Plant Developmental Genetics

Our research centers on the genetic and epigenetic control of plant reproduction. We are interested in both sexual reproduction and apomixis, a form of asexual reproduction through seeds. We use Arabidopsis thaliana and Zea may sas model systems, but also work with several other plant species.

Our studies have shown that both genetic and epigenetic mechanisms play a key role in plant reproduction. The long term goal of our research is to elucidate the role of positional information, cell-cell communication and epigenetic regulation of gene expression in plant morphogenesis and cellular differentiation. Furthermore we are investigating the role of epigenetic mechanisms in development, ecology, and evolution. Towards these goals we use a broad range of integrated, interdisciplinary approaches combining classical genetics, systems biology, ecology, chemistry and mathematics, and we collaborate both scientifically and technically with a number of institutions in Switzerland, as well as abroad. Our research is funded by a number of sources, notably the European Union, the Swiss National Science Foundation, SystemsX.ch, the Zürich-Basel Plant Science Center, and University Research Priority Program Systems Biology/Functional Genomics.

• Adaptive reduction of male gamete number in the selfing plant Arabidopsis thaliana
  Tsuchimatsu, T; Kakui, H; Yamazaki, M; Marona, C; Tsutsui, H; Hedhly, A; Meng, D; Sato, Y; Stadler, T;Grossniklaus, U; Kanaoka, MM; Lenhard, M; Nordborg, M; Shimizu, KK
  Nature Communications  8 June 2020., 10.1038/s41467-020-16679-7
• Dynamics of apomictic and sexual reproduction during primary succession on a glacier forefield in the Swiss Alps
  Sailer, Christian; Stocklin, Jurg; Grossniklaus, Ueli
  Scientific Reports 10.1038/s41598-020-64367-9  MAY 19 2020
• Cell type-specific genome scans of DNA methylation divergence indicate an important role for transposable elements
  Kartal O; Schmid MW; Grossniklaus U
  Genome Biology 2020 10.1186/s13059-020-02068-2
• A single touch can provide sufficient mechanical stimulation to trigger Venus flytrap closure
  Burri, Jan T.; Saikia, Eashan; Laeubli, Nino F.; Vogler, Hannes; Wittel, Falk K.; et al.
  Plos Biology 2020, 10.1371/journal.pbio.3000740
• Adaptive reduction of male gamete number in the selfing plant Arabidopsis thaliana
  Tsuchimatsu, T; Kakui, H; Yamazaki, M; Marona, C; Tsutsui, H; Hedhly, A; Meng, D; Sato, Y; Stadler, T;Grossniklaus, U; Kanaoka, MM; Lenhard, M; Nordborg, M; Shimizu, KK
  Nature Communications  8 June 2020., 10.1038/s41467-020-16679-7
• Acute heat stress during stamen development affects both the germline and sporophytic lineages in Arabidopsis thaliana (L.) Heynh.
  Hedhly, Afif; Nestorova, Anna; Herrmann, Anja; Grossniklaus, Ueli
  Environmental And Experimental Botany 10.1016/j.envexpbot.2020.103992 Published: MAY 2020
• A pseudomolecule-scale genome assembly of the liverwort Marchantia polymorpha
  Diop, Seydina I.; Subotic, Oliver; Giraldo-Fonseca, Alejandro; Waller, Manuel; Kirbis, Alexander; et al.
  Plant Journal  DOI: 10.1111/tpj.14602  Published: MAR 2020
• Structural basis for recognition of RALF peptides by LRX proteins during pollen tube growth
  Moussu, Steven; Broyart, Caroline; Santos-Fernandez, Gorka; Augustin, Sebastian; Wehrle, Sarah; Grossniklaus, Ueli; Santiago, Julia
  Proceedings Of The National Academy Of Sciences Of The United States Of America  DOI: 10.1073/pnas.2000100117  Published: MAR 31 2020
• Differential gene expression profiling of one- and two-dimensional apogamous gametophytes of the fern Dryopteris affinis ssp. affinis
  Wyder, Stefan; Rivera, Alejandro; Valdes, Ana E.; Jesus Canal, Maria; Gagliardini, Valeria; Fernandez, Helena; Grossniklaus, Ueli
  Plant Physiology And Biochemistry  148: 302-311 DOI: 10.1016/j.plaphy.2020.01.021 MAR 2020
• To preserve or to destroy, that is the question: the role of the cell wall integrity pathway in pollen tube growth
  Vogler, Hannes; Santos-Fernandez, Gorka; Mecchia, Martin A.; Grossniklaus, Ueli
  Current Opinion In Plant Biology,  DOI: 10.1016/j.pbi.2019.09.002
• Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies (vol 5, 50, 2018)
  Zhang, Lei; Cai, Xu; Wu, Jian; Liu, Min; Grob, Stefan; Cheng, F; Liang, JL; Cai, CC; Liu, ZY; Liu, B; Wang, F; Li, S; Liu, FY; Li, XM; Cheng, L; Yang, WC; Li, MH; Grossniklaus, U; Zheng, HK; Wang, XW
  Horticulture Research,  DOI: 10.1038/s41438-019-0210-y
• Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars
  Kuon, JE; Qi, WH; Schlapfer, P; Hirsch-Hoffmann, M; von Bieberstein, PR; Patrignani, A; Poveda, L; Grob, S; Keller, M; Shimizu-Inatsugi, R; Grossniklaus, U; Vanderschuren, H; Gruissem, W
  BMC BIOLOGY, 17 (1):10.1186/s12915-019-0697-6 SEP 18 2019
• The SMC5/6 Complex Subunit NSE4A Is Involved in DNA Damage Repair and Seed Development
  Diaz, M; Pecinkova, P; Nowicka, A; Baroux, C; Sakamoto, T; Gandha, PY; Jerabkova, H; Matsunaga, S; Grossniklaus, U; Pecinka, A
  PLANT CELL, 31 (7):1579-1597; 10.1105/tpc.18.00043 JUL 2019
• Invasive DNA elements modify the nuclear architecture of their insertion site by KNOT-linked silencing in Arabidopsis thaliana
  Grob, S; Grossniklaus, U
  GENOME BIOLOGY, 20 10.1186/s13059-019-1722-3 JUN 11 2019
• Seeds – An evolutionary innovation underlying reproductive success in flowering plants
  Baroux, C; Grossniklaus, U
  PLANT DEVELOPMENT AND EVOLUTION, 131 605-+; 10.1016/bs.ctdb.2018.11.017 2019
  Current Topics in Developmental Biology
• The Boechera Genus as a Resource for Apomixis Research
  Brukhin, V; Osadtchiy, JV; Florez-Rueda, AM; Smetanin, D; Bakin, E; Nobre, MS; Grossniklaus, U
  FRONTIERS IN PLANT SCIENCE, 10 10.3389/fpls.2019.00392 APR 2 2019
• Consistent Reanalysis of Genome-wide Imprinting Studies in Plants Using Generalized Linear Models Increases Concordance across Datasets
  Wyder, Stefan; Raissig, Michael T.; Grossniklaus, Ueli
  SCIENTIFIC REPORTS, 9 10.1038/s41598-018-36768-4 FEB 4 2019
• Contribution of epigenetic variation to adaptation in Arabidopsis
  Schmid, MW; Heichinger, C; Schmid, DC; Guthorl, D; Gagliardini, V; Bruggmann, R; Aluri, S; Aquino, C; Schmid, B; Turnbull, LA; Grossniklaus, U
  NATURE COMMUNICATIONS, 9 10.1038/s41467-018-06932-5 OCT 25 2018
• …

• Genetic and molecular mechanisms controlling female gametophyte development and function, focusing on cell specification and fertilization
• Investigation of the molecular basis of parental effects and genomic imprinting in plants
• Genetics and epigenetics of adaptation in a changing environment
• Identification of apomictic traits in maize using genetic approaches
• Systems biology of reproductive tissues of Arabidopsis thaliana

• Joint projects with mathematicians and computational scientists: B. Hellriegel (Verlag Birkhäuser, Basel), R. Smith (UniBe), T. Wicker (UZH), C. von Mering (UZH)
• Joint projects with ecologists: J. Stöcklin (UniBas), B. Schmid (UZH), L. Turnbull (UZH)  
• Joint projects with engineers and chemists: B. Nelson (ETHZ), N. Luedtke (UZH)