Developing Gene-tagged Molecular Markers For Functional Analysis Of Starch-synthesizing Genes In Rice(Oryza Sativa L.)

The granule-bound starch synthase (GBSS), starch branching enzymes 1 (SBE1) and 3 (SBE3) are three major enzymes involved in starch biosynthesis in rice endosperm. The granule-bound starch synthase encoded by the Wx gene controls the synthesis of amylose .while starch branching enzymes are mainly in charge of the synthese of amylopectin. Available sequences of Sbe 1 and Sbe3 genes encoding corresponding SBE1 and SBE3 have been used to identify homologous regions from genome databases of both the indica rice 93-11 and the japonica rice Nipponbare. Sequence diversities were exploited to develop gene-tagged markers to distinguish an indica allele from a Japonica allele for both Sbel and Sbe3 loci. With these newly developed gene-tagged markers and available Wx gene markers, the roles of these starch-synthesizing genes (Sbel, Sbe3, and Wx) in determining amylose content(AC) in the rice endosperm were evaluated using a double-haploid (DH) population derived from a cross between the indica rice Nanjing 11 and the japonica rice Balilla. Only the Wx and Sbe3 loci had significant effects on the AC variation. On average, indica Wx genotypes showed -9.1% higher AC than japonica Wx genotypes, while indica Sbe3 genotypes showed ~1.0% lower AC than japonica Sbe3 genotypes. A significant interaction was also observed between Wx and Sbe3 loci whereby the amylose content was 0.3% higher in Sbe3 than Sbe3 genotypes in the presence of the Wx allele, but it was lower by 2.3% in the presence of the W allele. Overall, polymorphisms at the Wx and Sbe3 loci together could account for 79.1% of the observed AC variation in the DH population. The use of gene-tagged markers in marker-assisted selection and gene functional analysis was also discussed.