CLASSIFICATION OF RICE GERMPLASM .1. ANALYSIS USING ALP AND PCR-BASEDRFLP

The potential of using a PCR-based approach to detect DNA polymorphism for rice germplasm classification was compared with that of Southern- based RFLP analysis. Thirty-five Iranian rice varieties were studied a long with 2 typical Indica and 3 typical Japonica varieties. Thirteen mapped RFLP markers were used as hybridization probes against Southern blots containing digests of one restriction endonuclease; 12 of the 1 3 probes detected polymorphism in the varieties. Fifteen sets of oligo nucleotides derived from sequences near the ends of the same probes an d of two other mapped probes were used as primers for PCR amplificatio n of total genomic DNA of the varieties. Amplicon length polymorphisms (ALPs) were detected with 6 of the 15 sets of primers. To identify ad ditional polymorphism, the PCR products were digested with nine differ ent restriction endonucleases recognizing 4- or 5-bp DNA sequences and analyzed by gel electrophoresis in agarose and polyacrylamide. RFLPs were detected for 11 sets of primers, due to point mutations and to ad dition/deletion events that were too small to be detected as ALPs. Bec ause PCR products are easily generated and may be analyzed in detail t hrough the use of restriction endonucleases that cut rice DNA frequent ly, PCR-based RFLP analysis is a useful tool for the classification of rice germplasm.