Single-nucleotide polymorphisms in rice starch synthase IIa that alter starch gelatinisation and starch association of the enzyme

Abstract

The starch synthase IIa (SSIIa) gene of rice (Oryza sativa L.) has been shown to be the alk gene that controls alkali disintegration of rice grains, although the effects of naturally occurring alk mutant alleles on enzyme function have yet to be determined. We genotyped 60 rice cultivars for two single-nucleotide polymorphisms (SNPs) in rice SSIIa, including one that results in an amino acid substitution. Incorporating data for three other SNPs previously genotyped in rice SSIIa, five haplotypes were found. We analysed the association of these SSIIa haplotypes with the chain-length distribution of amylopectin, the gelatinisation temperature of rice flour, the alkali spreading score, and the starch association of the enzyme. It was determined that two SNPs resulting in amino acid changes close to the C-terminus most likely alter SSIIa both in terms of activity and starch granule association. This in turn alters the branch-length distribution of amylopectin and the gelatinisation properties of starch.

Recent progress toward understanding the role of starch biosynthetic enzymes in the cereal endosperm

“…SSIIa is mainly present in cereal endosperms, while SSIIb is mainly found in photosynthetic tissues [6]. Both SSI and SSII are localised within the starch granules in many cereals [56][57][58]. SSIII has two genes responsible for its expression in the endosperms and leaves of rice.…”

Haplotype Analysis of <i>Wx</i> and <i>Alk</i> Genes and Amylopectin Chain-Length Distribution among Kazakhstan Glutinous Rice Lines

“…The glutinous parents had 'A' at SNP3 and 'GC' at SNP4, indicating that they had the non-functional alk allele (Umemoto & Aoki 2005) (Fig. 3).…”

Genetic Diversity of Rice Grain Quality

“…Four haplotypes have been defined based on two SNPs and a functional nucleotide polymorphism (FNP) in SSIIa. These haplotypes generally group rice varieties into high and low GT classes (Cuevas et al, 2010a ;Umemoto & Aoki, 2005;Waters et al, 2006), with a few exceptions (Figure 7). …”