DEVELOPMENT OF MICROSATELLITE MARKERS WITH LONG MOTIFS FOR SCOTS PINE BASED ON WHOLE-GENOME de novo SEQUENCING
N. V. Oreshkova1,2,3, E. I. Bondar1,3, V. V. Sharov1,3, K. V. Krutovsky3,4,5,6
1Krasnoyarsk Science Centre of the Siberian Branch of Russian Academy of Science, Krasnoyarsk, Russian Federation
2Krasnoyarsk Science Centre of the Siberian Branch of Russian Academy of Science, V. N. Sukachev Institute of Forest, Russian Academy of Sciences, Siberian Branch, Krasnoyarsk, Russian Federation
3Siberian Federal University, Krasnoyarsk, Russian Federation
4N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russian Federation
5G. F. Morozov Voronezh State Forest Engineering University, Voronezh, Russian Federation
6Georg-August University of Göttingen, Gottingen, Germany
Keywords: Pinus sylvestris L, genetic diversity, whole genome sequencing, heterozygosity, conifers, population genetic analysis, microsatellite markers, SSRs
Abstract
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 were 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.
|
