Sebastian Soyk received his PhD in 2013 from the ETH Zürich after carrying out his doctoral thesis in the group of 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. His research is supported by the Swiss National Science Foundation and a European Research Council Starting Grant.
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 how these 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 selected 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
Soyk, S.+, Lemmon, Z.H., Sedlazeck, F.J., Jiménez-Gómez, J.M., Alonge, M., Hutton, S.F., Van Eck, J., Schatz, M.C., and Lippman, Z.B.+ (2019). Duplication of a domestication locus neutralized a cryptic variant that caused a breeding barrier in tomato. Nature Plants 5, 471–479. http://dx.doi.org/10.1038/s41477-019-0422-z
Lemmon, Z.H., Reem, N.T. .*, Dalrymple.*, J., Soyk, S.*, Swartwood, K.E., Rodriguez-Leal, D., Van Eck, J., and Lippman, Z.B.. (2018). Rapid improvement of domestication traits in an orphan crop by genome editing. Nature Plants 4, 766–770. http://dx.doi.org/10.1038/s41477-018-0259-x
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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Ludivine Lebeigle - Technician Ludivine obtained her Bachelor’s degree in cellular biology and physiology in 2015 from the University of Dijon, where she studied the inflammatory response and cytotoxicity in response to natural plant defense stimulators in zebra fish. She obtained her Master’s degree in plant biology in 2017 from the INRA Centre of Dijon, where she focused on the identification and characterization of secondary metabolites in pea and faba bean varieties in the laboratory of Richard Thompson. Then she worked for one year as a research assistant at the Institute of Plant Sciences at the University of Bern, where she studied pollinator-mediated speciation and evolution of flower morphology in Petunia in the laboratory of Cris Kuhlemeier. She joined our group in August 2019. |
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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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Varjany Vashanthakumar - Student helper Varjany joined the lab in 2020 as a student helper and studies Biology at University of Lausanne. She is responsible for the seed collection and takes care of all plants in the greenhouse. |
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Estelle Vivien - Master Student Estelle obtained her Bachelor in Biology and started her Master in Molecular Life Sciences at UNIL. She did a First-Step project at the DBMV in Prof. Philippe Reymond’s lab where she studied plant defenses against insect oviposition. She joined the Soyk lab in March 2022 for her Masters thesis, where she investigates the role of transcription factors in the flowering time of tomato. |
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Stéphanie Afonso - Master Student Stéphanie passed her Bachelor’s degree in Organismal Biology in 2020 at the University of Dijon (France), where she became interested in plant biology and the evolution of organisms. At the same time, she began volunteering in associations for the protection of the fauna and flora in Dijon, both as active member and treasurer. She decided to continue her studies to obtained a Master's degree in Plant Biology with a specialisation in plant-microorganism-environment interactions in Dijon. There she joined the group of Sergio J. Ochatt in 2021 in the FILEAS team of INRAe (Dijon). She mainly used flow cytometry and fluorescence microscopy to study how the composition of plant cell walls changes when the formation of clathrin vesicles and membrane trafficking is disrupted. Stephanie joined the Soyk lab in January 2022 as an international Master’s degree internship student, where she studies how gene interactions influence plant architecture, with the aim to discover genetic suppressors of inflorescence branching in tomato. |
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Louis Currat - Laboratory technician apprentice Louis is a laboratory technician apprentice and joined the Soyk group in April. He previously worked with Richard Benton's group for three months and at the Genotyping facility during three months. He studies in Essanté, a School of Health. He loves sports, Japanese culture and Biology. |
Former members
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.
