STSM PROJECT PROPOSALS
You are interested in learning methods related to the WGs of Action FA1306? You want to be part of medium to large-scale phenotyping experiments and gain experience in labs with phenotyping expertise? Then check the STSM project proposals below and let these guide you in developing your STSM project and application!
Please coordinate your application together with the given contact persons!
3D imaging - algorithm development or validation of existing tools
Within the EPPN project our research group has developed a detailed full 3D reconstruction approach for plant phenotyping (link). We are able to create 3D models based on a multi-camera setup in less than 1/10 of a second. We are working on different developmental stages (seedling, young plants up to 70 cm). STSM participants are invited to join our research group to link this imaging approach to their on-going research projects in our group. Potential topics are; 3D models and the interaction with robotics for local measurement on plant parts and/ or other the automation of other manual tasks. Another topic can be the validation of measured architectural traits of plants comparing different genotypes and or treatments (leaf angle, leaf length, internode length, etc).
Work Group: 1
Offer: Training in 3D imaging and feature extraction
Duration: 2-3 months
Place: Wageningen UR, Netherlands
Contact: rick.vandezedde@wur.nl
Stress responses of wheat cultivars to drought, heat and different CO2 conditions
Four wheat cultivars will be subjected to different stress treatments (such as drought, heat and different CO2 conditions) and their reaction monitored by measurements of Gas exchange, porometry, chlorophyll content, water potential and fluorometry.
Work Group: 1
Offer: Training in plant cultivation, stress treatments, physiological measurements of stress responses
Duration: 3 months
Place: Copenhagen University, Denmark
Contact: ero@plen.ku.dk
Allele mining in allopolyploid crops via proteomics and transcriptomics data.
KULeuven is responsible for the management and safe storage of the Bioversity International collection of banana (Musa spp). Our mandate is to secure the crop’s gene pool and encourage its use. The latter, however, requires an in-depth knowledge of the variability among the accessions. As a proof of concept, 3 different genotypes have been challenged during 28 days to a mild drought stress and samples have been taken at different time points. At the early stage of stress and acclimation, high throughput RNA-sequencing from leaves and roots of all 3 genotypes under control and stress conditions as well as high throughput LCMSMS (orbitrap data) data have been obtained while the plants have been monitored online and off-line in terms of transpiration and growth.
Both omics datasets do not only contain a complementary set of quantitative information about gene expression and need to be integrated; they also contain useful information concerning the different alleles. In contrast to lower organisms with a haploid genome, higher eukaryotes - and especially plants with their flexibility towards polyploidy - tend to have several gene and protein isoforms and have different alleles that might make the difference for a specific trait. Functional genomics is an ideal way to find those alleles (Zivy et al 2015; Vanhove et al 2015, Carpentier & Amerika 2014, Carpentier et al 2011).
Work Group: 2
Offer: Training in proteomics (LC MSMS orbitrap) and transcriptomcics (mRNA seq) data analysis on musa data and possibility to run the proteomics of own samples.
Duration: 6 months
Place: Leuven Belgium
Contact: Sebastien.Carpentier@biw.kuleuven.be
Analysis of variance of cell walls in populations of emerging plants
Forschungszentrum Jülich IBG-2: Plant Sciences runs a program analysing the cell wall composition in various populations. STSM researcher might add phenotypic analysis as well as other omics analysis in this material.
Work Group: 2
Offer: Training in chemical analysis of cell walls as well as phenotypic analysis .
Duration: 3-6 months
Place: Jülich, Germany
Requirements: basic knowledge about biochemistry and cell walls; special skills will be trained; if required special skills for own samples/genotypes.
Contact: b.usadel@fz-juelich.de
Interaction of heat and chilling stress on physiology (soya/faba bean)
Offer: Training in physiological measurements
Duration: 3 months
Place: Dept of Food Science, Aarhus University, DK
Characterization of growth and photosynthesis in a panel of Arabidopsis thaliana accession in response to various temperature and CO2 regimes
Forschungszentrum Jülich IBG-2: Plant Sciences runs a screening program in automated growth chamber at various CO2 regimes. Growth, development and photosynthesis are measured. Additional analysis can be included by the STSM researcher including phenotypic analysis as well as omics analysis in this material.
Work Group: 3
Offer: Training in high-throughput Arabidopsis phenotyping in growth chambers, photosynthesis, growth analysis, data analysis and statistics; options to add additional genotypes and to collect samples for further omics analysis.
Duration: 3-6 months
Place: Jülich, Germany
Requirements: basic knowledge about Arabidopsis physiology, special skills will be trained; if required special skills for own samples/ genotypes.
Contact: f.fiorani@fz-juelich.de
Comparison of different barley varietas focusing on root sstems, biomass and yield in response to different nitrogen treatments
Forschungszentrum Jülich IBG-2: Plant Sciences runs a phentotyping program analysing root system responses in diverse genotypes to nitrogen treatments in the field STSM researcher might phenotypic analysis as well as omics analysis in this material.
Workgroup: 3
Offer: Training in barley root phenotyping in the field (incl. shovelmomics). Image base phenotyping, data analysis and statistics; options to collect samples for further omics analysis.
Duration: 1 month
Place: Jülich, Germany
Requirements: basic knowledge about barley root physiology, special skills will be trained; if required special skills for own samples/genotypes.
Contact: t.wojciechowski@fz-juelich.de