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Analysis of molecular variance and population structure in southern Indian finger millet genotypes using three different molecular markers

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Abstract

The genetic relationship among 42 genotypes of finger millet collected from different geographical regions of southern India was investigated using random amplified polymorphic DNA (RAPD), inter simple sequence repeats (ISSR), and simple sequence repeats (SSR) markers. Ten RAPD primers produced 111 polymorphic bands. Five ISSR primers produced a total of 61 bands. Of these, 23 bands were polymorphic. The RAPD and ISSR fingerprints revealed 71.3 and 37.4% polymorphic banding patterns, respectively. Thirty-six SSR primers yielded 83 scorable alleles in which 62 were found to be polymorphic. Out of 36 SSR primers used, 14 primers (46.6%) produced polymorphic bands. The SSR primer UGEP7 produced a maximum number of six alleles. Mean polymorphic information content (PIC) of RAPD, ISSR and SSR were 0.44, 0.28, and 0.14, respectively. Molecular variances among the population were 2, 11, and 1% for RAPD, ISSR, and SSR markers, respectively. SSR produced 99% molecular variance within individuals. RAPD and ISSR markers produced a low level of molecular variance within individuals. The STRUCTURE (model-based program) analysis revealed that the 42 finger millet genotypes could be divided into a maximum of four subpopulations. Based on the Bayesian statistics, each RAPD and SSR marker produced three subpopulations (K=3), while ISSR marker showed four subpopulations (K=4). This study revealed that RAPD and SSR markers could narrow down the analysis of population structure and it may form the basis for finger millet breeding and improvement programs in the future.

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Authors and Affiliations

  1. Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600034, India

    Host Antony David Rajendran, Ramakrishnan Muthusamy, Antony Caesar Stanislaus, Sivasankaran Kuppusamy & Savarimuthu Ignacimuthu

  2. Centre for Plant Sciences and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK

    Antony Caesar Stanislaus

  3. Pondicherry Centre for Biological Sciences, Jawahar Nagar, Pondicherry, India

    Thirugnanasambantham Krishnaraj

  4. State Bio-control Laboratory, Perunthalaivar Kamaraj Krishi Vigyan Kendra (PKKVK), Kurumbapet, Puducherry, India

    Thirugnanasambantham Krishnaraj

  5. International Scientific Partnership Program (ISPP), Deanship of Scientific Research, College of Science, King Saud University, Riyadh, Saudi Arabia

    Savarimuthu Ignacimuthu

  6. Department of Botany and Microbiology, Addiriyah chair for Environmental studies, College of Science, King Saud University, Riyadh, Saudi Arabia

    Naif Abdullah Al-Dhabi

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  1. Host Antony David Rajendran
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  2. Ramakrishnan Muthusamy
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Correspondence to Savarimuthu Ignacimuthu.

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Rajendran, H.A.D., Muthusamy, R., Stanislaus, A.C. et al. Analysis of molecular variance and population structure in southern Indian finger millet genotypes using three different molecular markers. J. Crop Sci. Biotechnol. 19, 275–283 (2016). https://doi.org/10.1007/s12892-016-0015-6

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  • DOI: https://doi.org/10.1007/s12892-016-0015-6

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