Variation on Starch Properties and the Relationship to Single Nucleotide Polymorphism in SSIIa in Waxy Rice Collected from Central of Vietnam

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Twenty two waxy rice cultivars originated from Central Vietnam were used for studying the variation on starch properties and the relationship to single nucleotide polymorphism in the SSIIa gene. A wide range of alkali digestibility level among 22 waxy rice cultivars was observed and recorded as low, intermediate and high alkali digestibility groups. All 22 waxy rice cultivars has significantly higher proportion of fa (DP≦12) and markedly lower proportion of fb1 chains with DP from 12 to 24 whereas the little difference was observed in proportion fb2 (25≦DP≦36) and fb3 (DP≧37) between waxy cultivars tested and IR36. The nucleotide changes in three exons (exon 1, exon 2 and exon 8) were observed in 22 waxy rice cultivars. Of the six single nucleotide polymorphism (SNPs) in the coding region, two SNPs, C/T (at site 516 bp) in exon 2 and G/T (at site 3903) in exon 8, were silent substitution while other four caused amino acid replacement. The SNP at position 264 bp in exon 1, was found an G–to–C transition causing change of glutamic to aspartic while the SNP at 3,799 bp in exon 8, resulting in glycine to serine change. The SNP at 4,198 bp, causing methionine to valine. The SNP at 4,329–4330 bp was observed a GC–to–TT transition leading to change of glycine–leucine change to glycine–phenylalanine. The study suggested that the wide variation on alkali digestibility and amylopectin fine structure in waxy rice starch was caused by the nucleotide diversity of SSIIa gene besides of other starch synthase genes involving in amylopectin synthesis.