Cutting-edge technologies for detection of plant viruses in vegetatively propagated crop plants

Abstract

Plant virus diseases cause enormous loss which is estimated to be US$60 billion in crop yields worldwide each year. Seed is a propagating material in most of the crop plants, whereas most of the horticultural crops are vegetatively propagated. Horticultural crops like banana, bamboo, citrus, and grapes; commercial crops like sugarcane, black pepper, cardamom, orchids, and bulbous ornamentals; and tuber crops like potato, cassava, yam, etc., have been known to be infected by a range of viruses that belong to different genera and families. In these crops, the primary mode of transmission of viruses is through the use of infected plant propagule like corms, tubers, cutting, grafts, etc. An effective virus management strategy requires an accurate, rapid, and sensitive diagnosis for which understanding the disease cycle of etiological agents and its molecular nature, genome sequence and structure, coat protein information and sequences, etc. should be known in advance to design a detection strategy. Enzyme-linked immunosorbent assay (ELISA) or polymerase chain reaction (PCR) has been widely used for detection of plant viruses. These methods are time-consuming and laborious and require special skills such as in prior information on taxonomy to detect the pathogen responsible for the disease. On-site or point-of-care methods of detection are not new but limited to clinical use for human diseases. But recently this lateral flow devices (LFDs) are being made available for a number of viruses infecting plants. However, the widespread usage of this technology is delayed probably due to its limitation on robustness and lack of high-throughput nature. In this chapter, we have reviewed the recent developments on the early diagnosis using cutting-edge technologies like on-the-spot diagnostic tool lateral flow immunoassay (LFIA), loop-mediated isothermal amplification (LAMP), and multiplex technologies like microarray, microsphere immunoassay, etc. LAMP method is highly specific and requires less time to complete the indexing; however, this technique is yet to replace ELISA and PCR completely in agriculture possibly due to its specificity and viral variants that might escape from detection, and other possible reasons may be that the researchers and policy makers have not yet been convinced. Recent technologies such as rolling circle amplification which is dependent on a circular DNA genome and random hexamers do not require sequence data of the target, and similarly the next-generation sequencing also does not require a priori knowledge on the sequence of the causal agents. Principles and application of these cutting-edge technologies are reviewed in this chapter. The objective of the present chapter is not to cover all the details of diagnostics but to highlight the current status of various cutting-edge diagnostic techniques that can be applied for the biosecurity, by the quarantine departments, international exchange of germplasm, and on-site field detection by farmers, and use in the certification programs.