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
+ Author Affiliations
- 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.


Cao H, Imparl-Radosevich J, Guan HP, Keeling PL, James MG, Myers AM (1999) Identification of the soluble starch synthase activities of maize endosperm. Plant Physiology 120, 205–215.
CrossRef | PubMed | open url image1

Commuri PD, Keeling PL (2001) Chain-length specificities of maize starch synthase I enzyme: studies of glucan affinity and catalytic properties. The Plant Journal 25, 475–486.
CrossRef | PubMed | open url image1

Gao Z, Zeng D, Cui X, Zhou Y, Yan M, Huang D, Li J, Qian Q (2003) Map-based cloning of the ALK gene, which controls the gelatinization temperature of rice. Science in China Series C 46, 661–668.
CrossRef | open url image1

Guan HP, Preiss J (1993) Differentiation of the properties of the branching isozymes from maize (Zea mays). Plant Physiology 102, 1269–1273.
PubMed |
open url image1

Hirose T, Terao T (2004) A comprehensive expression analysis of the starch synthase gene family in rice (Oryza sativa L.). Planta 220, 9–16.
CrossRef | PubMed | open url image1

Imparl-Radosevich JM, Keeling PL, Guan HP (1999) Essential arginine residues in maize starch synthase IIa are involved in both ADP-glucose and primer binding. FEBS Letters 457, 357–362.
CrossRef | PubMed | open url image1

Jiang H, Dian W, Liu F, Wu P (2004) Molecular cloning and expression analysis of three genes encoding starch synthase II in rice. Planta 218, 1062–1070.
CrossRef | PubMed | open url image1

Juliano BO (1998) Varietal impact on rice quality. Cereal Foods World 43, 207–222. open url image1

Little RR, Hilder GB, Dawson EH (1958) Differential effect of dilute alkali on 25 varieties of milled white rice. Cereal Chemistry 35, 111–126. open url image1

Morell MK, Kosar-Hashemi B, Cmiel M, Samuel MS, Chandler P, Rahman S, Buleon A, Batey IL, Li Z (2003) Barley sex6 mutants lack starch synthase IIa activity and contain a starch with novel properties. The Plant Journal 34, 173–185.
CrossRef | PubMed | open url image1

Mu-Forster C, Huang R, Powers JR, Harriman RW, Knight M, Singletary GW, Keeling PL, Wasserman BP (1996) Physical association of starch biosynthetic enzymes with starch granules of maize endosperm. Plant Physiology 111, 821–829.
CrossRef | PubMed | open url image1

Nakamura Y, Takeichi T, Kawaguchi K, Yamanouchi H (1992) Purification of two forms of starch branching enzyme (Q-enzyme) from developing rice endosperm. Physiologia Plantarum 84, 329–335.
CrossRef | open url image1

Nichols DJ, Keeling PL, Spalding M, Guan HP (2000) Involvement of conserved aspartate and glutamate residues in the catalysis and substrate binding of maize starch synthase. Biochemistry 39, 7820–7825.
CrossRef | PubMed | open url image1

Okamoto K, Kobayashi K, Hirasawa H, Umemoto T (2002) Structural differences in amylopectin affect waxy rice processing. Plant Production Science 5, 45–50. open url image1

Tetlow IJ, Wait R, Lu Z, Akkasaeng R, Bowsher CG, Esposito S, Kosar-Hashemi B, Morell MK, Emes MJ (2004) Protein phosphorylation in amyloplasts regulates starch branching enzyme activity and protein–protein interactions. The Plant Cell 16, 694–708.
CrossRef | PubMed | open url image1

Umemoto T, Terashima K (2002) Activity of granule-bound starch synthase is an important determinant of amylose content in rice endosperm. Functional Plant Biology 29, 1121–1124.
CrossRef | open url image1

Umemoto T, Yano M, Satoh H, Shomura A, Nakamura Y (2002) Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties. Theoretical and Applied Genetics 104, 1–8.
CrossRef | PubMed | open url image1

Umemoto T, Aoki N, Lin HX, Nakamura Y, Inouchi N, Sato YI, Yano M, Hirabayashi H, Maruyama S (2004) Natural variation in rice starch synthase IIa affects enzyme and starch properties. Functional Plant Biology 31, 671–684.
CrossRef | open url image1

Vandeputte GE, Vermeylen R, Geeroms J, Delcour JA (2003) Rice starches. I. Structural aspects provide insight into crystallinity characteristics and gelatinisation behaviour of granular starch. Journal of Cereal Science 38, 43–52.
CrossRef | open url image1

Yamamori M, Fujita S, Hayakawa K, Matsuki J, Yasui T (2000) Genetic elimination of a starch granule protein, SGP-1, of wheat generates an altered starch with apparent high amylose. Theoretical and Applied Genetics 101, 21–29.
CrossRef | open url image1

Rent Article (via Deepdyve) Export Citation Cited By (75)