Department of Chemistry and Biotechnology

We study genetic, molecular and cellular aspects of plant-pathogen interactions. As experimental host plant species, we use different cereals as well as model plants (Arabidopsis thaliana and tobacco).

We identify and characterize, using next-generation sequencing techniques, viruses infecting cereal crops in Estonia and neighbouring countries.

We identify and characterize, using next-generation sequencing techniques, viruses infecting cereal crops in Estonia and neighbouring countries. We are the coordinators of EUPHRESCO ERA-Net project “Epidemiology and diagnosis of viruses infecting cereal crops”, which gathers together 24 international partner organizations.

We study especially sobemoviruses, and are members of ICTV. Thanks to the PARROT project “Emergence and divergence of sobemoviruses“ we have reinforced our cooperation with the French National Research Institute for Sustainable Development.

In plant molecular biology, we do research on ABCE proteins that are involved in translation and RNA silencing suppression.

We take part in an EEA-RESEARCH-64 project entitled “Improving adaptability and resilience of perennial ryegrass for safe and sustainable food systems through CRISPR-Cas9 technology (EditGrass4Food)”,  supported by European Economic Area and Norway Grants (EEA/Norway). Our partners are the University of Latvia, the Norwegian University of Life Sciences and the Lithuanian Research Centre for Agriculture and Forestry. Perennial ryegrass (Lolium perenne) is the dominant forage grass species in Europe due to its high regrowth capacity and high nutritive value. However, perennial ryegrass exhibits poor performance under unfavourable environmental conditions. Using CRISPR-based editing we will validate candidate genes involved in northern adaptation of perennial ryegrass. We focus on genes involved in the mechanisms of freezing tolerance and biomass growth under water deficit. By improving forage production benefits directly dairy and meat industries. Therefore, this project contributes to sustainable food systems.

We coordinate the EMP project entitled “An innovative platform for Estonia-Norway research-based teaching in bioinformatics and gene editing”. Our partner is NMBU. TalTech and NMBU students participated in a bioinformatics course that took place in Norway in May 2022. Next Spring students will attend our course on CRISPR/Cas technologies. 

We cooperate with Estonian Crop Research Institute to develop contemporary precision gene editing and genotyping methods (CRISPR/Cas, SSR, KASP, SNPs) for fast and cost-effective genomic selection in barley breeding.

We are part of a project of the Department of Marine Systems that aims to characterise green algae isolated from lakes in Sweden.

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

• Cecilia Sarmiento – senior researcher, research group leader
• Triin Vahisalu – senior researcher
• Irena Jakobson  – researcher
• Lenne Nigul – engineer
• Signe Nõu – engineer
• Kairi Kärblane – engineer
• Ferenz Sustek – PhD student, early-stage researcher
• Anna Ivanova-Pozdejeva – PhD student (together with Estonian Crop Research Institute)
• Evelyn Pil – PhD student (together with the Department of Marine Systems)
• Mirjam Nuter – MSc student
• Greete Urvak – MSc student
• Grete Jõgisoo – MSc student (together with Estonian Crop Research Institute)
• Marlene Kaljumäe – MSc student (together with the Department of Marine Systems)
• Pille Leesmäe – MSc student (together with the Department of Marine Systems)
• Laura Johanna Kadak – MSc student (together with the Department of Marine Systems)
• Mihhail Drozdov – BSc student
• Katariina Laretei – BSc student (together with the Department of Marine Systems)
• Kristian Pärt – BSc student (together with the Department of Marine Systems)
• Mariliis Pukk – BSc student (together with the Department of Marine Systems)

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.; Bull, S.E.; Eeckhaut, T.; Fladung, M.; Galovic, V.; Linkiewicz, A. and Lukan, 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

Merits, A.; Abroi, A.; Kurg, R.; Žusinaite, E.; Truve, E.; Sarmiento, C.; Sõmera, M.; Saar, T.; Viltrop, A.; Lutsar, I.; Avi, R.; Karki, T.; Huik, K.; Kõljalg, S.; Brilene, T.; Roots, I.; Inno, H. (2022). Üldine ja Meditsiiniline viroloogia. Tartu: Tartu Ülikooli kirjastus [ilmumas].

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.

Sõmera, M.; Massart, S.; Tamisier, L.; Sooväli, P.; Sathees, K.; Kvarnheden, A. (2021). A Survey Using High-Throughput Sequencing Suggests That the Diversity of Cereal and Barley Yellow Dwarf Viruses Is Underestimated. Frontiers in Microbiology , 12. DOI: 10.3389/fmicb.2021.673218.

Sõmera, M.; Kvarnheden, A.; Desbiez, C.; Blystad, D.-R.; Sooväli, P.; Kundu, J. K.; Gantsovski, M.; Nygren, J.; Lecoq, H.; Verdin, E.; Spetz, C.; Tamisier, L.; Truve, E.; Massart, S. (2020). Sixty Years after the First Description: Genome Sequence and Biological Characterization of European Wheat Striate Mosaic Virus Infecting Cereal Crops. Phytopathology, 110, 68−79. DOI: 10.1094/PHYTO-07-19-0258-FI.

Project "Improving adaptability and resilience of perennial ryegrass for safe and sustainable food systems through CRISPR-Cas9 technology - EditGras4Food"
Project No. EEA-RESEARCH-64
Implementation period 01/05/2021-30/04/2024
Funding total funding 1 000 000 euros (for TalTech: 225 500)

Due to an increase in the consumption of food, feed, fuel and to meet global food security needs, there is a necessity to breed for high yielding crops that can adapt to future climate changes. Perennial ryegrass (Lolium perenne) is the dominant forage grass species in Europe due to its high regrowth capacity, rapid establishment, tolerance to frequent cutting and grazing, and high nutritive value for ruminant livestock. However, perennial ryegrass exhibits poor performance under unfavourable environmental conditions compared to other cool season forage grass species, thus the changing climate pose a substantial challenge to perennial ryegrass cultivation in the Nordic/Baltic region. In this project, we intend to utilize unique pre-breeding material, developed by the members of our consortium in the ongoing Nordic/Baltic Public-Private Partnership project on pre-breeding of perennial ryegrass and CRISPR-based editing to validate candidate genes involved in northern adaptation of perennial ryegrass. We will focus on genes involved in the mechanisms of freezing tolerance and biomass growth under water deficit. Moreover, we will investigate changes during abiotic stress periods at the transcriptome level to reveal gene regulatory pathways and networks. This project aims at improving perennial ryegrass for winter hardiness, persistence and biomass formation under water-limited conditions. This will enable us to utilize the gained information in future genomic selection programs to develop ryegrass cultivars with improved freezing and drought tolerance and persistence. It will also help breeders and agriculture in general in the Nordic/Baltic region to prepare for meeting new demands due to climate change and changing societal demands. Importantly, by improving forage production, dairy and meat industries will directly benefit and therefore this project contributes to safe and sustainable food systems.

The aim of the project is to utilize transcriptomics and functional genomics to increase sustainability in agriculture through improvement of perennial ryegrass with better adaptation to frost and drought for current and future climates.

Main objectives:

1. Establish a diverse perennial ryegrass core association panel by utilization of data from ongoing projects (WP1)
2. Screen the association panel in order to detect haplotype-resolved single-nucleotide
   variants and structural variation in the targeted genes/alleles for freezing and drought
   genes (WP1)
3. Identify novel genes and characterize drought and freezing tolerance genes by
   comparing their expression for pathway related genes in non-edited and mutant plants
   (WP2)
4. Develop CRISPR-Cas9 constructs and generate CRISPR-edited perennial ryegrass
   mutants for freezing and mild drought tolerance (WP3)
5. Validate and characterize the role of the genes and their sequence variations in the
   freezing and drought mechanisms (WP4)

TalTech is involved in WP3, WP4 and WP5

Baltic Research Programme’s project Improving adaptability and resilience of perennial ryegrass for safe and sustainable food systems through CRISPR-Cas9 technology - EditGrass4Food  is financially supported by European Economic Area (EEA) Grants.
The project is developed in cooperation with University of Latvia as promoter, Norwegian University of Life Sciences and Lithuanian Agriculture and Forestry Sciences Center.

Links:

• https://eeagrants.lv/
• https://eeagrants.org/
• www.editgrass4food.lu.lv

Contact person: Cecilia Sarmiento (cecilia.sarmiento@taltech.ee)
Responsable for communication: Ferenz Sustek (fesust@taltech.ee)

This project aims to develop tools for teaching two cutting-edge technologies needed in almost all the fields of Life Sciences. The project is coordinated by TalTech and NMBU as partner. During the project, material for lectures and practical work in the laboratories will be developed. These tools will be tested in two 10 days long intensive courses for MSc and PhD students. The tools developed will be presented at the end of the project in a seminar in TalTech with PhD students presenting their work. A special emphasis will be given to gene editing technologies, including science policy, since this topic is of interest to different stakeholders.