Genome wide association studies in sugarcane host pathogen system for disease resistance: an update on the current status of research

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.