Department of Chemistry and Biotechnology

We study the genetic, molecular and cellular aspects of plant-microbe interactions. For this, we use various cereals, potato, tomato, and faba bean plants as hosts, as well as Arabidopsis thaliana and different tobacco species as experimental model plants.

Multifunctional ABCE genes remain a subject of study, but our main focus is on applying CRISPR-Cas technology to achieve optimal plant tolerance to both abiotic and biotic stresses. Specifically, transcriptomics and functional genomics are being employed to enhance the frost and drought tolerance of perennial ryegrass, thereby supporting agricultural sustainability. This project is conducted in collaboration with scientists from Latvia, Norway, and Lithuania.

One of our major projects is MARTA (Modern Breeding Tools for Smart Food Security), which aims to generate novel breeding knowledge and a toolbox of modern breeding methods to promote the development of climate- and disease-resistant, high-quality, sustainable and high-yielding plant varieties. Our tasks include developing new breeding techniques to obtain PVY-resistant potato and drought-tolerant faba bean plants. MARTA is funded by the Ministry of Regional Affairs and Agriculture of Estonia, led by METK (The Centre of Estonian Rural Research and Knowledge), with partners including the University of Tartu, the Estonian University of Life Sciences, and TalTech.

Within the framework of the Marie Skłodowska-Curie Actions (MSCA) COFUND programme INNOCHEMBIO, we have started research on obtaining PVY-resistant tomato plants using CRISPR-Cas techniques. This work is carried out in cooperation with the Genetics and Improvement of Fruit and Vegetables Unit in Avignon (INRAE). A second INNOCHEMBIO project, conducted in collaboration with the University of Helsinki, focuses on unraveling novel mechanisms in plant stress signaling and translating this knowledge into crop improvement, with a focus on faba bean.

Under a cooperation agreement with METK, genes determining disease resistance and yield in spring and winter wheat are being investigated using phytopathological methods and genotyping tools. We also develop precision breeding and genotyping tools in collaboration with METK to enable rapid and cost-effective genomic selection in barley breeding.

In addition, we continue research on sobemoviruses in collaboration with the French National Research Institute for Sustainable Development (Montpellier) and are members of ICTV.

We are part of a project at the Department of Marine Systems aimed at characterizing green algae isolated from lakes in Sweden.

Being part of the TARISTU24-TK28 project (Plant Biology and Valorization Infrastructure, coordinated by Tartu University, partners METK and Estonian University of Life Sciences, Avaleht | Taim) has enabled us to procure a biolistics system for plant transformation as well as growth chambers. A tissue culture chamber is being acquired and renovation of plant rooms is carried out.

As part of TAIM (Plant Biology Infrastructure) we offer two services:

• Determination of viral disease agents on plants using the next-generation sequencing
• Genome editing in plants or plant viruses using CRISPR-Cas9 technology

Members

Group Leader: Cecilia Sarmiento (Tenured Associate Professor, Programme Director)

Researchers: Triin Vahisalu (Senior Researcher), Irena Jakobson (Researcher), Jelena Mõttus (Researcher), Kairi Kärblane (Engineer), Lenne Nigul (Engineer) 

PhD Students, Early Stage Researchers: Nicoletta Cau, Jose Gutierrez, Ferenz Sustek

PhD Students: Anna Ivanova-Pozdejeva (together with METK); Marlene Kaljumäe, Pille Leesmäe and Evelyn Pil (together with the Department of Marine Systems)

MSc Students: Martin Paggi; Grete Jõgisoo (together with METK); Laura Johanna Kadak, Katariina Laretei and Kristian Pärt (together with the Department of Marine Systems) 

BSc Students: Ailika Külm; Daniil Orlovski (together with Jekaterina Mazina-Šinkar); Ilona Fjodorova and Aleksandrina Smirnova (together with the Department of Marine Systems)

Engineer: Signe Nõu

Assistant: Riina Turi
 

Sustek-Sánchez, F.; Eelmets, E.; Nigul, L.; Kärblane, K.; Laasmaa, M.; Balode-Sausina, M.; Berzina, S. A.; Ducis, D.; Kaktina, E.; Jaškūne, K.; Rognli, O. A.; Rostoks, N.; Sarmiento, C. (2026). Isolation and transformation of perennial ryegrass (Lolium perenne L.) protoplasts for the in vivo assessment of guide RNAs editing efficiency. Frontiers in Plant Science, 16, 1−14. https://doi.org/10.3389/fpls.2025.1744085

Van der Sman, P.; Järvekülg, L.; Stražev, A.; Puurand, T.; Pata, P.; Sarmiento, C.; Adams, I.; Sõmera, M. (2026). A Survey of Potato Virus Y Strains in Estonian Seed Potatoes. Plant Health Progress, 1−8. https://doi.org/10.1094/PHP-06-25-0175-S

Rubino, L.; Abrahamian, P.; An, W.; Aranda, M. A.; Ascencio-Ibañez, J. T.; … (2025). Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses from the Plant Viruses Subcommittee. Journal of General Virology, 106 (7), 002114. https://doi.org/10.1099/jgv.0.002114

Pashapu, A. R.; Statkevičiūtė, G.; Sustek-Sánchez, F.; Kovi, M. R.; Rognli, O. A.; Sarmiento, C.; Rostoks, N.; Jaškūnė, K. (2024). Transcriptome profiling reveals insight into the cold response of perennial ryegrass genotypes with contrasting freezing tolerance. Plant Stress, 14, 100598. https://doi.org/10.1016/j.stress.2024.100598

Jakobson, L.; Mõttus, J.; Suurväli, J.; Sõmera, M.; Tarassova, J.; Nigul, L.; Smolander, O.P. and Sarmiento, C. (2024). Phylogenetic insight into ABCE gene subfamily in plants. Frontiers in Genetics, 15, 1408665. DOI: 10.3389/fgene.2024.1408665

Ghafari, M., Sõmera, M., Sarmiento, C., Niehl, A., Hébrard, E., Tsoleridis, T., Ball, J., Moury, B., Lemey, P., Katzourakis, A. and Fargette, D. (2024). Revisiting the origins of the Sobemovirus genus: A case for ancient origins of plant viruses. PLoS Pathogens, 20(1), e1011911. DOI: 10.1371/journal.ppat.1011911

Frei, M.; Sarmiento, C.; Kärblane, K.; Niehl, A.; & Sõmera, M. (2023). Sequencing and biological characterization of historical cynosurus mottle virus isolates from Germany. Archives of Virology, 168(10), 265. DOI: 10.1007/s00705-023-05893-5

Cardi, T.; Murovec, J.; Bakhsh, A.; Boniecka, J.; Bruegmann, T.; … (2023). CRISPR/Cas-mediated plant genome editing: outstanding challenges a decade after implementation. Trends in Plant Science, 28(10), 1144-1165. DOI: 10.1016/j.tplants.2023.05.012

Jaślan, J; Marten, I.; Jakobson, L.; Arjus, T.; Deeken, R.; Sarmiento, C.; De Angeli, A.; Brosché, M.; Kollist, H.; Hedrich, R. (2023) ALMT‐independent guard cell R‐type anion currents. New Phytologist, 239(6), 2225-34. DOI: 10.1111/nph.19124

Sustek-Sánchez, Ferenz; Rognli, Odd Arne; Rostoks, Nils; Sõmera, Merike; Jaškūnė, Kristina; Kovi, Mallikarjuna Rao; Statkevičiūtė, Gražina; Sarmiento, Cecilia. (2023). Improving abiotic stress tolerance of forage grasses – prospects of using genome editing. Frontiers in Plant Science, 14. DOI: 10.3389/fpls.2023.1127532

Guarino, F.; Cicatelli, A.; Castiglione,S.; Agius, D. R.; Orhun, G. E.; Fragkostefanakis, S.; Leclercq, J.; Dobránszki, J.; Kaiserli, E.; Lieberman-Lazarovich, M.; Sõmera, M.; Sarmiento, C.; Vettori, C.; Paffetti, D.; Poma, A. M. G.; Moschou, P. N.; Gašparović, M.; Yousefi, S.; Vergata, C.; Berger, M. M. J.; Gallusci, P.; Miladinović, D.;  Martinelli, F. (2022). An Epigenetic Alphabet of Crop Adaptation to Climate Change. Frontiers in Genetics, 13. DOI: 10.3389/fgene.2022.818727

Sõmera, M.; Fargette D.; Hébrard, E.; Sarmiento, C.; ICTV Report Consortium (2021). ICTV Virus Taxonomy Profile: Solemoviridae. Journal of General Virology, 102 (12). DOI: 10.1099/jgv.0.001707.

Sarmiento, C.; Sõmera, M.; Truve, E. (2021). Solemoviruses (Solemoviridae). In: Bamford, D.; Zuckerman, M. (Ed.). Encyclopedia of Virology, 4th edition. Elsevier. DOI: 10.1016/B978-0-12-809633-8.21288-0.

Mõttus, J.; Maiste, S.; Eek, P.; Truve, E.; Sarmiento, C. (2021). Mutational Analysis of Arabidopsis thaliana ABCE2 Identifies Important Motifs for its RNA Silencing Suppressor Function. Plant Biology, 23 (1), 21−31. DOI: 10.1111/plb.13193.