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

Abstract

Sugarcane is the world’s most widely grown sugar crop and accounts for almost 75% of world sugar production. Diseases are the major productivity constraints for sugarcane that considerably reduce cane yield and sugar recovery and identification of resistance is the important and sustainable approach to manage the diseases. More recently, research group headed by Brazilian researchers have characterized the whole genome sequences of a commercial sugarcane cv SP 80-3280 and mapped 3,73,869 genes or ninety nine percent of the total genome. Similarly, revolutionary changes in genomics, approaches through recent NGS techniques combined with availability of complete genomes of various sugarcane pathogens available to date viz., Colletotrichum falcatum, Sporisorium scitamineum, Xanthomonas albilineans, Leifsonia xyli subsp. xyli, Sugarcane mosaic virus, etc have provided new avenues for the understanding organization of disease resistance gene clusters and their genetic mechanism involved in development of new resistance strategies for the management of sugarcane diseases. Genome wide association study (GWAS), which studies the whole genome for polymorphisms related with composite characters. In the omics era, whole genome sequencing of host and pathogens combined with evolution of different statistical methods for their analyses led to the emergence of GWAS, a potent method for pinpoint genomics region having usual difference of resistant loci in various plants. This review summarizes the literature available from last two decades on genome wide association studies in sugarcane with respect to disease resistance and also deals with novel single nucleotide polymorphism and quantitative trait loci’s hot spots identified for economically important diseases of sugarcane