Development of Microsatellite Genetic Markers in Siberian Stone Pine (Pinus sibirica Du Tour) Based on the de novo Whole Genome Sequencing

Тип публикации: статья из журнала

Год издания: 2016

Идентификатор DOI: 10.1134/S1022795416120036

Ключевые слова: genome, microsatellite markers, whole genome sequencing, Siberian stone pine, genetic diversity, heterozygosity, NGS

Аннотация: 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 microsatellite 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.

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Издание

Журнал: RUSSIAN JOURNAL OF GENETICS

Выпуск журнала: Vol. 52, Is. 12

Номера страниц: 1263-1271

ISSN журнала: 10227954

Место издания: NEW YORK

Издатель: MAIK NAUKA/INTERPERIODICA/SPRINGER

Авторы

  • Belokon M.M. (Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia)
  • Politov D.V. (Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia)
  • Mudrik E.A. (Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia)
  • Polyakova T.A. (Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia; Fed Forestry Agcy, Russian Ctr Forest Hlth, Pushchino 141207, Russia)
  • Shatokhina A.V. (Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia)
  • Belokon Yu. S. (Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia)
  • Oreshkova N.V. (Russian Acad Sci, Sukachev Inst Forest, Siberian Branch, Krasnoyarsk 660036, Russia; Siberian Fed Univ, Genome Res & Educ Ctr, Krasnoyarsk 660036, Russia)
  • Putintseva Yu. A. (Russian Acad Sci, Sukachev Inst Forest, Siberian Branch, Krasnoyarsk 660036, Russia; Siberian Fed Univ, Genome Res & Educ Ctr, Krasnoyarsk 660036, Russia)
  • Sharov V.V. (Siberian Fed Univ, Genome Res & Educ Ctr, Krasnoyarsk 660036, Russia)
  • Kuzmin D.A. (Siberian Fed Univ, Genome Res & Educ Ctr, Krasnoyarsk 660036, Russia)
  • Krutovsky K.V. (Russian Acad Sci, Vavilov Inst Gen Genet, Moscow 119991, Russia; Siberian Fed Univ, Genome Res & Educ Ctr, Krasnoyarsk 660036, Russia; Georg August Univ Gottingen, D-37077 Gottingen, Germany; Texas A&M Univ, College Stn, TX 77843 USA)

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