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Molecular characterization of Vigna radiata (L.) Wilczek genotypes based on nuclear ribosomal DNA and RAPD polymorphism

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Abstract

Mungbean germplasm characterization, evaluation and improvement are fundamentally based on morpho-agronomic traits. The lack of break-through in mungbean production has been due to non-availability of genetic variability for high yield potential. Forty-four genotypes of mungbean [Vigna radiata (L.)Wilczek] were subjected to random amplified polymorphic DNA (RAPD) analysis to assess the genetic diversity and relationships among the genotypes. Multilocus genotyping by twelve RAPD primers generated 166 markers and detected an average of intraspecific variation amounting to 82% polymorphism in banding patterns. Dendrogram obtained from cluster analysis delineated all the 44 genotypes into six clusters. Higher values of Nei’s gene diversity (h) and Shannon information index (i) and genetic distance analysis validate existence of wide genetic diversity among mungbean genotypes tested. Besides internal transcribed spacer (ITS) length variations, single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELS) were detected at number of sites in nuclear rDNA region and the sequences of representatives of each sub-cluster and all distinct genotypes have been submitted to NCBI database and assigned Gen accession numbers HQ 148136-148147. Multiple sequence alignment revealed further lineages of distinct genotypes with main RAPD clusters. The measures of relative genetic distances among the genotypes of mungbean did not completely correlate the geographical places of their development. The homogeneous phenotypic markers proved insufficient in exhibiting genetic divergence among mungbean genotypes studied. RMG-62, RMG-976, and NDM-56 have been identified as potential source of parents for crop improvement. RAPD primers, OPA-9 and OPA-2 as polymorphic genetic markers and number of pods/plant and number of seeds/plant as dependable phenotypic markers have been identified for improving yield potentials. This genetic diversity will be of significance in developing intraspecific crosses in mungbean crop improvement programme.

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Acknowledgments

The authors are thankful to Dr. M. M. Roy, Director, Central Arid Zone Research Institute, Jodhpur for providing necessary laboratory and field facilities and CSIR for providing financial assistance to carry out this study.

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Authors and Affiliations

  1. Central Arid Zone Research Institute, Jodhpur, Rajasthan, India

    Aparna Raturi, S. K. Singh & Rakesh Pathak

  2. Banasthali Vidyapith, Tonk, 304022, Rajasthan, India

    Vinay Sharma

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  1. Aparna Raturi
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  2. S. K. Singh
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Correspondence to S. K. Singh.

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Raturi, A., Singh, S.K., Sharma, V. et al. Molecular characterization of Vigna radiata (L.) Wilczek genotypes based on nuclear ribosomal DNA and RAPD polymorphism. Mol Biol Rep 39, 2455–2465 (2012). https://doi.org/10.1007/s11033-011-0996-7

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