Genome-wide identification and characterization of major RNAi genes highlighting their regulatory factors in Cowpea (Vigna unguiculata (L.) Walp.)

In different regions of the world, cowpea (Vigna unguiculata (L.) Walp.) is an important vegetable and an excellent source of protein. It lessens the malnutrition of the underprivileged in developing nations and has some positive effects on health, such as a reduction in the prevalence of cancer and cardiovascular disease. However, occasionally, certain biotic and abiotic stresses caused a sharp fall in cowpea yield. Currently, short RNAs (sRNAs) are thought to play a crucial role in controlling how stress-related genes are expressed in plants as they go through various developmental phases. Major RNA interference (RNAi) genes like Dicer-like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) are essential for sRNA synthesis processes and shield plants from biotic and abiotic stresses. In this study, applying BLASTP search and phylogenetic tree analysis with reference to the Arabidopsis RNAi (AtRNAi) genes, we discovered 28 VuRNAi genes, including 7 VuDCL, 14 VuAGO, and 7 VuRDR genes in cowpea. We looked at the domains, motifs, gene structures, chromosomal locations, sub-cellular locations, gene ontology (GO) terms and regulatory factors (transcription factors, micro-RNAs, and cis-acting factors) to characterize the VuRNAi genes and proteins in cowpea. Predicted VuDCL1, VuDCL2(a, b), VuAGO7, VuAGO10 and VuRDR6 genes might have an impact on cowpea growth, development of the vegetative and flowering stages and antiviral defense. The VuRNAi gene regulatory features miR395 and miR396 might contribute to grain quality improvement, immunity boosting, and pathogen infection resistance under salinity and drought conditions. Predicted cis-acting elements (CAEs) from the VuRNAi gene associated with light responsiveness (LR), stress responsiveness (SR) and hormone responsiveness (HR) might play a role in plant growth and development, improving grain quality and production and protecting plants from biotic and abiotic stresses. Therefore, our study provides crucial information about the functional roles of VuRNAi genes and their regulatory components, which would aid in the development of future cowpeas that are more resilient to biotic and abiotic stress.