Sequence-tagged sites and low-cost DNA marker technology for rice

Abstract

Sequence-tagged sites (STSs) facilitate the conversion of a genetic map into a physical map, provide a common basis for the comparison of diverse types of mapping data, are stored and disseminated as electronic data, and are amplified from genomic DNA by polymerase chain reaction (PCR). STSs find application as DNA markers in breeding programs and germplasm management because they offer speed, convenience, reliability, and low cost in genomic analysis, but these applications are currently limited by the small number of STSs available. We report here the terminal sequencing of 354 DNA markers of the Cornell-IRRI genetic map of rice and the conversion of 100 of them into STSs by synthesis of pairs of PCR primers. PCR was used to amplify the corresponding loci from genomic DNA of IR36 (indica), Taichung 65 (japonica), and Oryza longistaminata (AA genome wild species). More than half of the RZ clones amplified DNA segments that were 0.1-2.0 kbp larger than expected, presumably because of the presence of introns. Amplicon length polymorphisms were detected between O. sativa and O. longistaminata for about one quarter of the clones. The applications of STSs are illustrated by reference to 1) DNA marker-aided selection for pyramiding of bacterial blight resistance genes, 2) breeding for gall midge resistance, 3) monitoring the inheritance of transgenes, and 4) analysis of genetic variation of AA genome wild species.