Nucleotide polymorphisms in the waxy gene of NaN3-induced waxy rice mutants

Spontaneous and induced waxy phenotype, associated with endosperm containing little or no amylose, has been recognized in rice (Oryza sativa L.). Mutation of a dominant gene Wx into a recessive gene wx, which causes the inactivation or absence of granule bound starch synthase, is believed to be responsible for the change in endosperm starch leading to the waxy grain. In the present study, the nucleotide polymorphism in the Wx gene of rice genotype Tainung 67 (wild type) and its 35 NaN3-induced wx mutants were examined. Iodine staining confirmed that all the mutants had waxy grain trait. The G-to-T single base substitution analysis indicated that the wild type genotype Tainung 67 and its waxy mutants carried Wxb allele. Moreover, 23-bp duplication in exon 2 was detected in all the waxy mutants. Microsatellite polymorphism (CT)n was also detectable on the Wx gene of the tested genotypes and mutants, with at least 5 classes of (CT)n microsatellites identified at the Wx locus. Electrophoretic analyses also confirmed the observed nucleotide polymorphsim. Thus, nucleotide polymorphsim exist among NaN3-induced waxy mutants in rice. However, only the 23-bp duplication in exon 2 may be used as a molecular marker to characterize waxy grain trait in rice genotypes.