Structural genomics and genome sequencing

Sugarcane exemplifies many challenges associated with genetic and genomic analysis of angiosperms, being a recently formed autopolyploid with a large genome, and with its most economically important forms being aneuploid interspecific hybrids. Despite nearly two decades of vigorous activity, current genetic maps remain “incomplete” (with some chromosomes/segments lacking informative sequence-tagged polymorphism) and physical mapping tools are of insufficient depth to cover each allele in any one genotype. Nonetheless, considerable advances have been made by reduced-representation sequencing of cDNA and repetitive DNA. The virtually-complete sequencing of a close relative (sorghum) provides a valuable framework for deducing the probable arrangement of much of the sugarcane genome. Refined sequencing strategies and rapidly dropping costs enhance the likelihood that one or more sugarcane genomes will be sequenced in the near future, and the worldwide sugarcane community continues to discuss various possible sequencing strategies involving different cost levels, different genotypes, and with different expected outcomes. A major contribution is expected from sugarcane genomics regarding the understanding of allelic variation and expression profile in such a complex genomic context. A singular opportunity in the postgenomic era for sugarcane will be to reveal the early events in the adaptation of a genome to the duplicated (polyploid) state, and how this adaptation might relate to productivity of biomass and specific metabolites such as sucrose.