Chapter 8 - Molecular Characterization of Sugarcane Viruses and Their Diagnostics

Abstract

Sugarcane (Saccharum spp. hybrid) is an important field crop grown for sugar and biofuel in more than 110 countries in the world under varied agroclimatic conditions. Viral diseases, namely, mosaic caused by sugarcane mosaic virus, sugarcane streak mosaic virus (SCSMV), and sorghum mosaic virus in different countries; leaf fleck by sugarcane bacilliform virus; and yellow leaf disease by sugarcane yellow leaf virus, are the important diseases reported across the sugarcane-growing regions. Vegetative propagation favors transmission of these diseases through planting materials and subsequent generations. Increasing titer of virus(es) in the canes adversely affects cane growth, leading to varietal degeneration in popular varieties and thereby severe losses to sugarcane cultivation. With the advancements in molecular diagnosis, impact caused by these viruses has been clearly established in the recent years. Several molecular diagnostics right from PCR to qRT-PCR are being widely used to detect the viruses; further, all the viruses have been characterized up to complete genome level. The complete genome analyses revealed the existence of genomic variation within the population of the same virus even in the same geographic region indicating occurrence of new strains. SCSMV earlier described as unassigned member of Potyviridae was characterized as a new genus, “Susmovirus,” and the same was renamed as Poacevirus in the family based on its distinct sequence variation to the existing genera. In case of other viruses, new virus species, genotypes, and strains of the viruses were reported. New recombinants were reported based on its nucleotide and amino acid sequence variations. Under Indian context, all the viruses were characterized based on complete genomes, and existing variability among the viruses has been brought out. Characterization of the viruses led to developing molecular tools especially PCR and qRT-PCR assays and developing recombinant antisera for the viruses and duplex/multiplex RT-PCR assays for different viruses. These assays have helped in the production of healthy planting materials through tissue culture techniques. Now, it is established that tissue-culture-derived planting materials free from the viruses exhibit varietal vigor and the viral diseases can be efficiently managed by this approach. Further, works are required to develop sensitive diagnostics for field level diagnosis of the viruses to address the problems in the field and seed selection at the farmer's holdings.