Abstract: DNAs of “NK58S” and “NK58” (Oryza sativa L. ssp. japonica) were digested with Eco RⅤ, Dra Ⅰ, Hind Ⅲ, Xba Ⅰ, Msp Ⅰ or Hpa Ⅱ and probed with a cDNA clone of “IR36” (O. sativa L. ssp. indica) phyA gene. Polymorphism was found only when the DNAs were digested with Hpa Ⅱ . Msp Ⅰ and Hpa Ⅱ are isoschizomers whose recognition sites are CCGG. They are sensitive differently to the methylation of the second C, i.e. CpG in the recognition site. The experimental results indicated that the methylation level of CpGs in phyA gene of “NK58S” was lower than that of “NK58”. The possible function of the demethylation of “NK58S” phyA gene was discussed. DNA fragments in the upstream region from the transcription starting site of phyA gene were obtained by PCR amplification from IR36, “NK58” and “NK58S”. The PCR product of “NK58S” (PCR2) was one bp longer than that of IR36 (PCR1), moreover, 8 nucleotides were different between PCR2 and PCR1. RFLP analysis with PCR1 as a probe showed that there was variation between the 5′-flanking region of phyA gene of “NK58S” and that of IR36. According to the sequences of PCR2 and IR36 phyA gene, this variation might be caused by insertion or deletion.

Key words: Rice, Phytochrome gene, RFLP, DNA methylation