes encoding putative seminal fluid proteins (e.g. endopeptidases, serpins, antimicrobial peptides), and those involved in reproductive regulation (e.g. testis-specific serine kinases); while juveniles displayed enhanced expression of genes related to energy metabolism and growth. Further analysis of endocrine pathways revealed non-canonic mechanisms compared to insect models, particularly in ecdysteroid and sesquiterpenoid biosynthesis and regulation. Expression patterns in genes involved in cuticle formation were also identified, reflecting their role in developmental transitions and sexual differentiation. Allergen and allergen-related gene expression showed an overall increase in feeding juveniles, as well as sex-biased expression, with Der p 27 upregulated in females. These findings provide insight into the physiological roles of allergens in digestion, immunity, and muscle formation, among other functions. Additionally, seven new horizontally transferred genes, including a DNA-repair photolyase linked to females, and novel multigene families (e.g. 119 male-specific beta-propeller proteins, 70 hypothetical cuticular proteins, 23 tetraspanin-like proteins, 5 female-associated putative odorant-binding proteins) were identified.

CONCLUSIONS

This study provides the first genome-wide transcriptomic analysis of a HDM across life stages and sexes, expanding our understanding of the molecular mechanisms underlying mite development, sexual reproduction, and allergen expression. The generated data, fully available via supplementary spreadsheet and the ORCAE online platform, provide a valuable foundation for future allergy research and the development of new mite control strategies.

Spray-Induced Gene Silencing for Postharvest Protection: dsRNA Stability and Insecticidal Efficacy

Sprayable double-stranded RNA (dsRNA) pesticides, based on RNA interference (RNAi), have shown promise in preharvest crop protection, yet their use for postharvest grain storage remains underexplored. In this study, we evaluated the efficacy and stability of sprayable dsRNA in protecting stored rice grains from the lesser grain borer (Rhyzopertha dominica). Results showed significant insecticidal activity, with 72% mortality observed after ingestion of grains stored for 60 days post-treatment, compared to 90% mortality in freshly treated grains. To assess dsRNA persistence, we developed a sensitive detection method for low-input samples. Approximately 73% of the initial dsRNA remained detectable after 60 days of storage, with increased absorption into the rice hull over time. These findings demonstrate the durability and effectiveness of sprayable dsRNA in stored grain protection and underscore its potential as a sustainable alternative to chemical pesticides for postharvest pest management.

Comparative transcriptome analysis provides a glance into the regulation of the Krüppel homolog 1 on the reproduction and diapause of the predatory ladybeetle, Coccinella septempunctata

As a typical natural predator of agricultural pests, the lady beetle, Coccinella septempunctata, has been commercially mass-reared and widely employed in in pest management. The lady beetles can enter a long-term reproductive diapause phase in response to short photoperiods and low temperatures, for maintaining population during the overwintering process. Insect diapause is a physiological adaptative strategy that is characterized by a cessation of ovarian development, lipid accumulation and extended lifespan. Diapause regulating improve the long-term storage of C. septempunctata and release of natural enemies at the right time. In our previous research, as a main output of the juvenile hormone pathway, Krüppel homolog 1 (Kr-h1) was a key component of reproduction and diapause in C. septempunctata. However, the molecular mechanisms underlying the regulation of C. septempunctata reproduction and diapause by Kr-h1 transcription factor remains unknown. In this study, we utilized RNA-Sequencing to investigate the transcriptomic changes in C. septempunctata following RNA interference targeting the Kr-h1 gene. DEGs analysis revealed significant transcriptional alterations between the Kr-h1 knockdown group and the control group. Noteworthy findings include the downregulation of three genes related to reproduction (follicle cell protein,vitelline membrane protein, and vitellogenin) in the dsKr-h1 group, while genes involved in lipid metabolism, such as lipase and fatty acid synthase, were upregulated. These results suggested that Kr-h1 plays a critical role in the regulation of both reproductive processes and lipid metabolism in C. septempunctata. Our findings provided valuable insights into the molecular mechanisms regulating reproduction and diapause in C. septempunctata and contributed to the expanding understanding of the role of CsKr-h1 in insect physiology.

dsRNAEngineer: a web-based tool of comprehensive dsRNA design for pest control

Over the past two decades, many double-stranded (ds)-RNAs have been synthesized to silence target genes for exploration of gene functions in pests. Some of these dsRNAs are lethal to pests, leading to a new category of pesticides. The generation of these environmentally friendly pesticides requires precise in silico design of dsRNA molecules that target pests but not non-pest organisms. Current efforts in dsRNA design focus mainly on the analysis of the target gene sequence, lacking comprehensive analysis of all transcripts of the whole transcriptome per given species, causing low efficiency and imprecise dsRNA target exploration. To address these limitations, we created the dsRNAEngineer online platform (https://dsrna-engineer.cn), which allows comprehensive and rational dsRNA design, incorporating hundreds of pest and non-pest transcriptomes. Developed functionalities include screen-target (screen conserved genes for cotargets of various pest species), on-target, off-target, and multi-target to generate optimal dsRNA for precise pest control.

Coat protein I genes are essential for the morphogenesis of the intestinal tract in Locusta migratoria

The coat protein I (COPI) complex is crucial in several significant physiological processes in eukaryotes. The assembly of COPI vesicles is initiated by the recruitment of adenosine diphosphate-ribosylation factor 1 (Arf1) to the membrane. Previous studies have primarily focused on the roles of COPI in yeast, humans, insects, and beyond Drosophila. However, the function of COPI during the development of insects remains largely unknown. In this study, we first identified eight COPI assembly genes, including α-, β-, β'-, γ-, δ-, ε-, ζ-COPI, and Arf1 in Locusta migratoria. Quantitative reverse-transcription polymerase chain reaction revealed that these genes were uniformly expressed in multiple tissues, including wing pads, leg, foregut, midgut, hindgut, and gastric cecum, and on all developmental days in 5th-instar nymphs. The injection of double-stranded RNAs (dsRNAs) against LmCOPI and LmArf1 induced high silencing efficiency in the 3rd- and 5th-instar nymphs. Locusts treated with dsLmCOPIs and dsLmArf1 exhibited feeding cessation, leading to 100 % mortality. LmCOPIs and LmArf1 knockdown resulted in midgut and gastric cecum atrophy. Histological observation and hematoxylin-eosin staining indicated that the midgut and gastric cecum exhibited deformed structures, with defective microvilli and midgut peritrophic matrix. These results suggest that LmCOPIs and LmArf1 significantly affect the intestinal tract morphogenesis in locust nymphs. Thus, COPI assembly genes are promising RNA interference targets for managing L. migratoria, reducing the dependence on chemical pesticides for pest control.

Superior target genes and pathways for RNAi-mediated pest control revealed by genome-wide analysis in the beetle Tribolium castaneum

BACKGROUND

An increasing human population, the emergence of resistances against pesticides and their potential impact on the environment call for the development of new eco-friendly pest control strategies. RNA interference (RNAi)-based pesticides have emerged as a new option with the first products entering the market. Essentially, double-stranded RNAs targeting essential genes of pests are either expressed in the plants or sprayed on their surface. Upon feeding, pests mount an RNAi response and die. However, it has remained unclear whether RNAi-based insecticides should target the same pathways as classic pesticides or whether the different mode-of-action would favor other processes. Moreover, there is no consensus on the best genes to be targeted.

RESULTS

We performed a genome-wide screen in the red flour beetle to identify 905 RNAi target genes. Based on a validation screen and clustering, we identified the 192 most effective target genes in that species. The transfer to oral application in other beetle pests revealed a list of 34 superior target genes, which are an excellent starting point for application in other pests. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analyses of our genome-wide dataset revealed that genes with high efficacy belonged mainly to basic cellular processes such as gene expression and protein homeostasis - processes not targeted by classic insecticides.

CONCLUSION

Our work revealed the best target genes and target processes for RNAi-based pest control and we propose a procedure to transfer our short list of superior target genes to other pests. © 2024 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.