Understanding the specific functions played by individual starch synthase isoforms in maize and Arabidopsis will provide important evidence for how highly organized starch structure is made. Starch synthases (SS) catalyze the transfer of the glucosyl moiety from ADP-Glc to the terminus of a growing alpha-(1, 4)-linked glucan linear chain. At least five classes of SSs are identified in higher species, referred to as GBSS, SSI, SSII, SSIII, and SSIVN. They have high similarity in the catalytic and starch-binding domains of the C-termini but differ at their N-termini. All of these enzymes are highly conserved in plant kingdom, which indicates that they might have specific functions during starch biosynthesis;To investigate the functions of SSII, changes in starch biosynthesis caused by mutation of the sugary 2 (su2) gene in maize, two allelic su2-mutations were characterized. Su2 was shown to code for SSIIa, and both mutant alleles cause loss of SSIIa activity. Starch was characterized with respect to structural changes to the amylopectin (Ap) component of starch granules, changes of the amylopectin:amylose (Am) compositional ratio, and pleiotropic effects on other starch metabolizing enzymes. Loss of SSII resulted in Ap with more short chains of degree of polymerization (DP) 5-11 and fewer intermediate chains of DP12-25. Increased Am:Ap ratio was also observed in the mutant starches. The changes in Ap structure and Am:Ap ratio are similar to the effects of SSII deficiency in other species. The results demonstrate that some function of SSII is necessary for the normal accumulation of chains of DP12-25 in Ap;A similar approach was used in Arabidopsis to study the function of both SSII and SSIII. Six SS genes were identified in the Arabidopsis genome. To examine the specific functions of different SS isoforms or the functional interactions among them, either single mutations or a combination of double mutations in SS genes were studied. (Abstract shortened by UMI.)