Progress and Prospects of Association Mapping in Sugarcane ( Saccharum Species Hybrid), a Complex Polyploid Crop

Sugarcane is one of the most important economic crops and contributes more than 80% of the sugar globally. Developing superior sugarcane varieties is a long-term process due to polyploidy, high chromosome numbers, large complex genome size and also many other practical constraints like long breeding cycle, etc. The recent advancements in molecular markers, next-gen sequencing tools and development of robust statistical models have the potential to lead to affordable genomics-assisted breeding in sugarcane. In order to identify genes linked to trait(s) of interest, association mapping has good prospects as a feasible approach in sugarcane. Association mapping (AM) is a recent technique that identifies quantitative trait loci (QTLs) by investigating marker–trait associations that arise due to the linkage disequilibrium between the genotypic polymorphic loci and the phenotypic variation in a diverse panel of genotypes. In last decade, the understanding of association mapping has increased significantly, due to which focussed efforts are now been made in developing association mapping population, genome-wide association studies and detection of QTLs for several important traits in sugarcane. In contrast to linkage mapping, detecting QTLs through AM approach in sugarcane has certain advantages as historical phenotypic data could be used and there is no need to artificially develop a structured segregating population. The last few years have witnessed a more concerted effort in AM studies in sugarcane where a range of marker tools like SSRs, DArT, GBS, targeted sequence enrichment, etc. were exploited to find out QTLs linked to traits of economic importance. In this review, the recent developments in the area of association mapping in sugarcane and the various methodologies and statistical tools that are being adopted have been discussed.