A cell atlas of temperature-dependent gene activities in the flower

• Applicant: Professorin Dr. Kerstin Kaufmann
• Subject Area: Plant Cell and Developmental Biology
• Term: from 2021 to 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 458750707

Plants are exposed to an environment that is inherently heterogeneous depending on the local habitat. Therefore, plants have evolved intricate adaptive mechanisms, and different organs and cell types vary in their environmental response programs. An excellent example for this is the environmental robustness of flower development, which is a key factor in determining the habitat range of plants. Once the decision to bloom has been made, floral organ development need to be robustly maintained irrespective of the local environment. However, it is still largely unknown how gene activity in different cell types and individual cells is controlled by environmental factors such as temperature.Novel single-cell omics technologies have started to unravel the intrinsic cellular heterogeneity in multicellular organisms. However, plant cells pose specific challenges to single cell omics, because the isolation of single cells is aggravated by the presence of a cell wall. We have established single nucleus RNA-seq in plants, which allows us to ‘freeze’ the native transcript states in nuclei and thereby overcomes the limitation of commonly used protoplasting techniques that result in the activation of many stress-related genes. Thus, this method allows us to study environmental responses in transcriptional activity. This project aims at using our snRNA-seq method to generate a cellular atlas of transcriptional changes associated with temperature adaptation in the flower. The goal is to generate temperature-dependent cell type atlases of gene activity in three species: the model plant Arabidopsis thaliana, its close relative Cardamine hirsuta and the crop plant species Solanum lycopersicum. In addition, we make use of the rich knowledge of natural variation within Arabidopsis by interrogating different ecotypes that reflect adaptations to different local environments within the large global habitat range of this species. By combining information on cell-type specific differences in gene activities with information on natural genetic variation, we can identify candidate genes involved in mediating temperature robustness of flower development. This project will provide an innovative proof-of-concept for using single cell omics technologies to understand cell-type specificity of environmental responses in plants, allowing these methods to be applied to other environmental conditions and biological questions in the future.

• DFG Programme: Research Grants