Relative efficiency of RAPD and ISSR markers in assessment of DNA polymorphism and genetic diversity among Pseudomonas strains

Abstract

This study presents the results from comparison of random amplified polymorphic DNA (RAPD), random amplified polymorphic DNA (RAPD) and RAPD-ISSR markers together in determining the genetic diversity and polymorphism among strains of fluorescent Pseudomonas. In order to compare the efficiencies of these markers, 17 different isolates were investigated using RAPD and ISSR. In RAPD marker analysis, 147 out of 222 bands (63.85%) were polymorphic and the RAPD based genetic similarity (RAPD-GS) ranged from 0.11 to 0.73. In ISSR analysis, a total of 134 alleles were detected, among which 105 alleles (77.9%) were polymorphic. The ISSR derived genetic similarity (ISSR-GS) ranged from 0.38 to 0.81. Cluster analysis indicated that all the 17 isolates could be distinguished by both RAPD and ISSR markers and worked effectively to determine high level of polymorphism in Pseudomonas. But ISSR was found to be slightly better than RAPD in assessing genetic diversity among the isolates while the combination of these techniques will give the comprehensive genetic analysis of Pseudomonas. Principal component analysis (PCA) was employed to evaluate the resolving power of the markers to differentiate between them.

Key words: Fluorescent Pseudomonas, Molecular markers, RAPD , ISSR,  PCR, Genetic diversity, Phylogeny, Principal component analysis. 

Abbreviation: RAPD (DNA), Random amplified  polymorphic deoxyribonucleic  acid;  ISSR,  inter-simple   sequence  repeat; PCA, principal components analysis; UPGMA, unweighted pair groups method using arithmetic averages