Integration of sucrose accumulation processes across hierarchical scales: towards developing an understanding of the gene-to-crop continuum

Although we have a working knowledge of the general biology of sugarcane and are fairly efficient in crop production, we are only beginning to produce the detailed biochemical and genetic information that will be needed to develop technologies necessary for long-term success of the sugarcane industry. A true understanding of sucrose accumulation will be achieved only through a combination of experimental and computational analyses of comprehensive datasets to gain information on the underlying molecules and processes. Currently, systems-level approaches towards understanding biology are gaining momentum primarily because of the tremendous increases in computing power, advances in information sciences and rapid progress being made in molecular biology to facilitate data management, analyses and modeling from high-throughput genome sequencing and proteomics. Large-scale sequencing projects have not only provided complete sequence information for a number of genomes, but they are also producing integrated pathway-genome databases and models that provide organism-specific connectivity maps of metabolic and, to a lesser extent, other cellular networks. To date, the processes that generate mass, energy, information transfer and cell-fate specification have been analyzed only at the cell or microorganism levels, where they are shown to be seamlessly integrated through a complex network of cellular constituents and reactions. Despite the key role of these networks in sustaining cellular functions, their large-scale structure is essentially unknown. Fifty years of sugarcane research have identified and characterized a suite of physiological processes and enzymes involved in sucrose accumulation. More recently, genes encoding these enzymes have been isolated, cloned and used in experiments to transform sugarcane to increase or decrease expression of the enzyme with the goal of altering sucrose accumulation. However, results of this reductionist approach towards understanding sucrose accumulation have fallen short of expectations, apparently because of the complex interactions among the multitude of simultaneous processes. Recent rapid expansion of sugarcane molecular datasets and the beginning of a systems approach to metabolic modeling of sucrose accumulation point the way for future research efforts to integrate processes from gene to crop performance.