Carbohydrate research is increasingly focused on changing the biochemical nature of starch to create more efficient substrates for biofuel production, healthier foods for human consumption and more efficient livestock feed. A key factor in these processes is the rate at which starch is digested by amylases. Starch digestibility is influenced heavily by genetically controlled factors including starch granular and molecular structure and composition. We have begun to characterize genes involved in controlling formation of protein-lined channels connecting the starch granule surface to the central cavity of the granule where digestion is initiated. In addition to starch biosynthetic proteins, these channels contain actin and tubulin, suggesting they are formed by invaginations of the amyloplast created by cytoskeletal elements as the amyloplast expands during starch granule formation. Characterizing the differences between B73 and Mo17 in relative degree of channelization using the IBM population suggests two major loci, on Chromosomes 2 and 3, and a number of minor loci that contribute to channelization. We have defined more dramatic differences among other inbred lines and will be using the NAM lines to map the loci involved and isolate the relevant genes.