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Starch, which is composed of amylose and amylopectin, is the key determinant of rice quality. Amylose is regulated by the  Waxy  ( Wx ) gene, whereas amylopectin is coordinated by various enzymes including eight soluble starch synthases (SSSs), of which SSSI accounts for ∼70% of the total SSS activity in cereal endosperm. Although great progress has been made in understanding  SSSI  gene expression and function, allelic variation and its effects on gene expression, rice physicochemical properties and qualities, and interactions with the  Wx  gene remain unclear. Herein,  SSSI  nucleotide polymorphisms were analyzed in 165 rice varieties using five distinct molecular markers, three of which reside in an  SSSI  promoter and might account for a higher expression of the  SSSI i   allele in  indica  ssp. than of the  SSSI j   allele in  japonica  ssp. The results of  SSSI  promoter- Beta-Glucuronidase  (β-GUS) analysis were consistent with the expression results. Moreover, analysis of near isogenic lines (NILs) in the Nipponbare (Nip) background showed that Nip ( SSSI i  ) and Nip ( SSSI j  ) differed in their thermal properties, gel consistency (GC), and granule crystal structure. Knockdown of  SSSI  expression using the  SSSI -RNA interference (RNAi) construct in both  japonica  and  indica  backgrounds caused consistent changes in most tested physicochemical characteristics except GC. Moreover, taste value analysis (TVA) showed that introduction of the  SSSI  allele in  indica  or knockdown of  SSSI  expression in  japonica  cultivars significantly reduced the comprehensive taste value, which was consistent with the superior taste of  japonica  against  indica . Furthermore, to test the potential interaction between  SSSI  and different  Wx  alleles, three NILs within the  Wx  locus were generated in the  indica  cv. Longtefu (LTF) background, which were designated as LTF ( Wx a  ), LTF ( Wx b  ), and LTF ( wx ). The  SSSI -RNAi construct was also introduced into these three NILs, and physiochemical analysis confirmed that the knockdown of  SSSI  significantly increased the rice apparent amylose content (AAC) only in the  Wx a   and  Wx b   background and caused different changes in GC in the NILs. Therefore, the effect of  SSSI  variation on rice quality also depends on its crosstalk with other factors, especially the  Wx  gene. These findings provide fundamental knowledge for future breeding of rice with premium eating and cooking qualities.

Rice Soluble Starch Synthase I: Allelic Variation, Expression, Function, and Interaction With Waxy