SSR based molecular profiling of elite cultivars of basmati rice (Oryza sativa L.)

Abstract

The experiment was conducted to assess the available genetic variability amongst Indian Basmati rice and identify co-dominant and reproducible robust simple sequence repeat markers for drought resistance and their utilization in marker assisted selection for developing drought resistant / tolerant aromatic rice cultivars in various parts of India as well as in world. DNA was isolated from fresh and young leaf tissues of 35 cultivars of basmati rice using the CTAB procedure of Doyle and Doyle with slightly modifications. The DNA was further quantified by spectrophotometer at 260 nm and 280 nm. The quality and quantity of DNA were checked by agarose gel electrophoresis. Out of 60 SSR markers, 18 were found to be polymorphic and the rest 42 primers were monomorphic. One of the main purposes of SSR markers in genomic study is the characterization of genetic resources to help gene bank management. The informative (18) SSR markers were capable to discriminate the entire cultivars of basmati rice used in this research work. A total of 52 alleles at 18 loci could be scored. The allelic richness per locus diversified from 2 to 5 with an average of 2.89 alleles per locus. The amplitude of Polymorphism Information Content (PIC) value is 0.066 (RM 1068) to 0.730 (RM 1059) with an average of 0.505. The Jaccard’s similarity coefficient ranged from 0.79 to 0.95. Polymorphic finding content showed a positive correlation (r =0.69) with number of alleles at the SSR locus. However it is recommended that SSR markers can be efficiently utilized for this purpose. The maximum similarity coefficient was observed between Jeerakasab and Kalanamak with a coefficient value of 95% and the minimum similarity was found between Jeerakasab and Pusa basmati-1 with a coefficient value of 79%.