Biology Reference
In-Depth Information
that strong stickiness and softness are preferred
among Japanese consumers.
A wide range of variation in physicochem-
ical properties related to cooking characteris-
tics between indica and japonica cultivars and
between glutinous and non-glutinous cultivars
has been observed (Juliano et al. 1964; Cham-
pagne et al. 1999; Lisle et al. 2000). Several
QTLs for physicochemical properties have been
reported in populations derived from crosses
between indica and japonica rice cultivars (Bao
et al. 1999; Bao et al. 2000). Many QTLs were
detected near genes related to starch synthe-
sis, such as Waxy ( Wx , which encodes granule-
bound starch synthase) and alkali disintegra-
tion ( Alk , which encodes starch synthase IIa),
both on the short arm of chromosome 6. These
genes are responsible for the main differences
in the physicochemical properties of cooked
rice between indica and japonica cultivars, and
may conceal other genetic factors with smaller
effects. There have been a few reports of phe-
notypic variation in these cooking traits among
non-glutinous japonica rice cultivars (Lin et al.
2005; Kang et al. 2006), but the genetic basis of
this variation could not be determined, possibly
because of low levels of DNA polymorphism in
the materials. In general, japonica cultivars show
less phenotypic variation in grain physicochemi-
cal properties than do indica cultivars (Bao et al.
2004). Several instruments for testing the pasting
properties of rice grain can clearly detect differ-
ences between indica and japonica cultivars, but
not between japonica cultivars. This gap is an
impediment to an in-depth genetic analysis of
the traits in japonica rice cultivars.
grain, many studies of rice cooking characteris-
tics and grain appearance have focused on the
starch components, primarily amylose and amy-
lopectin. Amylose is considered the most impor-
tant factor affecting cooking and sensory qual-
ity in rice. The granule-bound starch synthase I
enzyme (GBSSI) is required for amylose syn-
thesis in rice, and the gene encoding GBSSI was
named Waxy ( Wx ) when it was first discovered
through classical genetic studies (Ikeno 1914).
The amylose content of rice cultivars is classi-
fied as waxy (0-2%), very low (3-9%), low (10-
19%), intermediate (20-25%), or high (
25%)
(Fitzgerald et al. 2003). Glutinous rice cultivars
and waxy mutant lines carry a deletion in the
Wx gene that is fatal to the activity of GBSSI
(Mikami et al. 1999), and consequently they con-
tain no amylose. In non-glutinous rice cultivars,
a single-nucleotide polymorphism (SNP) at the
splice site of intron 1 defines two alleles, Wx a
and Wx b , and differentiates intermediate- and
high-amylose cultivars from low-amylose cul-
tivars (Isshiki et al. 1998). Wx a is distributed
predominantly in indica cultivars and Wx b in
japonica cultivars. A recent association study
identified an SNP in exon 6 that differentiates
high- and intermediate-amylose cultivars (Chen
et al. 2008; Mikami et al. 2008). By using
near-isogenic lines, it was shown that this SNP
decreases the level of GBSSI protein, lower-
ing the amylose content from high to interme-
diate (Mikami et al. 2008). An SNP in exon
4 is associated with an opaque phenotype and
defines the Wx allele of the very-low-amylose
cultivars (Mikami et al. 2008). Cultivars with
very low amylose show even less GBSSI activ-
ity than low-amylose cultivars (Mikami et al.
1999).
Other genes besides Wx also affect the amy-
lose content. For example, dull ( du ) mutants
have low amylose content (Satoh and Omura
1981; Okuno and Yano 1984), and several du
mutant genes have been mapped and isolated
(Yano et al. 1988; Zeng et al. 2007; Isshiki et al.
2008). The mutant gene du1 is a member of a
family of pre-mRNA processing genes, and du3
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ComponentsofRiceEndosperm
The major components of polished rice grain are
starch (up to 95% of dry weight), protein (5-7%),
and lipids (0.5-1%). The chemical components
of rice grain (endosperm) affect many cooking
characteristics and sensory qualities (Han and
Hamaker 2001; Martin and Fitzgerald 2002).
Because starch is the main component of the
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