Semi-random PCR markers for DNA fingerprinting of rice hybrids and theirs corresponding parents

Molecular markers technology provides novel tools for DNA fingerprinting of rice hybrids to assess hybrid seed purity. Semi-random PCR primers targeting intron-exon splice junctions (ISJ) were used to analyze the rice genome with the aim of evaluating potential of these markers for identification and classification of rice hybrids. A total of 21 primers were tested for screening eight hybrid combination and their corresponding parents. Among 185 amplification products, 42.7% have polymorphic bands. The average number of bands per primer and genotype were 15.41 and 11.56, respectively. The genetic similarity between lines ranged from 0.47 to 0.95 with an average similarity index of 0.75. Cluster analysis based on Dice's similarity coefficient using UPGMA procedure grouped the cultivar into 5 clusters. A set of 5 semi-random primers characterized all the genotypes from each other, which can be used for identification of these hybrid and their parental lines. IT/10-1 and IT31/15 multilocus primers were the most-informative loci for DNA profiling and differentiation. Because of its rapidity and reliability of semi- random primers, it seems to be a suitable method for DNA typing and discrimination of rice hybrids.