Skip to main content
SpringerLink
Log in

Development of microsatellite genetic markers in Siberian larch (Larix sibirica Ledeb.) based on the de novo whole genome sequencing

  • Plant Genetics
  • Published:
Russian Journal of Genetics Aims and scope Submit manuscript

Abstract

This special issue of the journal is devoted to the outstanding population geneticist Yuri Petrovich Altukhov, who paid much attention in his research to the development of molecular genetic markers for population studies. Over the past time markers and methods of their development have undergone significant change. Thanks to modern methods of whole genome sequencing, it has become possible to develop markers of very different types—selectively neutral, as well as functional. Among them, microsatellite markers remain the most informative, convenient, reproducible, relatively inexpensive, and polymorphic. Whole genome sequencing greatly facilitates their discovery and development. This paper is devoted to the development of new microsatellite markers for a very important species of boreal forest—Siberian larch (Larix sibirica Ledeb.). Using a draft assembly of the larch genome, several thousand contigs containing microsatellite loci with di-, tri, tetra-, and pentanucleotide motifs were selected. A total of 59 pairs of PCR primers were tested for loci with dinucleotide motifs as the most variable. From them, 11 pairs were finally selected for 11 loci with dinucleotide repeats, which showed a high level of polymorphism and can be used in various population genetic studies and to identify the origin of wood and plant material. This study was done at the Laboratory of Forest Genomics of the Genome Research and Education Center of the Siberian Federal University with the support of the Department of Forest Genetics and Forest Tree Breeding of the Georg-August University of Göttingen, the Department for Monitoring of Forest Genetic Resources of the Forest Protection Center of the Krasnoyarsk Territory, and the Laboratory of Forest Genetics and Selection of the Sukachev Institute of Forest of the Siberian Branch of the Russian Academy of Sciences within the framework of the project “Genomics of the Key Boreal Forest Conifer Species and Their Major Phytopathogens in the Russian Federation” funded by the Government of the Russian Federation (grant no. 14.Y26.31.0004).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Khasa, D.P., Newton, C.H., Rahman, M.H., et al., Isolation, characterization, and inheritance of microsatellite loci in alpine larch and western larch, Genome, 2000, vol. 3, no. 43, pp. 439–448. doi 10.1139/g99-131

    Article  Google Scholar 

  2. Isoda, K. and Watanabe, A., Isolation and characterization of microsatellite loci from Larix kaempferi, Mol. Ecol. Notes, 2006, vol. 6, no. 3, pp. 664–666. doi 10.1111/j.1471-8286.2006.01291.x

    Article  CAS  Google Scholar 

  3. Chen, C., Liewlaksaneeyanawin, C., Funda, T., et al., Development and characterization of microsatellite loci in western larch (Larix occidentalis Nutt.), Mol. Ecol. Resour., 2009, vol. 9, no. 3, pp. 843–845. doi 10.1111/j.1755-0998.2008.02289.x

    Article  CAS  PubMed  Google Scholar 

  4. Oreshkova, N.V. and Belokon, M.M., Assessment of the genetic variation of Siberian larch using microsatellite markers, Vestn. Mos. Gor. Univ. Lesa—Lesnoy Vestn., 2012, vol. 84, no. 1, pp. 118–122.

    Google Scholar 

  5. Oreshkova, N.V., Belokon, M.M., and Jamiyansuren, S., Genetic diversity, population structure, and differentiation of Siberian larch, Gmelin larch, and Cajander larch on SSR-marker data, Russ. J. Genet., 2013, vol. 49, no. 2, pp. 178–186. https://doi.org/10.1134/S1022795412120095.

    Article  CAS  Google Scholar 

  6. Krutovsky, K.V., Oreshkova, N.V., Putintseva, Y., et al., Preliminary results of de novo whole genome sequencing of the Siberian larch (Larix sibirica Ledeb.) and the Siberian stone pine (Pinus sibirica Du Tour), Siberian Journal of Forest Science, 2014, vol. 1, no. 4, pp. 79–83.

    Google Scholar 

  7. Oreshkova, N.V., Putintseva, Yu.A., Kuzmin, D.A., et al., Genome sequencing and assembly of Siberian larch (Larix sibirica Ledeb.) and Siberian pine (Pinus sibirica Du Tour) and preliminary transcriptome data, in Proceedings of the 4th International Conference on Conservation of Forest Genetic Resources in Siberia, Barnaul, 2015, pp. 127–128.

    Google Scholar 

  8. Sadovsky, M.G., Putintseva, Y.A., Birukov, V.V., et al., De novo assembly and cluster analysis of Siberian larch transcriptome and genome, in Lecture Notes in Bioinformatics, 2016, vol. 9656, pp. 455–464.

    CAS  Google Scholar 

  9. Bolger, A.M., Lohse, M., and Usadel, B., Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 2014, vol. 30, no. 15, pp. 2114–2120. doi: 10.1093/bioinformatics/btu17

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Wang, X., Lu, P., and Luo, Z. GMATo: a novel tool for the identification and analysis of microsatellites in large genomes, Bioinformation, 2013, vol. 9, no. 10, pp. 541–544.

    Article  PubMed  PubMed Central  Google Scholar 

  11. Martins, W.S. Lucas, D.C.S., Neves, K.F.S., and Bertioli, D.J., WebSat—a web software for microsatellite marker development, Bioinformation, 2009, vol. 3, no. 6, pp. 282–283.

    Article  PubMed  PubMed Central  Google Scholar 

  12. Devey, M.E., Bell, J.C., Smith, D.N., et al., A genetic linkage map for Pinus radiata based on RFLP, RAPD, and microsatellite markers, Theor. Appl. Genet., 1996, vol. 92, no. 6, pp. 673–679. doi 10.1007/BF00226088

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Genome Research and Education Center, Siberian Federal University, Krasnoyarsk, 660036, Russia

    N. V. Oreshkova, Yu. A. Putintseva, V. V. Sharov, D. A. Kuzmin & K. V. Krutovsky

  2. Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Krasnoyarsk, 660036, Russia

    N. V. Oreshkova

  3. Georg-August University of Göttingen, Göttingen, 37077, Germany

    K. V. Krutovsky

  4. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119333, Russia

    K. V. Krutovsky

  5. Texas A&M University, College Station, TX, 77843-2138, USA

    K. V. Krutovsky

Authors
  1. N. V. Oreshkova
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yu. A. Putintseva
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. V. V. Sharov
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. D. A. Kuzmin
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. K. V. Krutovsky
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to N. V. Oreshkova.

Additional information

Published in Russian in Genetika, 2017, Vol. 53, No. 11, pp. 1278–1284.

The article was translated by the authors.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Oreshkova, N.V., Putintseva, Y.A., Sharov, V.V. et al. Development of microsatellite genetic markers in Siberian larch (Larix sibirica Ledeb.) based on the de novo whole genome sequencing. Russ J Genet 53, 1194–1199 (2017). https://doi.org/10.1134/S1022795417110096

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S1022795417110096

Keywords

Search

Navigation