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Sugarcane is the world’s most widely grown sugar crop accounts for almost 75% of world sugar production. Diseases are the major productivity constraints for sugarcane that considerably reduce yield and sugar recovery. Identification of disease resistance is an important and sustainable approach for disease management. More recently, Brazilian researchers have characterized the whole genome sequences of a commercial sugarcane cv SP80-3280 and mapped 373,869 genes or ninety nine percent of the total genome. Use of next- generation sequencing (NGS) techniques have facilitated the availability of complete genomic information of various sugarcane pathogens, have led to the understanding of organization of the disease resistance gene clusters for unraveling the genetic mechanism involved in developing new resistance strategies to manage sugarcane diseases. Genome wide association study (GWAS) reveal polymorphisms related with composite characters in the whole genome. In the omics era, whole genome sequencing of host and pathogens combined with the availability of bioinformatics tools for their analyses led to the emergence of GWAS, a potent method for identifying genomics region covering resistance loci in various plants. This review summarizes the literature generated during last the 10 years on GWAS in sugarcane related to disease resistance and along with novel single nucleotide polymorphism and quantitative trait loci’s hotspots identified for economically important diseases of sugarcane.

Dragon fruit (Hylocereus spp.) is an important fruit crop for its high nutrition and profitability grown in India and many other countries. Dragon fruit stem samples exhibiting chlorosis and mottling symptoms, collected from Sangareddy district of Telangana, India revealed a flexuous rod-shaped virus with a length of ~ 600 nm in electron microscopic examination. The RT-PCR based detection of Cactus virus X using specific primers resulted in the production of ~ 900 bp amplicons covering the full length triple gene block protein 3 and coat protein regions. Further, cloning and sequence information of the ~ 900 bp amplicon revealed the presence of Cactus virus X (CVX) in dragon fruit. To our knowledge, this is the first record of CVX causing particular disease in dragon fruit from India.

Among 10 proteins encoded by Papaya ringspot virus (PRSV), only coat protein (CP) has been studied extensively from mainly the papaya-originated isolates i.e. PRSV-P. In this study, besides CP, the helper component proteinase (HC-pro) and nuclear inclusion protein-a (NIa-pro) coding regions from 19 PRSV-P and -W isolates originating from different geo-climatic locations and hosts were analyzed. Unlike CP, both HC-pro and NIa-pro did not reveal the variability in their length. HC-pro and NIa-pro sequences revealed less than 10% deduced amino acid (daa) diversity worldwide, the CP was found highly variable (up to 20% daa diversity). Highest variability in CP sequence was noticed among the cucurbit-originating PRSV-P Indian isolates, especially from Warm semi-arid climate, which was attributed to a large number of aa insertions/deletions. However, papaya-originating PRSV-P isolates from the Oceanic climate were less variable (up to 5% daa diversity). In NIa-pro, besides already known host/pathotype-specific switching of aa Lys/Asp27, switching of Lys27 → Arg27 and Asp27 → Glu27 was identified within P and W pathotypes. Additionally, a novel aa switching from Ser/Met134 → Thr134 between P and W pathotypes respectively was identified. The phylogeny of PRSV isolates was largely based on the geo-climatic locations and hosts. Through recombination detection analysis, three recombinant isolates were detected based on both NIa-pro and CP sequences, which possessed cucurbit-originated PRSV (either -P or -W) isolates as one of their parents (either major or minor.) Patterns of codon usage among the three protein coding sequences generated further revealed that the CP gene is under maximum selection pressure (with six sites) followed by NIa-pro gene (with one site). This investigation shows that the genetic recombination between the isolates originating from different hosts and geo-climatic locations as well as mutations are the significant mechanisms playing their role in generating diverse populations of PRSV.