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.
Highlights
Fluorescent Pseudomonas are plant, animal and human pathogens; exhibit plant growth-promoting and plant pathogen-suppressing properties, useful in biological control and express metabolic versatilities valued in biotechnology and bioremediation
Polymerase chain reaction (PCR) with 10-mer oligo nucleotide Random amplified polymorphic DNA (RAPD) primers produced a total of 222 loci of which 63.8% were polymorphic with cumulative size range of 308 to 1466 bp (Table 2)
The potential ability of two molecular markers that is, Inter-simple sequence repeat (ISSR) and RAPD were tested to evaluate the genetic diversity of the most commonly used biocontrol agent, fluorescent Pseudomonas. This assessment showed that the percent polymorphism, primer information content (PIC) and average expected gene diversity (Hi) values were slightly higher in case of ISSR
Summary
Fluorescent Pseudomonas are plant, animal and human pathogens; exhibit plant growth-promoting and plant pathogen-suppressing properties, useful in biological control and express metabolic versatilities valued in biotechnology and bioremediation. Pseudomonas includes species with functions of ecological, economic, and health-related importance (Siddiqui et al, 2005). 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.
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