Rice

Molecular biology of Rice tungro viruses: Although Rice tungro viruses were studied extensively in India from mid-1960s, there was little information available on their genomic features. Our work brought out for the first time important differences between Rice tungro bacilliform virus (RTBV) isolates from various geographical regions of our country (Joshi and Dasgupta, 2001). We also devised PCR-RFLP to distinguish between various isolates of RTBV (Joshi et al., 2003) and extended the study to look at infectivity and symptom production in various rice varieties by the tungro viral isolates (Niazi et al., 2005). We showed by sequence analysis of RTBV isolates from Andhra Pradesh and West Bengal that they, while retaining high identities with each other, were significantly different from those from south-east Asian countries (Nath et al., 2002). Interestingly, remarkable sequence conservation was found in the Rice tungro spherical virus (RTSV) isolates collected in India and the Southeast Asian countries, both in the nucleotide and in the coat protein sequences (Verma and Dasgupta, 2007a, b). In RTBV, additional sequence information generated on an isolate from Tamil Nadu, suggested it to be a product of recombination (Sharma et al., 2011) and sequence information on an isolate from Punjab reaffirmed the sequence conservation in RTBV isolates within the country (Mathur and Dasgupta, 2013). We also devised a SYBR Green – based method to accurately estimate the RTBV and RTSV titers (Sharma and Dasgupta, 2012).

Rice transformation: Considering the primary importance of rice as a food source for the growing population in the Asian countries, we have developed tools for the efficient gene transfer and transformation of four popular rice varieties, widely cultivated in India (Tyagi et al., 2007; Baskaran and Dasgupta, 2012).

Transgenic resistance against the tungro viruses: Using the principles of RNA interference, we demonstrated resistance against Rice tungro bacilliform virus (RTBV) in transgenic rice plants (Tyagi et al., 2008). We also showed RTBV resistance in plants expressing the RTBV coat protein (Ganesan et al., 2009). Rice plants expressing the RNA of Rice tungro spherical virus (RTSV) showed resistance against RTSV and low transmission of the tungro virus complex (Verma et al., 2012). The RNAi RTBV transgenics were used as parents to diversify the resistance to five popular rice varieties (Roy et al., 2012; Jyothsna et al., 2013; Valarmathi et al., 2016), where the resistance was retained, there by adding agronomic value to the varieties.

The prime concern for the tungro resistance in plants is whether the engineered resistance developed is against either of the virus (RTBV or RTSV) or both. The resistance against any one of the virus may render the plant in threat from the other virus. Hence, the strategy for simultaneous targeting of RTBV and RTSV appears to be promising for effective and durable tungro resistance. In this context, we designed ihpRNA constructs containing sequences from both RTBV and RTSV for simultaneous targeting of both viruses and achieved significant resistance against both the viruses as indicated by the low virus levels and less symptoms compared to the control (Sharma et al., 2018). We are the first to do the simultaneous targeting of two unrelated viruses, which together cause tungro disease, using a single construct as the transgene. The diversification of RNA interference-based transgenic resistance in popular rice lines against RTBV has been described by Valarmathi et al., 2016; Kumar et al., 2019.

Virus induced gene silencing for rice: We published a review on the phenomenon of Virus induced gene silencing, which is an emerging technique for plant gene silencing (Purkayastha and Dasgupta, 2009). Subsequently, we have modified an isolate of Rice tungro bacilliform virus (RTBV) from West Bengal so that it can be used to silence any rice gene upon agroinoculation (Purkayastha et al., 2010). Subsequently, we have worked out a detailed protocol for the gene silencing process (Purkayastha et al., 2013) and demonstrated the role of physical conditions and the orientation of the insert for the silencing process (Kant and Dasgupta, 2017). The commercial implications of this have been recognized and an Indian patent has been awarded to this discovery (Indian patent no. 278167). We have published a review on VIGS in monocots (Kant and Dasgupta, 2019).