Laboratory of Plant System Biology

Elena Z. Kochieva
Professor, Dr.Sci. (Biology)
Head of Laboratory
INB, room 408
Телефон +7 (499) 135-30-50, +7 (499) 135-62-19

Main research areas:

  • Assessment of the genome diversity to address the issues of plant species taxonomy and phylogeny
  • Genotyping studies of bioresource collections
  • Studies of plant speciation and genome evolution
  • Studies of molecular and genetic mechanisms underlying plant development
  • Analysis of plant response to biotic and abiotic stresses
  • Development of molecular markers for genes of agricultural importance for MAS strategies in Solanaceae


Main achievements:

  • Biodiversity and phylogeny of wild and cultivated Solanaceae, Lemnaceae, Fabaceae, Fagopyrum, and Allium species were assessed, using AFLP, SSR, ISSR, SNP, S-SAP, etc.
  • In collaboration with the PRI (the Netherlands), RGA-profiling was developed, and the RGA gene family was analyzed in various plant families.
  • Molecular genotyping of more than 300 potato, tomato, pepper, and pea cultivars was performed. A methodology has been developed for EcoTILLING  in Solanaceae species resistance genes.
  • Carbohydrate metabolism genes were identified and characterized for a wide range of Solanaceae, Fabaceae, and Poaceae species and cultivars. Molecular markers for fruit/grain sugar and starch content were developed.
  • In Brassica, Solanum and Allium species, CSD-protein genes were identified. In Solanum species and cultivars, genes for PVX and G. pallida resistance were identified and analyzed.
  • In the leek Allium porrum L. accessions, differing in ascorbic acid content, the key genes of the L-galactose pathway of vitamin C biosynthesis were identified and characterized.
  • Homologs of the carotenoid and anthocyanin biosynthesis key genes were identified and characterized in a wide range of Solanaceae species and varieties.
  • Complete chloroplast genomes of Allium species (A. porrum, A. altaicum, A. obliquum, A. sativum, A. ramosum and A. regelianum) were determined.
  • The lab participated in sequencing and analysis of mycoheterotroph Monotropa hypopitys nuclear, chloroplast and mitochondrial genomes. The chloroplast genome variability was determined in Monotropa accessions and related Ericaceae photosynthetic species. Transcriptomes and miRNA libraries of various tissues of Monotropa hypopitys were sequenced and analyzed; MADS-box, YABBY, LEAFY and WOX gene families, as well as conserved miRNAs microRNA library was sequenced; species-specific and conservative microRNAs, including those associated with flowering and endomycorrhizal symbiosis, were identified and functionally characterized.
  • MADS-box and YABBY gene families were identified and characterized in cultivated and wild Solanum and Capsicum species. Donors of alleles of agronomic importance were determined, and molecular markers linked to the vegetation period and fruit multi-locule trait have been developed and verified.
  • In collaboration with the PRI (the Netherlands), sunflower and chrysanthemum MADS-box gene families were identified and characterized, including reverse genetics methods. Inflorescence miRNA family was characterized in WT and three lines of transgenic early-flowering chrysanthemums.


Selected publications:

  1. Slugina M.A., Shchennikova A.V., Meleshin A.A., Kochieva E.Z. Homologs of vacuolar invertase inhibitor INH2 in tuber-bearing wild potato species and Solanum tuberosum: gene polymorphism and co-expression with saccharolytic enzyme genes in response to cold stress. Scientia Horticulturae. 2020. 269:109425.
  2. Slugina M.A., Meleshin A.A., Shchennikova A.V., Kochieva E.Z. The Opposite Effect of Low Temperature on the Pho1a starch phosphorylase gene expression in Solanum tuberosum L. tubers and Petota species leaves. American Journal of Potato Research. 2020. 97:78-87.
  3. Slugina M.A., Shchennikova A.V., Kochieva E.Z. Differences in the sucrose synthase gene SUS1 expression pattern between Solanum lycopersicum and wild tomato species. Theoretical and Experimental Plant Physiology. 2019. 31(4):455-462.
  4. Slugina M.A., Shchennikova A.V., Kochieva E.Z. The expression pattern of the Pho1a genes encoding plastidic starch phosphorylase correlates with the degradation of starch during fruit ripening in green-fruited and red-fruited tomato species. Functional Plant Biology. 2019. 46(12):1146-1157.
  5. Filyushin M.A., Beletsky A.V., Kochieva E.Z. Characterization of the complete chloroplast genome of leek Allium porrum L. (Amaryllidaceae). Mitochondrial DNA Part B: Resources. 2019. 4(2):2602-2603.
  6. Slugina M.A., Shchennikova A.V., Pishnaya O.N., Kochieva E.Z. Assessment of the fruit-ripening-related FUL2 gene diversity in morphophysiologically contrasted cultivated and wild tomato species. Molecular Breeding. 2018. 38(7):82.
  7. Slugina M.A., Shchennikova A.V., Kochieva E.Z. LIN7 cell-wall invertase orthologs in cultivated and wild tomatoes (Solanum section Lycopersicon). Plant Molecular Biology Reporter. 2018. 36(2):195-209.
  8. Filyushin M.A., Beletsky A.V., Mazur A.M., Kochieva E.Z. Characterization of the complete plastid genome of lop-sided onion Allium obliquum L. (Amaryllidaceae). Mitochondrial DNA Part B: Resources. 2018. 3(1):393-394.
  9. Shchennikova A.V., Slugina M.A., Beletsky A.V., Filyushin M.A., Mardanov A.V., Shulga O.A., Kochieva E.Z., Ravin N.V., Skryabin K.G. The YABBY genes of leaf and leaf-like organ polarity in leafless plant Monotropa hypopitys. Int J Genomics. 2018. 2018:7203469.
  10. Shulga O.A., Shchennikova A.V., Beletsky A.V., Mardanov A.V., Kochieva E.Z., Filyushin M.A., Ravin N.V., Skryabin K.G. Transcriptome-wide characterization of the MADS-box family in pinesap Monotropa hypopitys reveals flowering conservation in non-photosynthetic myco-heterotrophs. Journal of Plant Growth Regulation. 2018. 37(3):768-783.
  11. Savelyeva E., Kalegina A., Boris K., Kochieva E., Kudryavtsev A. Retrotransposon-based sequence-specific amplified polymorphism markers for the analysis of genetic diversity and phylogeny in Malus Mill. (Rosaceae). 2017. Genet Resour Crop Evol 64(7):1499–1511.
  12. Beletsky A.V., Filyushin M.A., Gruzdev E.V., Mazur A.M., Prokhorchouk E.B., Kochieva E.Z., Mardanov A.V., Ravin N.V., Skryabin K.G. De novo transcriptome assembly of the mycoheterotrophic plant Monotropa hypopitys. Genomics Data. 2017. 11:60-61.
  13. Slugina M.A., Shchennikova A.V., Kochieva E.Z. TAI vacuolar invertase orthologs: the interspecific variability in tomato plants (Solanum section Lycopersicon). Molecular Genetics and Genomics. 2017. 292(5):1123-1138.
  14. Shulga O.A., Nedoluzhko A.V., Shchennikova A.V., Gruzdeva N.M., Shelenkov A.A., Sharko F.S., Sokolov A.S., Pantiukh E.S., Rastorguev S.M., Prokhortchouk E.B., Skryabin K.G. Profiling of microRNAs in wild type and early flowering transgenic Chrysanthemum morifolium by deep sequencing. Plant Cell, Tissue and Organ Culture. 2017. 128(2):283-301.
  15. Filyushin M.A., Slugina M.A., Shchennikova A.V., Kochieva E.Z. YABBY3-Orthologous Genes in Wild Tomato Species: Structure, Variability, and Expression. Acta naturae. 2017. 9(4):101-109.
  16. Ravin N.V., Gruzdev E. V., Beletsky A.V., Mazur A.M., Prokhorchouk E.B., Filyushin M.A., Kochieva E.Z., Kadnikov V.V., Mardanov A.V., Skryabin K.G. The loss of photosynthetic pathways in the plastid and nuclear genomes of the non-photosynthetic mycoheterotrophic eudicot Monotropa hypopitys. BMC Plant Biology. 2016. 16(3):153-161.
  17. Shcherban A.B., Kochieva E.Z., Salina E.A. Diversification of the Homoeologous Lr34 Sequences in Polyploid Wheat Species and Their Diploid Progenitors. Journal of Molecular Evolution. 2016. 82(6):291-302.
  18. Shchennikova A.V., Beletsky A.V., Shulga O.A., Mazur A.M., Prokhorchouk E.B., Kochieva E.Z., Ravin N.V., Skryabin K.G. Deep-sequence profiling of miRNAs and their target prediction in Monotropa hypopitys. Plant Molecular Biology. 2016. 91(4-5):441-458.
  19. Filyushin M.A., Beletsky A.V., Mazur A.M., Kochieva E.Z. The complete plastid genome sequence of garlic Allium sativum L. Mitochondrial DNA Part B: Resources. 2016. 1(1):831-832.
  20. Goryunova S.V., Salentijn E.M.J., Chikida N.N., Kochieva E.Z., van der Meer I.M., Glissen L.J.W.J., Smulders M.J.M. Expansion of the gamma-gliadin gene family in Aegilops and Triticum. BMC Evolutionary Biology. 12(1):215.
  21. Goloveshkina E.N., Shchennikova A.V., Kamionskaya A.M., Skryabin K.G., Shulga O.A. Influence of ectopic expression of Asteraceae MADS box genes on plant ontogeny in tobacco. Plant Cell Tiss Organ Cult. 2012. 109(1):61-71
  22. Immink R.G.H., Tonaco I.A.N., de Folter S., Shchennikova A., van Dijk A.D.J., Busscher-Lange J., Borst J.W., Angenent G.C. SEPALLATA3: the ‘glue’ for MADS box transcription factor complex formation. Genome Biology. 2009. 10(2):R24
  23. Urbanus S.L., Folter S.D., Shchennikova A.V., Kaufmann K., Immink R.G.H., Angenent G.C. In planta localisation patterns of MADS domain proteins during floral development in Arabidopsis thaliana. BMC Plant Biol. 2009. 9(1):5
  24. de Folter S., Shchennikova A.V., Franken J., Bussher M., Baskar R., Grossniklaus U., Angenent G.C., Immink R.G. A Bsister MADS-box gene involved in ovule and seed development in petunia and Arabidopsis. The Plant J. 2006. 47:934-946
  25. Ferrario S., Shchennikova A.V., Franken J., Immink R.G., Angenent G.C. Control of floral meristem determinacy in Petunia by MADS-box transcription factors. Plant Physiol. 2006. 140(3):890-898
  26. Shchennikova, A. V., Shulga, O. A., Immink, R., Skryabin, K. G., Angenent, G. C. Identification and characterization of four chrysanthemum MADS-box genes, belonging to the APETALA1/FRUITFULL and SEPALLATA3 subfamilies. Plant Physiology. 2004. 134(4):1632-1641
  27. Van Der Linden C.G., Wouters D.C.A.E., Mihalka V., Kochieva E.Z., Smulders M.J.M., Vosman B. Efficient targeting of plant disease resistance loci using NBS profiling. Theoretical and Applied Genetics. 2004. 109(2):384-393
  28. Ferrario S., Immink R.G.H., Shchennikova A., Busscher-Lange J., Angenent G.C. The MADS box gene FBP2 is required for the SEPALLATA function in petunia. The Plant Cell J. 2003. 15(4):914-925
  29. Tsugeki R., Kochieva E.Z., Fedoroff N.V. A transposon insertion in the arabidopsis ssr16 gene causes an embryo-defective lethal mutation. The Plant J. 1996. 10(3):479-489