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Comparative analysis of microsatellites in five different antagonistic Trichoderma species for diversity assessment

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Abstract

Microsatellites provide an ideal molecular markers system to screen, characterize and evaluate genetic diversity of several fungal species. Currently, there is very limited information on the genetic diversity of antagonistic Trichoderma species as determined using a range of molecular markers. In this study, expressed and whole genome sequences available in public database were used to investigate the occurrence, relative abundance and relative density of SSRs in five different antagonistic Trichoderma species: Trichoderma atroviride, T. harzianum, T. reesei, T. virens and T. asperellum. Fifteen SSRs loci were used to evaluate genetic diversity of twenty isolates of Trichoderma spp. from different geographical regions of India. Results indicated that relative abundance and relative density of SSRs were higher in T. asperellum followed by T. reesei and T. atroviride. Tri-nucleotide repeats (80.2 %) were invariably the most abundant in all species. The abundance and relative density of SSRs were not influenced by the genome sizes and GC content. Out of eighteen primer sets, only 15 primer pairs showed successful amplification in all the test species. A total of 24 alleles were detected and five loci were highly informative with polymorphism information content values greater than 0.40, these markers provide useful information on genetic diversity and population genetic structure, which, in turn, can exploit for establishing conservation strategy for antagonistic Trichoderma isolates.

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Authors and Affiliations

  1. ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh, 275103, India

    Shalini Rai, Prem Lal Kashyap & Alok Kumar Srivastava

  2. ICAR-Indian Institute of Wheat and Barley Research (IIWBR), Karnal, Haryana, 132001, India

    Sudheer Kumar

  3. Sam Higginbottom Institute of Agriculture, Technology and Sciences (SHIATS), Allahabad, 211007, India

    Pramod W. Ramteke

Authors
  1. Shalini Rai
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  2. Prem Lal Kashyap
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  3. Sudheer Kumar
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  4. Alok Kumar Srivastava
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  5. Pramod W. Ramteke
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Correspondence to Prem Lal Kashyap.

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Rai, S., Kashyap, P.L., Kumar, S. et al. Comparative analysis of microsatellites in five different antagonistic Trichoderma species for diversity assessment. World J Microbiol Biotechnol 32, 8 (2016). https://doi.org/10.1007/s11274-015-1964-5

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  • DOI: https://doi.org/10.1007/s11274-015-1964-5

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