Duplicated coding sequence in the waxy allele of tropical glutinous rice (Oryza sativa L.)

Rice starch consists of annylopectin and amylose, the latter component being controlled by the Waxy (Wx(a)) gene. Two alleles Wx(b) and Wx(b) were found to regulate the quantitative level of the Wx protein as well as the amylose content. A comparison of the genomic sequences of rice Wx genes responsible for the synthesis of grain amylose was made between two pairs of glutinous and non-glutinous reverse mutants. By comparing their 5' splice codons in the first intron, the low-amylose and glutinous rices were characterized as the Wx(b) allele based on the G-to-T base substitution, which caused an aberrant splicing. When the entire genomic sequences of Wxb were compared, a unique duplication of 23 bp was found to be present only in the glutinous mutants. This 23 bp insertion was truly unique for tropical glutinous rice because of its similarity between the 800 bp sequences around the duplicated sequences of 24 glutinous varieties and two annual diploid wild rice accessions. This in-frame duplication created a premature translation stop codon at 78 bp downstream. The insertion was unique and none of the structure was identical to any transposon or retrotransposon ever reported in rice before. This unique duplicated sequence opens up opportunities to develop PCR-based markers useful for classifying grain amylose in rice. (C) 2003 Elsevier Ireland Ltd. All rights reserved.