The CRC Transregio TRR 341 “Plant Ecological Genetics: Genetics of Adaptation to Novel Environmental Challenges” is inviting applications for 10 doctoral research positions across several leading universities and research institutes in Germany. The interdisciplinary research program investigates how plants adapt genetically and ecologically to rapidly changing environments. PhD researchers will explore the mechanisms behind adaptation, including molecular variation, plant–microbe interactions, climate stress responses, evolutionary genetics, and ecological diversification. The available positions are distributed across research locations in:

• Cologne
• Bochum
• Düsseldorf
• Potsdam
• Marburg
• Quedlinburg
• Start Date: As soon as possible Application Deadline: July 10, 2026

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About CRC Transregio TRR 341

The CRC Transregio TRR 341 brings together researchers from multiple German universities and scientific institutions to understand how plants respond to new environmental challenges. The research consortium combines expertise from:

• Plant genetics
• Evolutionary biology
• Ecology
• Molecular biology
• Genomics
• Computational biology
• Plant physiology

The overall goal is to uncover the genetic mechanisms that allow plants to survive and adapt under changing environmental conditions, including climate stress, soil variation, competition, and resource limitations.

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Research Theme: Genetics of Plant Adaptation

Plants constantly face environmental challenges such as:

• Changing climates
• Nutrient limitations
• Soil chemical variation
• Competition from neighboring plants
• Herbivore pressure
• Human-driven landscape changes

TRR 341 investigates how genetic variation influences plant adaptation and ecological success. The PhD projects combine experimental approaches with modern genomic technologies, including:

• Genome analysis
• Transcriptomics
• Proteomics
• Quantitative genetics
• Machine learning
• Field experiments
• Controlled laboratory studies

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Available PhD Projects:

Project A02: Fitness and Competition Effects of Molecular Variants of Leaf Area in Barley

Location: Julius Kühn Institute, Groß Lüsewitz, Sanitz
Supervisors: Benjamin Stich and Asis Shrestha. This project investigates how genetic variation affecting leaf size influences plant fitness and competitive ability in barley. Research activities include:

• Identifying molecular variants responsible for leaf size differences
• Studying physiological consequences of genetic variation
• Evaluating agricultural impacts across different ecological environments
• Investigating competition effects using barley mixtures
• Candidates interested in this project must apply through both the TRR 341 portal and the Julius Kühn Institute recruitment system. Contact: Benjamin.Stich(at)julius-kuehn(dot)de and/or Asis.Shrestha(at)julius-kuehn(dot)de

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Project A07: Adaptive Responses to Plant Density and the Role of Soil Microbiota

Location: University of Cologne
Supervisor: Bart Thomma with Ute Höcker – Contact: bthomma(at)uni-koeln(dot)de This project examines how plants respond to high-density environments and how soil microorganisms influence competitive interactions. The research will explore:

• Belowground signaling mechanisms
• Plant–microbe interactions
• Soil microbial contributions to competition
• Plant–soil feedback effects
• Density-dependent growth responses in Arabidopsis thaliana

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Project A09: Ecological Adaptation to Local Soil pH in Arabidopsis halleri

Location: Ruhr University Bochum
Supervisor: Ute Krämer – Contact: ute.kraemer(at)ruhr-uni-bochum(dot)de This project studies how the extremophile plant Arabidopsis halleri adapts to alkaline soils where nutrient availability, particularly iron acquisition, is challenging. Research methods may include:

• Quantitative trait locus mapping
• Hydroponic plant experiments
• Transcriptomics
• Molecular biology
• Physiological and biochemical analyses
• Genome assembly and computational analysis

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Project A10: Sulfur Homeostasis Networks in Arabidopsis Adaptation

Location: University of Cologne
Supervisor: Stanislav Kopriva – Contact: skopriva(at)uni-koeln(dot)de This project investigates how Arabidopsis accessions adapt to different sulfur availability conditions. The research focuses on:

• Sulfur metabolism
• Sulfate transport systems
• Plant fitness consequences
• Physiological and molecular responses
• Genetic variation among Arabidopsis populations

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Project A13: Adaptive Potential of the Leaf Proteome Under Stress

Location: University of Cologne
Supervisor: Tatjana Hildebrandt – Contact: t.hildebrandt(at)uni-koeln(dot)de This project explores how plants adjust protein metabolism to survive stressful and resource-limited environments. The PhD researcher will combine:

• Genome-wide association studies (GWAS)
• QTL mapping
• Functional validation
• Proteomics
• Amino acid metabolism analysis

The goal is to understand how protein plasticity contributes to plant adaptation.

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Project B01: Ecological Diversification in Heterogeneous Habitats

Location: University of Cologne
Supervisor: Juliette de Meaux – Contact: jdemeaux(at)uni-koeln(dot)de This project combines ecology and population genomics to study how environmental conditions shape genetic diversity in plant communities. Research includes:

• Community genomics approaches
• Analysis of urban plant populations
• Comparison with agricultural landscapes in the Åland archipelago, Finland
• Machine learning identification of adaptive genomic regions

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Project B02: Adaptive Significance of Phenotypic Variation in Scandinavian Arabis alpina

Location: Max Planck Institute for Plant Breeding Research, Cologne
Supervisor: Andrea Fulgione – Contact: fulgione(at)mpipz.mpg(dot)de This project examines adaptation of Arabis alpina to harsh Arctic-alpine environments. The researcher will use:

• Population genetic modelling
• Whole-genome sequence analysis
• Greenhouse experiments
• Growth chamber experiments
• Field studies

The project aims to identify the evolutionary significance of adaptive traits and genetic variants.

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Project B04: Adaptation Through Gene Flow in Endangered Arabis Species

Location: University of Cologne / Max Planck Institute / University of Potsdam
Supervisors: Juliette de Meaux, Andrea Fulgione, Anja Linstädter – Contact: jdemeaux(at)uni-koeln(dot)de and/or anja.linstaedter(at)uni-potsdam(dot)de  or fulgione(at)mpipz.mpg(dot)de  This project investigates how hybridization contributes to adaptation in endangered grassland plants. Research focuses on:

• Adaptive introgression
• Transcriptomics
• Ecological genetics
• Molecular mechanisms of adaptation
• Genetic mapping populations

The study examines two endangered species:

• Arabis nemorensis
• Arabis sagittata

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Project B07: Ecological Genetics of Hordeum murinum

Location: Heinrich-Heine-University Düsseldorf
Supervisors: Timo Hellwig, Maria von Korff Schmising, Anna Lampei Bucharova – Contact: timo.hellwig(at)hhu(dot)de  and/or  Maria.Korff.Schmising(at)uni-duesseldorf(dot)de This project investigates climate adaptation in Hordeum murinum, a wild relative of barley. The PhD researcher will combine:

• Fine mapping of adaptive genes
• Comparative genomics
• Genetic analysis
• Phenotypic evaluation

The research will compare adaptive variation between Hordeum murinum and cultivated barley relatives.

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Project B09: Evolutionary Trade-Offs Between Drought Adaptation and Herbivory Resistance

Location: Heinrich-Heine-University Düsseldorf
Supervisor: Elena Hamann – Contact: Elena.Hamann(at)hhu(dot)de  This project investigates whether drought adaptation influences plant defense against herbivores. Using Brassica rapa populations, the researcher will combine:

• Resurrection experiments
• Common garden studies
• Herbivory experiments
• Metabolomics
• Transcriptomics

The project aims to understand how plants balance growth, stress tolerance, and defense strategies.

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Candidate Profile and Eligibility Requirements

Applicants should have a strong academic background in areas such as:

• Plant biology
• Ecology
• Evolutionary genetics
• Molecular biology
• Biotechnology
• Genomics
• Bioinformatics
• Related life science disciplines

Successful candidates should demonstrate:

• Strong interest in evolutionary and ecological research
• Motivation for interdisciplinary scientific work
• Ability to analyse biological data
• Interest in experimental approaches

Experience with molecular biology, computational analysis, or ecological fieldwork will be advantageous depending on the selected project.

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Benefits of Joining TRR 341

Selected PhD researchers will benefit from:

• Participation in an internationally recognized research consortium
• Training in modern plant science methods
• Collaboration across multiple German research institutions
• Access to advanced laboratory and computational facilities
• Opportunities for scientific publications
• Conference participation and networking
• Interdisciplinary doctoral training

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Application Information

Number of Positions: 10 PhD positions
Program: CRC Transregio TRR 341
Field: Plant Ecological Genetics
Start Date: As soon as possible
Application Deadline: July 10, 2026

Applicants should review individual project requirements and submit applications according to the instructions provided by the consortium and relevant institutions. Please send your application (without a photo) with proof of the required qualifications online with the reference number Wiss2605-14 to [https://jobportal.uni-koeln.de/bewerben/2632 . Please provide the following as proof of qualification: a letter of motivation, a CV (including the con- tact details of two references), degree certificates and transcript of records. If you wish to apply to multiple projects, please also provide the list of project your are applying to ordered by your preferences. Please feel free to indicate your motivation for each project either in the letter of motivation or the list.

For general questions: TRR 341 Office Email: trr341-office@uni-koeln.de Candidates are encouraged to contact individual project leaders for informal enquiries.

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Frequently Asked Questions (FAQ)

1. What are the TRR 341 PhD positions about?

The positions focus on plant ecological genetics and investigate how plants adapt to environmental challenges through genetic, molecular, and ecological mechanisms.

2. How many PhD positions are available?

The TRR 341 consortium is recruiting 10 doctoral researchers across several German universities and research institutes.

3. Which universities and institutes participate?

The positions are located in Cologne, Bochum, Düsseldorf, Potsdam, Marburg, and Quedlinburg, depending on the project.

4. What academic background is required?

Applicants should generally have a degree in plant science, biology, ecology, genetics, molecular biology, biotechnology, bioinformatics, or a related discipline.

5. Are these funded PhD positions?

Yes. These are doctoral research positions within a major German collaborative research program funded through the CRC Transregio framework.

6. What research methods will PhD students use?

Depending on the project, methods may include genomics, transcriptomics, proteomics, molecular biology, field experiments, computational analysis, and machine learning.

7. Can international applicants apply?

Yes. The research consortium welcomes applications from qualified candidates worldwide.

8. What is the application deadline?

The deadline for applications is July 10, 2026.

9. When do the PhD positions start?

The positions are expected to begin as soon as possible after selection.

10. Can applicants contact project supervisors before applying?

Yes. Candidates are encouraged to contact project leaders for informal enquiries regarding specific research projects.