ABSTRACT
Sugarcane (Saccharum spp. hybrid) is the major sugar and bioenergy crop grown throughout tropical and subtropical environments. In sugarcane, vegetative propagation, long breeding cycle, and complex polyploidy genome of the crop are the major bottlenecks in successful crop cultivation and development of new varieties. Fortunately, variability generated through hybridization in the F1 generation can be maintained through vegetative propagation in sugarcane for generations in the field. However, the vegetative cuttings (setts) used for planting also harbour most of the serious pathogens affecting sugarcane crop in the field, except fungi-causing foliar diseases. Hence, various diseases caused by fungi, bacteria, viruses, and phytoplasmas severely affect sugarcane productivity across the globe. No country is free from the ill effects of diseases in sugarcane. Under the Indian scenario, Colletotrichum falcatum causing red rot of stalks is the major disease affecting crop production and field life of the varieties. Hence, detailed studies were initiated to understand the basis of red rot resistance. Initially, phytoalexins and pathogenesis-related proteins involved in red rot resistance were identified and characterized, and later, molecular tools were employed to understand host resistance and identify putative resistant and susceptibility-related genes. C. falcatum genome and transcriptomes were characterized, and that led to identifying pathogenicity gene homologs/ proteins and candidate genes for fungicidal targets through a functional analysis approach. Similarly, interaction of smut pathogen Sporisorium scitamineum with sugarcane has been established using various omic tools. A clear understanding on the pathogen identity and variation has been brought out on Fusarium spp, causing wilt and pokkah boeng diseases in different countries. Likewise, bacterial pathogens and Puccinia spp associated with two rusts were characterized based on complete genomes. Application of genomics has helped characterize the viruses infecting sugarcane and viral genotypes/strains in different countries. Further, metagenomic applications discovered new viruses and strengthened quarantine procedures in sugarcane. Recently, complete genome of sugarcane grassy-shoot phytoplasma has been characterized from India. Pathogenomics have facilitated in developing accurate diagnostics against major sugarcane pathogens, and the diagnostics are applied in healthy seed production, disease monitoring, and quarantine in different countries. Overall, application of omics platform has been encouraging in sugarcane pathology, especially to understand host resistance and pathogen biology.
