Functional Plant Biology Functional Plant Biology Society
Plant function and evolutionary biology

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

Takayuki Umemoto A B and Noriaki Aoki A
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- Author Affiliations

A National Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan.

B Corresponding author. Email:

Functional Plant Biology 32(9) 763-768
Submitted: 16 November 2004  Accepted: 1 July 2005   Published: 26 August 2005


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.

Keywords: alk, alkali disintegration, alkali spreading score, amylopectin.


We thank Prof. Yasunori Nakamura for the gift of rice BEIIb antiserum; Prof. Yoichiro Sato, Dr Yanfeng Ding, Kazuyuki Okamoto, and Masakata Hirayama for their gifts of rice seeds and plant materials. We also thank Dr Sam Zeeman for critical reading of the manuscript. This work was supported by funds from the Ministry of Agriculture, Forestry, and Fisheries of Japan.


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