Abstract Starch characteristics determine the quality
of various products of rice, e.g., eating, cooking and
processing qualities. Our previous study indicated that
molecular markers inside or close to starch synthesiz-
ing genes can differentiate the starch properties of 56
waxy rices. Here we report microsatellite (or simple
sequence repeat, SSR) polymorphism in the Waxy
(Wx) gene, soluble starch synthase I gene (SS1) and
starch branching enzyme 1 gene (SBE1), single nucle-
otide polymorphism (SNP) in Wx and starch branching
enzyme 3 gene (SBE3), and a sequence tagged site
(STS) in starch branching enzyme 1 gene (SBE1)
among 499 nonwaxy rice samples and their relation-
ships with starch physicochemical properties. The
nonwaxy rice samples consist of landraces (n = 172)
obtained from germplasm centers and cultivars and
breeding lines (n = 327) obtained from various breed-
ing programs. Ten (CT)
n
microsatellite alleles, (CT)
8
,
(CT)
10
, (CT)
11
, (CT)
12,
(CT)
17
, (CT)
18
, (CT)
19
, (CT)
20
,
(CT)
21
, and (CT)
22
, were found at the Wx locus, of
which (CT)
11
was the most frequent, and (CT)
12
,
(CT)
21
and (CT)
22
were identified for the first time.
Four (CT)
n
microsatellite alleles were found at the
SBE1 locus, (CT)
8
, (CT)
9
, and (CT)
10
together with an
insertion sequence of CTCTCGGGCGA, and (CT)
8
alone without the insertion, of which (CT)
9
and the
insertion was a new allele identified in only one
rice, IR1552. Multiple microsatellites clustered at the
SS1 locus, and in addition to the three alleles previ-
ously detected (SSS-A = (AC)
2
...TCC(TC)
11
...(TC)
5
C(ACC)
11
, SSS-B = (AC)
3
...TCT(TC)
6
...(TC)
4
C(ACC)
9
,
and SSS-C = (AC)
3
...TCT(TC)
6
...(TC)
4
C(ACC)
8
),
one new allele (SSS-D = (AC)
2
...TCC(TC)
10
...(TC)
4-
C(ACC)
9
) was found. Analysis of the starch physico-
chemical properties of the samples with different
microsatellites, SNPs and STS groups indicated that
these molecular markers can differentiate almost all
the physicochemical properties examined, e.g., apparent
amylose content (AAC), pasting viscosity characteris-
tics, and gel textural properties. Wx SSR and Wx SNP
alone explained more variations for all physicochem-
ical properties than the other molecular markers. The
total six markers could explain 92.2, 81 and 86% of
total variation of AAC, gel hardness (HD), and gel
cohesiveness (COH), respectively, and they could
explain more than 40% of the total variation of hot
paste viscosity (HPV), cool paste viscosity (CPV),
breakdown viscosity (BD), setback viscosity (SB) and
gel adhesiveness (ADH). However, only 29% of the
total variation of peak viscosity (PV) and 37% of
pasting temperature (PT) could be explained by all
Communicated by M. Morell.
Electronic supplementary material
Supplementary material is
available in the online version of this article at http://dx.doi.org/
10.1007/s00122-006-0394-z and is accessible for authorized users.
J. S. Bao (&)
Institute of Nuclear Agricultural Sciences,
College of Agriculture and Biotechnology,
Zhejiang University, Hua Jiachi Campus,
Hangzhou 310029, People’s Republic of China
e-mail: jsbao@zju.edu.cn
H. Corke
Department of Botany, The University of Hong Kong,
Hong Kong, People’s Republic of China
M. Sun (&) Æ J. S. Bao
Department of Zoology, The University of Hong Kong,
Pokfulam Road, Hong Kong, People’s Republic of China
e-mail: meisun@hku.hk
Theor Appl Genet (2006) 113:1185–1196
DOI 10.1007/s00122-006-0394-z
123
ORIGINAL PAPER
Microsatellites, single nucleotide polymorphisms and a sequence
tagged site in starch-synthesizing genes in relation to starch
physicochemical properties in nonwaxy rice (Oryza sativa L.)
J. S. Bao Æ H. Corke Æ M. Sun
Received: 24 August 2005 / Accepted: 10 August 2006 / Published online: 9 September 2006
Ó
Springer-Verlag 2006