Molecular characterization of vitellogenin and its receptor with CRISPR-based sgRNA validation in the legume pod borer, Maruca vitrata (Geyer) (Lepidoptera: Crambidae)

Abstract Maruca vitrata , the legume pod borer, causes yield losses of up to 80% in grain legumes. Increasing insecticide resistance and environmental concerns necessitate sustainable pest management alternatives. In the present study, the complete vitellogenin (Vg) coding sequence (CDS), a key reproductive gene involved in oogenesis and embryonic development, was cloned and molecularly characterised from M. vitrata . The assembled Vg CDS (∼5.3 kb) shared 99.04% sequence identity with the reported M. vitrata Vg sequence (MG799570.1). Phylogenetic analysis demonstrated close evolutionary association with related Lepidopteran species, while protein domain analysis identified three conserved domains, namely LPD_N, DUF1943, and VWD. Among these, the single exon-encoded LPD_N domain was selected as the target region for CRISPR/Cas9-mediated editing. Homology models of Vg and vitellogenin receptor (VgR) (Global Model Quality Estimation (GMQE): 0.58 and 0.51) showed a favourable interaction by protein–protein docking (score: −295.66). Three single-guide RNAs (sgRNAs) were designed, synthesised through in-vitro transcription, and evaluated using in vitro cleavage assays. sgRNA1 targeting the LPD_N domain and sgRNA2 targeting the signal peptide region exhibited efficient site-specific cleavage activity, whereas sgRNA3 failed to induce cleavage because of an unfavourable secondary structure that likely impaired Cas9-sgRNA complex formation. Overall, this study provides the first CRISPR-oriented functional characterisation and sgRNA validation of the M. vitrata Vg gene, together with structural characterisation of VgR and Vg-VgR interaction analysis, providing preliminary molecular resources for future CRISPR/Cas9 studies and supporting future embryo microinjection and heritable genome editing for sustainable management of M. vitrata .