Oreshkova N. V., Bondar E. I., Sharov V. V., Krutovsky K. V. Development of Microsatellite Markers with Long Motifs for Scotch Pine Based on Whole-Genome de novo Sequencing
1 Fed. Res. Center Krasnoyarsk Sci. Center, Rus. Acad. Sci., Sib. Br.
Akademgorodok, 50, Krasnoyarsk, 660036 Russian Federation
2 V. N. Sukachev Inst. For., Rus. Acad. Sci., Sib. Br.
Fed. Res. Center Krasnoyarsk Sci. Center, Rus. Acad. Sci., Sib. Br.
Akademgorodok, 50/28, Krasnoyarsk, 660036 Russian Federation
Akademgorodok, 50a/2, Krasnoyarsk, 660036 Russian Federation
4 N. I. Vavilov Inst. Gen. Genet., Rus. Acad. Sci.
Gubkin str., 3, Moscow, 119333 Russian Federation
5 Voronezh St. Univ. For. & Technol. named after G. F. Morozov
Timiryazev str., 8, Voronezh 394087 Russian Federation
6 Georg-August University of Göttingen
Büsgenweg, 2, Göttingen, D-37077 Germany
E-mail: oreshkova@ksc.krasn.ru, bone-post@yandex.ru, vsharov@sfu-kras.ru,
Abstract
UDC 575.113:582.475.4
How to cite: Oreshkova N. V.1, 2, 3, Bondar E. I.1, 3, Sharov V. V.1, 3, Krutovsky K. V.3, 4, 5, 6 Development of microsatellite markers with long motifs for Scotch pine based on whole-genome de novo sequencing // Sibirskij Lesnoj Zurnal (Sib. J. For. Sci.). 2025. N. 1. P. 23–33 (in Russian with English abstract and references).
DOI: 10.15372/SJFS20250103
EDN: …
© Oreshkova N. V., Bondar E. I., Sharov V. V., Krutovsky K. V., 2025
Modern methods of whole-genome sequencing have made it possible to develop a large number of DNA markers, both selectively neutral and functional. Microsatellite loci are the most informative, reproducible, relatively inexpensive and highly polymorphic among other genetic markers. Whole-genome sequencing significantly simplifies their search and development. The article is devoted to the development of new microsatellite markers for Scots pine (Pinus sylvesrtis L.). Several thousand contigs containing microsatellite loci with tri-, tetra- and pentanucleotide motifs were selected in the draft genome assembly of Scots pine obtained by the authors. The search was specifically focused on loci with a repetitive motif length longer than two nucleotides, as the most reliable for genotyping even in a simple gel electrophoresis. A total of 39 primer pairs were tested. Of these, six loci with tri-, tetra- and pentanucleotide repeats were ultimately selected, which showed a high level of polymorphism, reliable genotyping, and additionally tested in two populations from the Severo-Yeniseisky and Kuraginsky districts in Krasnoyarsk Region (East Siberia, Russia) and compared with other populations and marker sets according to published data. The developed markers can be used in the future in various population genetic studies and for identifying the origin of wood and plant material.
Article
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