Genetics (Becker 2)

Department / Institute
Faculty of Biology
Subject area
Plant Sciences, Genetics, Molecular Biology, Computational Biology
Project title
Epigenomic associations with plant-microbe interaction
Name of supervisor
Prof. Dr. Claude Becker
Number of open positions
Language requirements
Proficiency in English
Academic requirements
4-year Bachelor's plus Master's Degree;
at the time of application, the last final exam should have taken place in the past 4 years.
Study model
Full doctoral study model: 36 or 48 months

Project description

Plants grow in a diverse community with microorganismic interactors, which range from pathogens to beneficial symbionts. In recent years, it has become apparent that the plant epigenome, the combination of chemical modifications to DNA and histones, plays a role in modulating both pathogenic and symbiotic interactions (reviewed in Ramos Cruz et al., Curr Opin Plant Biol 2021).

In this project, we want to identify which epigenomic loci are associated with the overall plant microbiome profile. Using a set of well-characterized Arabidopsis thaliana lines that have mosaic DNA methylation patterns, we will profile the overall root and leaf microbiome of these plants when grown in the same soil using metagenome sequencing via 16S rRNA and ITS profiling. We will then map microbial diversity and relative abundance to the epigenomic variation and combine these analyses with de novo generated transcriptome profiles. Our goal is to identify loci that are subject to epigenetic regulation and that modulate the overall interaction with microbial organisms. In a second phase, we will transition from the A. thaliana model to crop plants.

The project is embedded in a group with very diverse expertise, ranging from Bioinformatics and Genomics to Plant Genetics and Molecular Biology. We are looking for candidates with a solid background in molecular biology and genetics; expertise in computational data analysis and/or plant biology is a plus. Candidates should have an advanced level in spoken and written English.


Ramos-Cruz, D., Troyee, D., Becker, C. (2021) Epigenetics in plant organismic interactions. Curr Opin Plant Biol, 61: 102060. DOI: 10.1016/j.pbi.2021.102060

Wibowo, A.*, Becker, C.*, Durr, J., Price, J., Spaepen, S., Hilton, S., Putra, H., Papareddy, R., Saintain, Q., Harvey, S., Bending, G.D., Schulze-Lefert, P., Weigel, D., Gutierrez-Marcos, J. (2018) Partial maintenance of organ-specific epigenetic marks during plant asexual reproduction leads to heritable phenotypic variation. PNAS, 115: E9145-9152.

For further information, please contact Dr. Claude Becker:

Research group website

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