Sebastian Soyk received his PhD in 2013 from the ETH Zürich after carrying out his doctoral thesis in the group of Dr. Samuel Zeeman at the Institute of Agricultural Sciences. He then became a European Molecular Biology Organization post-doctoral fellow at the Cold Spring Harbor Laboratory in the group of Zachary Lippman. In August 2019 he joined the Center for Integrative Genomics at the University of Lausanne as a Swiss National Science Foundation Assistant Professor supported by a European Research Council Starting Grant. He joined the Department for Plant Molecular Biology in February 2023 as Tenure-track Assistant Professor.
Development, stem cells, domestication, gene editing, tomato
Research summary
Our research aims at understanding the genetic mechanisms that regulate flowering and flower production in plants, and the underlying developmental processes were shaped during crop domestication and breeding. More specifically, we study the development of inflorescences, the flower-bearing shoots, which arise when small groups of pluripotent stem cells at the growing tips cease the production of vegetative organs and transition to reproductive growth. The rate in which stem cells transition and differentiate finely balances vegetative and reproductive growth for optimized flower, fruit, and seed production. Many genes and gene variants that affect stem cell development were targets of selection during domestication and have potential in crop improvement. However, their effects often differ when introduced into disparate genetic backgrounds due to interactions with genetic modifiers. We use approaches in molecular genetics, genomics, and biochemistry to reveal and dissect signaling pathways and genetic interactions that regulate stem cell development in the model crop tomato, and advance our ability to fine-tune shoot and inflorescence architecture for optimized yields in tomato and other crops.
Representative publications
Alonge, M., Lebeigle, L., Kirsche, M., Aganezov, S., Wang, X., Lippman, Z.B., Schatz, M.C.+, Soyk, S.+ (2022). Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biology 23, 258. https://doi.org/10.1186/s13059-022-02823-7
Gaarslev, N., Swinnen, Soyk, S. (2021). Meristem transitions and plant architecture - learning from domestication for crop breeding. Plant Physiology 187(3):1045-1056. https://doi.org/10.1093/plphys/kiab388
Soyk, S.*, Lemmon, Z.H.*, Oved, M., Fisher, J., Liberatore, K.L., Park, S., Pistunov, A., Zemach, I., Jiang, K., Ramos, A., Van Eck, J., van der Knaap, E., Zamir, D., Eshed, Y., and Lippman, Z.B. (2017). Bypassing negative epistasis on yield in tomato imposed by a domestication gene. Cell 169(6): 1142-1155. http://dx.doi.org/10.1016/j.cell.2017.04.032
Soyk, S., Muller, N.A., Park, S.J., Schmalenbach, I., Jiang, K., Hayama, R., Zhang, L., Van Eck, J., Jimenez-Gomez, J.M., and Lippman, Z.B. (2017). Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato. Nature Genetics 49, 162–168. http://dx.doi.org/10.1038/ng.3733
+corresponding author
*equally contributing author
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Natalia González Gaarslev - PhD Student Natalia completed her Bachelor’s degree in Biology at Universidad Complutense de Madrid (UCM) in 2017. She enrolled in an exchange program at Högskolan i Gävle (HiG) to study Nordic Ecology. During the last year of her Bachelor’s degree she developed a strong interest towards the fields of genetics and molecular biology. Combining her lifelong passion for plants with these two fields, Natalia switched gears and enrolled in a joint Master’s program in Genetics and Molecular Plant Science at Uppsala University (UU), Stockholm University (SU) and Sveriges Lantbruksuniversitet (SLU). During her Master thesis work she developed skills in genomics and evolutionary biology. After graduating in July 2019, Natalia joined the Soyk Lab as a PhD student in 2020. She aims to identify genes that shape inflorescence architecture in tomato by studying natural genetic variation and gene expression dynamics.
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Gwen Swinnen - Post-doctoral Fellow Gwen obtained her Bachelor and Master degrees in Biochemistry and Biotechnology at Ghent University. During her Master thesis, she studied how to increase the activity of a jasmonate-related transcription factor to boost the production of specialized metabolites under supervision of Prof. Alain Goossens and Dr. Laurens Pauwels. She stayed for her PhD thesis, during which she examined the jasmonate-related transcriptional control of steroidal glycoalkaloid metabolism and organ size in tomato. Gwen joined the Soyk lab in July 2020, where she aims at exposing gene interactions that affect tomato inflorescence architecture and defining the molecular principles behind them.
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Anna Glaus - PhD Student Anna earned her bachelor’s degree in cell biology in 2019 from the University of Bern, where she investigated the viruses of the respiratory disease complex in Swiss cattle.
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Leana Keel - Helping student Leana is a third-year bachelor student in biology at UNIL. Since December 2022, she helps the lab with the transfer of the tissue cultures, the seed extraction, and taking care of the plants in the greenhouse. |
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Talia Stupp - Helping Student Talia is a third year student of a bachelor in biology at UNIL. She joined the lab in June 2023 and supports the group by extracting seeds, transferring explants in the tissue culture, and taking care of plants in the greenhouse. |
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Miguel Loera-Sánchez - Post-doctoral Fellow Miguel obtained his bachelor's degree in Genomic Biotechnology at the Autonomous University of Nuevo León (Mexico) in 2013. After spending an exchange year at the University of Göttingen (Germany) during his bachelor’s studies, he returned there and obtained his master’s degree in Microbiology and Biochemistry in 2015. In 2016 he joined the group of Prof. Bruno Studer at ETH Zurich. There he applied multiple genomic and targeted sequencing approaches to develop a method to assess genetic diversity in multiple grassland species. He obtained his doctoral degree in 2021 and stayed as a postdoctoral researcher at the same group until 2023. He joined the Soyk lab in July 2023, where he aims to decipher how domestication affected cis-regulatory elements of genes that influence plant architecture.
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Stéphanie Stolz - Lab Technician Stéphanie received her Master degree in Biology from UNIL in the 1990’s. She then worked as a scientific collaborator at Agroscope in Changins where she applied molecular approaches to analyse antifungal activities of leaf thionins in transgenic potato plants. In 1997, Stéphanie joined the group of Prof. Ted Farmer at the DBMV where she worked on projects related to plant defense. She supported the group as a lab technician for more than 20 years and collaborated with many scientists from all over the world. Stéphanie joined the Soyk lab in August 2023 and supports the group with her expertise in molecular biology and continues to enjoy the nice atmosphere of the DBMV. |
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Elia Lacchini - Post-doctoral Fellow During his Bachelor's in Crops Sciences at the University of Milan (Italy), Elia studied the impact of conservation agriculture practices on soil fertility, emissions, and plant yield. Later he got a Master’s in Plant Biotechnology in Martin Kater’s group, focusing on MADS-box transcription factors regulating rice flower development. There he then completed his PhD in 2018, working on genome editing and transformation protocols to improve the performance of the orphan crop Oryza glaberrima (African rice) by modifying inflorescence architecture, gaining interest for crop evolution and breeding. Next, during his postdoc in Alain Goossens’s group at VIB (Gent, Belgium), Elia identified and characterized novel biosynthetic enzymes enhancing the production of complex triterpenoid saponins from unconventional medicinal plants, with significant applications in gene therapy. In early 2024, Elia joined the Soyk lab, investigating how domestication and breeding affected the genetic background and interactions in tomato, impacting architecture and yield of reproductive meristems. |
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Ying completed her bachelor's degree in Horticulture at University of Henan Agriculture in 2015. Following this, she pursued her Master at Zhejiang University, focusing on grafting-induced transcriptional gene silencing in pear breeding. Her fascination with intracellular molecular transport led her to join Friedrich Kragler's research group at the Max Planck Institute of Molecular Plant Physiology. There she investigated how m5C modification regulates mRNAs to move over long-distance via the vasculature tissues and its modulation by developmental stage changes. She earned her doctoral degree in November 2022 and continued as a postdoctoral researcher in the same group until August 2023. She joined the Soyk lab in March 2024, where she aims to investigate how variation in cis-regulatory elements affects plant architecture in tomato. |
Former members
Antoine Chatillon - former helping student
Ludivine Lebeigle - former lab technician
Varjany Vashanthakumar - former student helper, now Master student at University of Bern
Estelle Vivien - former Master student
Stéphanie Afonso - former visiting Master student, now PhD student at INRAE Versailles
Louis Currat - former technician apprentice, now technician apprentice at UNIL
Marion Brechet - now at the DBMV of Université de Lausanne
Giti Ghazi Soltani - now at CHUV
Genschere: Der grosse Streit um kleine Schnitte (Neue Zürcher Zeitung)
Dialog Grün: De-novo-Domestikation: Erforschung und Erschliessung pflanzengenetischer Ressourcen (ETH Zürich)
Post-doctoral researchers and PhD students
We always welcome applications from motivated and talented students and postdocs, who are interested in joining the lab. Please send a cover letter describing your motivation to join the lab and a CV including a publication list in a single PDF file to Sebastian Soyk. Although internal funding may be available, all successful applicants will be strongly encouraged to apply for external sources of funding.
Master students
The Soyk lab offers First-Step and Master thesis projects to students in the Master of Science in Molecular Life Sciences program at UNIL. Please directly contact Sebastian Soyk for more details.
Undergraduate students
The Soyk lab participates in the Summer Undergraduate Research (SUR) program at UNIL and there may be additional opportunities during the rest of the year. Please directly contact Sebastian Soyk for more details.
