Assessment of molecular diversity chickpea (Cicer arietinum L.) Rhizobia and structural analysis of 16S rDNA sequences from Mesorhizobium ciceri strains
Akhilesh Yadav, Asha Lata Singh, Govind Kumar Rai, Major Singh Pol J Microbiol 2013; 62 (3): ICID: 1072790 Article type: Original article IC™ Value: 10.00
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The aims of this study were to investigate the diversity of chickpea rhizobia to correlate with the isolates site of origin, and to compare the molecular approaches in rhizobial strain identification and differentiation. Diversity of nineteen rhizobial isolates from Indian soils was assessed by molecular methods (16S rDNA-RFLP and SSR analysis) and phenotypical characterization across the isolates, for environmental tolerance such as temperatures, salinity and pH. These isolates were identified as different strains of Rhizobium, Bradyrhizobium, Agrobacterium and Mesorhizobium. All molecular methods generated analogous clustering of the isolates, supporting results of 16S rDNA sequence-based phylogeny. Twenty SSR loci of Mesorhizobium ciceri were selected for SSR analysis, which are distributed across the other rhizobial genome and clearly differentiated the different rhizobial strains. For structure analysis of 16S rDNA sequences from Mesorhizobium ciceri strains, the analysis data showed that nucleotide variables (signature sites) were detected in 20 positions and most of them were found in the first 820bp from 5' terminal. Interestingly, the 14 signature sites were located in two main regions: the first variable region V1 (position 527-584), while the second variable region V2 (position 754-813) were detected. Furthermore, the secondary structure and minimal free energy were determined in the two regions among the strains of two groups. These results will be useful in characterizing the micro-evolutionary mechanisms of species formation and increase our knowledge on the symbiotic relationship with the host plant, leading to an improvement in chickpea productivity.