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Molecular Marker-Based DNA Fingerprinting and Diversity Study of Rice Landraces Differing Salinity Tolerance

M. K. Saha1, S. N. Begum2, M. M. Islam3, M.S.R Khanom4, A. Z. Chowdhury5, U. Saha6,

Mondal S. K.7

 DOI :


The purpose of the research was to conserve the identity through molecular marker based DNA fingerprinting. Eight pair simple sequence repeat (SSR) primer and 7 randomly amplified polymorphic DNA (RAPD) primers were used to identify position of allele as well as to study genetic diversity among 35 genotypes differing salinity tolerance. All markers showed polymorphism with a mean number of 12.5 and 6.87 alleles per locus for SSR and RAPD respectively. When the DNA of genotypes were analyzed with SSR markers, tolerant landraces showed similar allelic position with salinity tolerant genotypes like Pokkali, FL478 or FL378 and salinity susceptible landraces showed similar position to popular salinity sensitive cultivar IR-29 or BRRI dhan29. From the SSR analysis, polymorphism information content (PIC) values ranged from 0.7334 (AP3206) to 0.8957 (RM336) where the highest gene diversity (0.9029) was observed in loci RM336 and the lowest gene diversity (0.7576) was observed in loci AP3206 with a mean diversity of 0.8604. In the mean time, RAPD analysis showed the highest gene frequency (1) among 5 loci viz. OPA04-5, OPB10-5, OPC02-8, OPC05-4 and OPC02-8 and the lowest gene frequency (0.0571) among 2 loci viz. OPB10-4 and OPC02-9 with mean gene diversity 0.3039. Cluster analysis based on SSR was more effective than RAPD markers in grouping landraces based on their salt tolerance due to co-dominance of SSR markers. The similarity and distinction between the landraces chosen for the study can be used as a precious tool and also recommend an appropriate selection of parents for mapping or breeding purposes.