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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Giti Ghazi Soltani - PhD Student Giti started her University studies in Agricultural Sciences with a focus on Plant Pathology at the University of Tabriz, Iran. Soon after she oriented towards insect taxonomy and obtained a Master’s degree from the University of Pierre and Marie Curie (UPMC) in Paris, where she investigated the taxonomy of a pollinator bee species that shows a ring distribution around the Mediterranean Sea. Then, she became interested in Molecular Plant Sciences and conducted a Master thesis in the group of Niko Geldner at UNIL in 2017, where she studied the function of an uncharacterized gene family in the model plant Arabidopsis thaliana with similarities to olfactory receptors of insect and putative roles in plant volatile perception. In November 2019 she joined the Soyk group as a PhD student. Here, she is interested in identifying genes and genetic interactions that regulate meristem development and plant architecture in the model crop tomato. |
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Marion Brechet - Master Student Marion obtained her Bachelor’s degree in Biological Sciences at UNIL in June 2019. Being a Master student in Molecular Life Sciences since September 2019, she joined our lab in February 2020 where she aims to characterize a gene involved in flowering transition and assess its role in the domestication of the model crop tomato. |
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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. |
