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 major enzymes involved in starch biosynthesis in rice endosperm. Available sequences of Sbe1 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 Sbe1 and Sbe3 loci. With these newly developed gene-tagged markers and available Wx gene markers, the roles of these starch-synthesizing genes (Sbe1, 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 cv. Nanjing11 and the japonica rice cv. Balilla. Only the Wx and Sbe3 loci had significant effects on the AC variation. On average, indica Wx ^a genotypes showed ∼9.1% higher AC than japonica Wx ^b genotypes, while indica Sbe3 ^a genotypes showed ∼1.0% lower AC than japonica Sbe3 ^b genotypes. A significant interaction was also observed between Wx and Sbe3 loci whereby the amylose content was 0.3% higher in Sbe3 ^a than Sbe3 ^b genotypes in the presence of the Wx ^a allele, but it was lower by 2.3% in the presence of the Wx ^b 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. This revised version was published online in July 2006 with corrections to the Cover Date.