A transposon-induced spontaneous mutation results in low β-amylase content in rice

Although germinating rice seeds typically show high β-amylase activity, some japonica rice cultivars have almost no β-amylase activity in the seedlings. This study was conducted to clarify the genetic basis for this suppression of β-amylases in germinating rice seeds. Quantitative trait locus (QTL) analysis using 'Nipponbare' (a japonica cultivar with very low β-amylase activity) × 'Kasalath' (an indica cultivar with normal β-amylase activity) backcross inbred lines revealed a major QTL (R2 = 0.64) at the marker interval C451-R1357 on chromosome 7, where the 'Nipponbare' allele dramatically decreased β-amylase activity. According to databases, this region is syntenic with the barley Bmy2 β-amylase locus, and carries two rice β-amylase genes (BAC83770 and BAC83773) in tight linkage. An RT-PCR experiment showed that 'Nipponbare' has suppressed BAC83773 expression (less than 1% that of 'Kasalath') but normal BAC83770 expression, indicating that BAC83773 is a candidate for the QTL. Insertion of a Mutator-like transposon in the BAC83773 promoter region was considered responsible for this suppression in 'Nipponbare' BAC83773 expression.