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Novel microsatellite markers identification and diversity characterization in Pteris cretica L.

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Abstract

To assess genetic variation, 33 novel microsatellite markers were identified through nucleotide sequencing of enriched genomic libraries of Pteris cretica. Di- repeats (79.7 %) were found to be most predominant followed by tri (15.8 %), tetra (2.3 %) and hexa (2.3 %) type of repeat motifs. Evaluating these markers in six populations (N = 48) of Western Himalayan range detected average polymorphism information content (PIC) of 0.32. Combined neighbor joining (NJ) and principal coordinate analysis (PCoA) grouped all the populations in two major clusters with high levels of intermixing of accessions in each cluster. This suggests that P. cretica populations of Western Himalaya have broadly been mixed with two sub-populations. High within population variance (98.7 %) and low genetic differentiation (Φst: 0.013), recorded in the analysis of molecular variance (AMOVA). For the first time, highly polymorphic novel genomic microsatellite markers were identified and utilized for revealing genetic diversity of P. cretica in Western Himalayan range in context of established hypothesis of genetic variations based on allozyme markers.

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Abbreviations

SSRs:

Simple sequence repeats

ESTs:

Expressed sequence tags

PIC:

Polymorphic information content

PCR:

Polymerase chain reaction

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Acknowledgments

The research work presented in the manuscript was funded by Department of Biotechnology (DBT) and Council of Scientific and Industrial Research (CSIR), Government of India. This is IHBT communication number 3624.

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    Authors and Affiliations

    1. Division of Biotechnology, CSIR - Institute of Himalayan Bioresource Technology, Post Box 6, Palampur, Himachal Pradesh, 176061, India

      Vishal Kumar, Abhishek Bhandawat, Himanshu Sharma, Akshay Nag & Ram Kumar Sharma

    2. Department of Biotechnology, Guru Nanak Dev University, Amritsar, 143005, India

      Vishal Kumar

    Authors
    1. Vishal Kumar
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    2. Abhishek Bhandawat
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    3. Himanshu Sharma
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    4. Akshay Nag
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    5. Ram Kumar Sharma
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    Corresponding author

    Correspondence to Ram Kumar Sharma.

    Additional information

    Vishal Kumar and Abhishek Bhandawat contributed equally to this work.

    Electronic supplementary material

    Below is the link to the electronic supplementary material.

    Supplementary Fig. 1

    Topographical location of forty eight P. cretica accessions sampled from Western Himalayan range (PPTX 324 kb)

    Supplementary Table 1

    Partitioning of diversity of 48 accessions. (DOCX 11 kb)

    Supplementary Table 2

    Analysis of molecular variance (AMOVA) of 48 P. cretica accessions (DOCX 12 kb)

    Supplementary Table 3

    Test for population differentiation. (DOCX 11 kb)

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    Kumar, V., Bhandawat, A., Sharma, H. et al. Novel microsatellite markers identification and diversity characterization in Pteris cretica L.. J. Plant Biochem. Biotechnol. 25, 104–110 (2016). https://doi.org/10.1007/s13562-015-0316-8

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    • DOI: https://doi.org/10.1007/s13562-015-0316-8

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