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.

• 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; et al.
  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
• Whole-mount Clearing and Staining of Arabidopsis Flower Organs and Siliques
  Hedhly, A; Vogler, H; Eichenberger, C; Grossniklaus, U
  JOVE-JOURNAL OF VISUALIZED EXPERIMENTS, (134):10.3791/56441 APR 2018
• Feeling the force: how pollen tubes deal with obstacles
  Burri, Jan T.; Vogler, Hannes; Laubli, Nino F.; Hu, Chengzhi; Grossniklaus, Ueli; Nelson, Bradley J.
  NEW PHYTOLOGIST, 220 (1):187-195; 10.1111/nph.15260 OCT 2018
• Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies
  Zhang, L; Cai, X; Wu, J; Liu, M; Grob, S; 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, 5 10.1038/s41438-018-0071-9 AUG 15 2018
• Aberrant imprinting may underlie evolution of parthenogenesis
  Kirioukhova, O; Shah, JN; Larsen, DS; Tayyab, M; Mueller, NE; Govind, G; Baroux, C; Federer, M; Gheyselinck, J; Barrell, PJ; Ma, H; Sprunck, S; Huettel, B; Wallace, H; Grossniklaus, U; Johnston, AJ
  SCIENTIFIC REPORTS, 8 https://doi.org/10.1038/s41598-018-27863-7 JUL 13 2018
• Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis-Associated Genes
  Kliver, S; Rayko, M; Komissarov, A; Bakin, E; Zhernakova, D; Prasad, K; Rushworth, C; Baskar, R; Smetanin, D; Schmutz, J; Rokhsar, DS; Mitchell-Olds, T; Grossniklaus, U; Brukhin, V
  GENES, 9 (4):10.3390/genes9040185 APR 2018
• LRX Proteins Play a Crucial Role in Pollen Grain and Pollen Tube Cell Wall Development
  Fabrice, TN; Vogler, H; Draeger, C; Munglani, G; Gupta, S; Herger, AG; Knox, P; Grossniklaus, U; Ringli, C
  PLANT PHYSIOLOGY, 176 (3):1981-1992; https://doi.org/10.1104/pp.17.01374 MAR 2018
• Extensive epigenetic reprogramming during the life cycle of Marchantia polymorpha 
  Schmid, Marc W.; Giraldo-Fonseca, Alejandro; Roevekamp, Moritz; et al. 
  GENOME BIOLOGY, 19: 10.1186/s13059-017-1383-z JAN 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)