Unraveling the sugarcane genome: Progress made so far and challenges ahead

Abstract

Sugarcane (Saccharum spp.) is a major crop grown for sugar and biofuel in tropical and subtropical regions around the world. Sugarcane has a high level of polyploidy, large and complex genome. There is a constant increase in demand of sugarcane worldwide, to meet this demand there is a need in improving the sugar- cane yield, sucrose content, increasing growth rate, abiotic and biotic stress toler- ance, etc. Researchers have been using conventional breeding efficiently to improve the sugarcane for many years. Present situation demands the improvement in sugar- cane varieties at faster rate than which the conventional breeding technique can provide. It is possible to achieve faster improvement only when researchers under- stand the genome of the plant. Genetics and genome studies have given a better path to develop better varieties. Understanding of sugarcane genome can help breeders to support the conventional breeding in selecting the parents and traits needed. In spite of the complexity, sugarcane genome is been successfully studied and in recent past good progress have been made by genome sequencing strategy, i.e., bacterial artificial chromosome (BAC) libraries. Study on genetic diversity among the spe- cies of sugarcane was carried out by RFLP, AFLP, RAPD, SRAP, TRAP and so on. In late 1990s fluorescent in situ hybridization (FISH) technique was used to physi- cally map two S. officinarum and three S. robustum clones. Later using molecular cytogenetic technique of FISH, many other clones were studied. Quantitative trait loci (QTLs) have been used to screen variety with sugar content, sugar yield, dis- ease resistance, etc. Researchers in Brazil have developed SUCEST database which consist of over 230,000 Expressed Sequence Tags (ESTs) which can be used for detection of molecular polymorphisms, gene expression profiles and gene discov- ery. In this chapter we discuss about the progress made so far and challenges faced during the study of sugarcane genome.