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Amylopectin is the principle component of starch. To elucidate the relationships between amylopectin and resistant starch content, six rice mutants with altered fine structure of amylopectin were selected for comparative studies with the primary wild type and two types of amylose-extender (ae) mutants. Significant differences in resistant starch content were observed among mutants with similarity or differences in amylose levels. Mutants high in resistant starch had significantly increased proportions of short amylopectin chains with DP≤12, decreased levels of intermediate chains with size of 13≤DP≤36, and decreased fractions of long chains with DP≥37. Additionally, there was a mutant different to ae, which was characterized by an increased level of short chains with 8≤DP≤12 and 13≤DP≤24, and a decreased proportion of long chains with DP≥37. The increased contents of short chains with 8≤DP≤12 and decreased of intermediate and long chains with 24≤DP were clearly associated with the increase of resistant starch in rice.