| Rice is one of the most important crops in the world that provides staple food for half of the world's population. Starch accounts for about 90% of milled rice, and it is a key determinant of processing, cooking and edible qualities of rice. Therefore improvement of starch properties is one of the most important goals in rice breeding. Starch is composed of linear amylose and branching amylopectin. It has been widely documented that both the proportion of amylose to amylopectin and the structure of amylopectin are determinants of rice starch texture. Synthesis of amylose is catalyzed by the granule-bound starch synthase (GBSS) that is encoded by the Wx gene. Recent investigations have shown that amylopectin is synthesized via a series of concerted reactions catalyzed by respective soluble starch synthase (SSS), starch branching enzyme (SBE) and starch debranching enzyme (DBE). Each of these three enzymes has multiple isoforms encoded by various alleles. Although many results have been published related to expression regulation of the Wx gene and its effects on starch quality, more researches are still needed to illustrate the expression regulations of genes involved in amylopectin biosynthesis and their effects on starch quality. The genome sequences available online for both indica (cultivar 93-11) and japonica (cultivar Nipponbare) rice subspecies provide unique opportunity for isolation and functionalanalysis of economically important genes. In the present studies, gene-tagged markers have been developed for each starch-synthesizing gene, and these markers were used to evaluate roles of starch-synthesizing genes in determining physiochemical properties. Moreover, a BAC library was constructed from a high quality rice cv. Suyunuo, and the starch-branching genes Sbel and Sbe3 from cv. Suyunuo were isolated and analyzed. The main results were detailed as following.(1) Variations in starch physicochemical properties were investigated between waxy mutant and its wild-type line for two rice varieties. The results demonstrated that waxy mutant showed higher GT (Gelatinization temperature) and GC (Gel consistency), and lower RVA (Rapid visco-analyzer) values than its wild-type line. As for the RVA profile, three characters including setback, consistence and cool viscosity varied greatly between waxy mutant and wild-type line, while slight difference was observed for peak viscosity or breakdown. It could be concluded that the Wx gene exerts pleiotropy on GC, GT, and starch paste viscosity. In addition, variations in breakdown and peak viscosity of RVA profile between two waxy mutants were even larger than those between the waxy mutant and its respective wild-type line. These results suggested that, apart from AC, amylopectin was also a key factor in determining cooking and eating qualities of rice. The Wx locus was characterized with both G/T single nucleotide polymorphism (SNP) at the putative leader intron 5' splice site and (CT)n microsatellite in the leader sequence. Analysis of G/T SNP showed that Yangfunuo 4 differed from its wild-type line IR[ 5 29-68-3-2 by a subsitution of G by T, while Yangnuo 2 exhibited the same nucleotide T with its wild-type Kinmaze. Variations in number of (CT)n repeats were also observed both between Yangfunuo 4 and ER1529-68-3-2 and between Yangnuo 2 and Kinmaze.(2) Gene-tagged molecular markers for both Sbel and Sbe3 have been developed based on sequence diversity between indica and japonica subspecies available online. All Sbe- and Wx- tagged markers have been used to investigate 40waxy rice cultivars. In the wx locus (null Wx locus in waxy rice), four classes of (CT)n repeats, including (CT)16, (CT)17, (CT)18, and (CT)19, were detected in the putative leader sequence. Moreover, a consistent sequence, AGTTATA, is also present at the 5' splice junction site of the putative leader intron. Overall, the wx locus has no effect on starch paste viscosity characteristics, GC and GT. Among all the 40 waxy rice cultivars, five genotypes are observed at the Sbel and Sbe3...
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