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A Comparative Analysis of ISSR and RAPD Markers for Study of Genetic Diversity in Shisham (Dalbergia sissoo)

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Abstract

Shisham (Dalbergia sissoo) is one of the most preferred timber tree species of South Asia. Two DNA-based molecular marker techniques, intersimple sequence repeat (ISSR) and random amplified polymorphism DNA (RAPD), were compared to study the genetic diversity in this species. A total of 30 polymorphic primers (15 ISSR and 15 random) were used. Amplification of genomic DNA of 22 genotypes, using ISSR analysis, yielded 117 fragments, of which 64 were polymorphic. Number of amplified fragments with ISSR primers ranged from five to ten and varied in size from 180 to 1,900 bp. Percentage polymorphism ranged from 0 to 87.5. The 15 RAPD primers produced 144 bands across 22 genotypes, of which 84 were polymorphic. The number of amplified bands varied from five to 13, with size range from 180 to 2,400 bp. Percentage polymorphism ranged from 0 to 100, with an average of 58.3 across. RAPD markers were relatively more efficient than the ISSR assay. The mental test between two Jaccard’s similarity matrices gave r ≥ 0.90, showing very good fit correlation in between ISSR- and RAPD-based similarities. Clustering of isolates remained more or less the same in RAPD and combined data of RAPD and ISSR. The similarity coefficient ranged from 0.734 to 0.939, 0.563 to 0.946, and 0.648 to 0.920 with ISSR, RAPD, and combined dendrogram, respectively.

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Acknowledgements

The authors are thankful to Dr. Ombir Singh, Division of Silviculture, Forest Research Institute, Dehradun, for providing the seed sources of different germplasms and to the Department of Biotechnology, Government of India, for providing financial support for conducting the investigation and fellowship to the first author.

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Authors and Affiliations

  1. Department of Plant Pathology, G. B. Pant University of Agriculture and Technology, Pantnagar, 263145, Uttarakhand, India

    Mohd Arif, N. W. Zaidi & U. S. Singh

  2. Forest Pathology Department, Forest Research Institute, Dehradun, India

    Y. P. Singh

  3. Department of Biosciences, Jamia Millia Islamia, New Delhi, India

    Qazi Mohd Rizwanul Haq

  4. South Asia Regional Project Coordinator, International Rice Research Institute, IRRI-India Office, NASC Complex, NAAS Blvd., Dev Prakash Shastri Marg, New Delhi, 110 012, India

    U. S. Singh

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  1. Mohd Arif
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  2. N. W. Zaidi
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Correspondence to U. S. Singh.

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Arif, M., Zaidi, N.W., Singh, Y.P. et al. A Comparative Analysis of ISSR and RAPD Markers for Study of Genetic Diversity in Shisham (Dalbergia sissoo). Plant Mol Biol Rep 27, 488–495 (2009). https://doi.org/10.1007/s11105-009-0097-0

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