Multiply Primed Rolling Circle Amplification (MPRCA) of Yellow mosaic virus genome from infected soybean in central Indian region divulges it as Mungbean yellow mosaic Indian virus-[sb] and its implications for RNAi mediated virus resistance

Abstract

Genome characterization of the yellow mosaic disease wreaking damage on soybean in Indore-a focal point of soybean cultivation and processing in India- employing Multiply Primed Rolling Circle Amplification (MPRCA) resulted in amplification of complete genomic components of the virus. RCA, when coupled with restriction enzyme digestion investigation, revealed two components each of ~2.7 Kb unit length of genomic components of the virus. The study further revealed the absence of β- satellite DNA genomic component of the virus. The RCA derived partial genomic region on further restriction enzyme digestion investigation revealed that Mungbean yellow mosaic Indian virus (MYMIV) is the species of begomovirus causing damage on soybean in the central Indian region, Indore. The RCA together with restriction enzyme digestion has wider implications for obtaining RNAi mediated viral gene silencing via complete genome sequence characterization to identify conserved genomic regions along with the discovery of ORFs encoding for Viral Derived Suppressor Proteins (VSPs). The potent siRNA inducing regions identified, employing web based siRNA design algorithms, revealed plausible small RNA effectors to obtain RNAi based, broad spectrum resistance against begomovirus infection and trait stable transgenics in soybean. In addition, the RCA products followed by partial digestion and cloning in binary vector offers a prospect to develop MYMIV based virus induced knock-out vectors with a potential implication for functional genomics study on soybean.