Email this article Development of microsatellite genetic markers in Siberian stone pine (Pinus sibirica Du Tour) based on the de novo whole genome sequencing
- Authors: Belokon M.M.1, Politov D.V.1, Mudrik E.A.1, Polyakova T.A.1,2, Shatokhina A.V.1, Belokon Y.S.1, Oreshkova N.V.3,4, Putintseva Y.A.3,4, Sharov V.V.4, Kuzmin D.A.4, Krutovsky K.V.1,4,5,6
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Affiliations:
- Vavilov Institute of General Genetics
- Russian Center of Forest Health
- Sukachev Institute of Forest
- Genome Research and Education Center
- Georg-August University of Göttingen
- Texas A&M University
- Issue: Vol 52, No 12 (2016)
- Pages: 1263-1271
- Section: Plant Genetics
- URL: https://journal-vniispk.ru/1022-7954/article/view/188027
- DOI: https://doi.org/10.1134/S1022795416120036
- ID: 188027
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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.
About the authors
M. M. Belokon
Vavilov Institute of General Genetics
Email: kkrutovsky@gmail.com
Russian Federation, Moscow, 119991
D. V. Politov
Vavilov Institute of General Genetics
Email: kkrutovsky@gmail.com
Russian Federation, Moscow, 119991
E. A. Mudrik
Vavilov Institute of General Genetics
Email: kkrutovsky@gmail.com
Russian Federation, Moscow, 119991
T. A. Polyakova
Vavilov Institute of General Genetics; Russian Center of Forest Health
Email: kkrutovsky@gmail.com
Russian Federation, Moscow, 119991; Pushkino, 141207
A. V. Shatokhina
Vavilov Institute of General Genetics
Email: kkrutovsky@gmail.com
Russian Federation, Moscow, 119991
Yu. S. Belokon
Vavilov Institute of General Genetics
Email: kkrutovsky@gmail.com
Russian Federation, Moscow, 119991
N. V. Oreshkova
Sukachev Institute of Forest; Genome Research and Education Center
Email: kkrutovsky@gmail.com
Russian Federation, Krasnoyarsk, 660036; Krasnoyarsk, 660036
Yu. A. Putintseva
Sukachev Institute of Forest; Genome Research and Education Center
Email: kkrutovsky@gmail.com
Russian Federation, Krasnoyarsk, 660036; Krasnoyarsk, 660036
V. V. Sharov
Genome Research and Education Center
Email: kkrutovsky@gmail.com
Russian Federation, Krasnoyarsk, 660036
D. A. Kuzmin
Genome Research and Education Center
Email: kkrutovsky@gmail.com
Russian Federation, Krasnoyarsk, 660036
K. V. Krutovsky
Vavilov Institute of General Genetics; Genome Research and Education Center; Georg-August University of Göttingen; Texas A&M University
Author for correspondence.
Email: kkrutovsky@gmail.com
Russian Federation, Moscow, 119991; Krasnoyarsk, 660036; Göttingen, D-37077; College Station, TX, 77843-2138
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