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Russian Journal of Genetics

, Volume 52, Issue 12, pp 1263–1271 | Cite as

Development of microsatellite genetic markers in Siberian stone pine (Pinus sibirica Du Tour) based on the de novo whole genome sequencing

  • M. M. Belokon
  • D. V. Politov
  • E. A. Mudrik
  • T. A. Polyakova
  • A. V. Shatokhina
  • Yu. S. Belokon
  • N. V. Oreshkova
  • Yu. A. Putintseva
  • V. V. Sharov
  • D. A. Kuzmin
  • K. V. KrutovskyEmail author
Plant Genetics

Abstract

Siberian stone pine, Pinus sibirica Du Tour is one of the most economically and environmentally important forest-forming species of conifers in Russia. To study these forests a large number of highly polymorphic molecular genetic markers, such as microsatellite loci, are required. Prior to the new high-throughput next generation sequencing (NGS) methods, discovery of microsatellite loci and development of micro-satellite markers were very time consuming and laborious. The recently developed draft assembly of the Siberian stone pine genome, sequenced using the NGS methods, allowed us to identify a large number of microsatellite loci in the Siberian stone pine genome and to develop species-specific PCR primers for amplification and genotyping of 70 microsatellite loci. The primers were designed using contigs containing short simple sequence tandem repeats from the Siberian stone pine whole genome draft assembly. Based on the testing of primers for 70 microsatellite loci with tri-, tetra- or pentanucleotide repeats, 18 most promising, reliable and polymorphic loci were selected that can be used further as molecular genetic markers in population genetic studies of Siberian stone pine.

Keywords

genome microsatellite markers whole genome sequencing Siberian stone pine genetic diversity heterozygosity NGS 

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Copyright information

© Pleiades Publishing, Inc. 2016

Authors and Affiliations

  • M. M. Belokon
    • 1
  • D. V. Politov
    • 1
  • E. A. Mudrik
    • 1
  • T. A. Polyakova
    • 1
    • 2
  • A. V. Shatokhina
    • 1
  • Yu. S. Belokon
    • 1
  • N. V. Oreshkova
    • 3
    • 4
  • Yu. A. Putintseva
    • 3
    • 4
  • V. V. Sharov
    • 4
  • D. A. Kuzmin
    • 4
  • K. V. Krutovsky
    • 1
    • 4
    • 5
    • 6
    Email author
  1. 1.Vavilov Institute of General GeneticsRussian Academy of SciencesMoscowRussia
  2. 2.Russian Center of Forest HealthFederal Forestry AgencyPushkinoRussia
  3. 3.Sukachev Institute of ForestSiberian Branch of the Russian Academy of SciencesKrasnoyarskRussia
  4. 4.Genome Research and Education CenterSiberian Federal UniversityKrasnoyarskRussia
  5. 5.Georg-August University of GöttingenGöttingenGermany
  6. 6.Texas A&M UniversityCollege StationUSA

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