Efficient detection of DNA polymorphism in cabbage and rice cultivars by PCR-RF-SSCP (PRS)

Abstract.

PCR (polymerase chain reaction)-RF(restriction fragment)-SSCP (single-strand conformation polymorphism) – designated here as PRS – is a combined method of SSCP and PCR-RFLP (restriction fragment length polymorphism) – designated as CAPS (cleaved amplified polymorphic sequence) – and was efficient in detecting intraspecific variation of the SLR1 gene in Brassica oleracea. One to six nucleotide changes in restriction fragments of the SLR1 gene were detected as different bands in PRS. In an analysis of randomly chosen DNA fragments in cabbage, PRS detected DNA polymorphism between different cultivars with more than 60% of the primer pairs used except for a combination of two cultivars having highly similar characteristics. In rice, no DNA polymorphism was found between two Japonica cultivars, while more than 80% of the primer pairs showed DNA polymorphism between Japonica cultivars and Indica cultivars. PRS had a 1.5- to twofold greater ability to detect DNA polymorphism in these cabbage and rice cultivars than CAPS. The present study indicated that PRS is potentially useful for the identification of crop cultivars and genetic mapping of DNA fragments including genes of interest.