The functions of rice SSIIa alleles in starch biosynthesis modulated by the distinct genetic backgrounds

Natural variations in rice starch synthase IIa (SSIIa) gene confer different enzyme activities, leading to biosynthesis of starch with altered structures. To investigate the interaction effects of SSIIa and other starch synthesis-related genes on starch structural and functional properties, indica rice genotypes with different allelic combinations of SSIIa, Waxy (Wx), and branching enzyme IIb (BEIIb) were analyzed. Although SSIIa alleles exerted minimal effects on starch structures in the background of Wx^b/BEIIb, SSIIa^TT specifically reduced gelatinization enthalpy by enhancing amylose synthesis in the background of Wx^a/BEIIb. Furthermore, the SSIIa × BEIIb interaction significantly modulated amylopectin B1 chain content: SSIIa^TT increased B1 chains and decreased B3 chains, compensating for the deficiency of amylopectin synthesis caused by be2b. Although SSIIa^GC elevated gelatinization temperature across diverse allele combinations, this effect was attenuated by be2b. This study demonstrates that SSIIa alleles interact with other starch synthesis-related genes to regulate starch biosynthesis, providing a novel theoretical foundation for biological modification of starch properties and improvement of rice quality.