![]() The primer OP-B11 gave the highest number of polymorphic fragments in the 18 inbred lines (14 fragments) with 93% polymorphism. ![]() A total of 106 amplified DNA fragments ranging in size from 1529 to 163 base pairs were present, whereas 83 fragments were polymorphic and 23 fragments were monomorphic. The results indicated distinct differences can be used for identification of maize inbred lines. Nine random primers were used to identify and characterize 18 maize inbred lines by randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) analysis. Because PCR products are easily generated and may be analyzed in detail through the use of restriction endonucleases that cut rice DNA frequently, PCR-based RFLP analysis is a useful tool for the classification of rice germplasm. RFLPs were detected for 11 sets of primers, due to point mutations and to addition/deletion events that were too small to be detected as ALPs. To identify additional polymorphism, the PCR products were digested with nine different restriction endonucleases recognizing 4- or 5-bp DNA sequences and analyzed by gel electrophoresis in agarose and polyacrylamide. Amplicon length polymorphisms (ALPs) were detected with 6 of the 15 sets of primers. ![]() Fifteen sets of oligonucleotides derived from sequences near the ends of the same probes and of two other mapped probes were used as primers for PCR amplification of total genomic DNA of the varieties. Thirteen mapped RFLP markers were used as hybridization probes against Southern blots containing digests of one restriction endonuclease 12 of the 13 probes detected polymorphism in the varieties. Thirty-five Iranian rice varieties were studied along with 2 typical Indica and 3 typical Japonica varieties. 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.
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