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Open PhD positions for DFG funded collaborative research centre of HHU Düsseldorf and University of Cologne

Plant Ecological Genetics

A1: Adaptive potential of the leaf economics spectrum in the Brassicaceae (HHU)

  • PhD position 1: In this project we will examine the relationship between the leaf economic spectrum and whole-plant performance. We will assess whether variation in the leaf economic spectrum is correlated with whole-plant performance and fitness in a given environment. To this end, we will assess the response of a broad range of Brassicaeae species to nitrogen input, water supply, and temperature regimes, as well as daily light integrals. These morphological and physiological measurements will be used to quantify the contribution of genetic and environmental variation and plasticity (G*E) variation to the overall variation in LES traits and eventually map genetic factors that are linked to phenotypic differentiation.

    Qualifications needed: MSc in biology or biochemistry, experience with plant eco-physiology and genetics is required

  • PhD position 2: In this project we will test the hypothesis that the mode of photosynthetic carbon assimilation (C3 vs. C3-C4 intermediate) contributes to adaptation of plants to urban environments. To test this hypothesis, we will evaluate physiological performance of selected accessions of Diplotaxis muralis, Diplotaxis viminea and Diplotaxis tenuifolia under conditions of water and nutrient limitations, and under competition, in growth chambers and in common garden experiments. Further, we will sample additional genotypes and develop populations from intra- and inter-specific crosses to enable mapping of the genes underpinning the traits analyzed in this work.

    Qualifications needed: MSc in biology or biochemistry, experience with plant eco-physiology and genetics is required

Contact: Andreas Weber, www.plant-biochemistry.hhu.de

 

A2: Fitness effect of molecular variants of leaf area and economics spectrum of Hordeum vulgare (HHU)

  • PhD project 1: As the flag leaf is often regarded as the most important supply of assimilates to the panicle, we will study in this project the covariation of flag leaf length and width with fitness traits in field experiments but also in growth chamber experiments under diverse, simulated environmental conditions.  With that we want to help answer the question to what extent do leaf-level resource economics in a species reflect whole-plant physiology, plant performance, and ultimately, fitness. In addition, with PhD2, the effect of the identified alleles for flag leaf length and width variation on plant fitness and other functional traits will be quantified.

    Qualifications needed: MSc in biology, agricultural sciences or related disciplines; experimental experience with plant physiological approaches is advantageous; proficiency in R programming and biostatistics is a plus; excellent communication skills in English (spoken and written); high motivation, team spirit, and independence

  • PhD project 2: In a newly developed multiparental mapping population, we observed a high diversity for flag leaf length and width and detected several major quantitative trait loci (QTL) for these traits. The objective of this PhD project is to isolate the underlying allelic variants and validate their role on flag leaf length and width using transgenesis or TILLING. Furthermore, in order to obtain first information about the potential mechanism of the underlying gene, we propose to perform a detailed characterization of the leaf and whole plant characteristics of selected plant material.

    Qualifications needed: MSc in biology, agricultural sciences or related disciplines; experimental experience with molecular biological and genetic approaches is advantageous; excellent communication skills in English (spoken and written); high motivation, team spirit, and independence

Contact: Benjamin Stich, www.quantitativegenetics.hhu.de

 

A3: Adaptive potential of temperature mediated plasticity in Cardamine hirsuta (MPIPZ)

  • PhD project 1: The aim of the first project is to determine the molecular and genetic basis of variation in plastic response in a recombinant inbred line population of Cardamine hirsuta. The student will focus on QTL analysis, fine-mapping and evaluating the gene expression response underpinning plasticity.

    Qualifications needed: MSc in plant biology or plant genetics or statistical genetics; expertise: QTL mapping, Molecular Biology including NGS sequence analysis

  • PhD project 2: The aim of the second project is to determine the developmental basis and physiological and fitness consequences of plasticity. The student will focus on the cellular and developmental basis of the plasticity response and perform field experiments to assess the adaptive potential of plasticity.

    Qualifications needed: MSc in plant biology, developmental biology; expertise: plant physiology, plant molecular biology, plant development

Contact: Miltos Tsiantis & Stefan Laurent, www.mpipz.mpg.de/tsiantis & www.mpipz.mpg.de/laurent

 

A4: Ecological importance and genetic basis of adaptive myxospermic strategies to drought stress in the Camelineae tribe and the Brassicaceae family (HHU)

  • PhD project: Analysis of general seed traits and mucilage quantification of Brassicaceae under control and abiotic stress conditions. The project encompasses biochemical analyses drawing on cell wall analytics as well as genomic and whole seed analyses and challenges and comparison between species and ecological niches.

    Qualifications needed: MSc in biology, biochemistry or similar; ideally knowledge in molecular biology techniques and cloning strategies; ideally experience in plant sciences and quantitative data analysis in e.g. R

Contact: Björn Usadel, www.biological-data-science.hhu.de

 

A5: The genetic basis of ecological variation in meiotic recombination rates (MPIPZ)

  • PhD project: Recombination of standing variation in adapting populations is an important factor for the emergence of genotypes with improved fitness. Recently, we have developed an efficient method that enables us to characterize genetic variation in recombination rates using parallel single-cell sequencing of thousands of pollen genomes within a single sequencing experiment. We will apply this method to study variation in genome-wide meiotic recombination rates and unravel the genetic diversity of recombination in plant genomes in benign and challenging environments.

    Qualifications needed: MSc in computational biology or bioinformatics; experiences in the analysis of next-generation sequencing data; proficiency in at least one scripting language (e.g. Python) and Linux; high proficiency in spoken and written English; experiences in plant biology and single-cell -omics are of advantage

Contact: Korbinian Schneeberger, www.mpipz.mpg.de/schneeberger

 

A9: Evolutionary adaptation to local soil pH in Arabidopsis halleri (RUB)

Molecular Genetics and Physiology of Plants: Two PhD positions are available in the group of Professor Ute Krämer to unravel within-species trait diversification and its genetic basis in the heavy metal hyperaccumulator Arabidopsis halleri, an outcrossing perennial extremophile. The project addresses natural populations on soils contrasting in carbonate content (soil pH).

  • PhD project 1: Plant Ecological Genetics – Fieldwork, reciprocal soil exchange, genetics, and computational analysis of genome sequence data (e.g. genome annotation and analysis, genome-environment associations).

    Qualifications needed: MSc in biology or related; knowledge and practical hands-on experience in Ecology, Genetics, computational sequence data analysis, work with plants

  • PhD project 2: Plant Molecular Physiology and Genomics – Comparative molecular physiology and transcriptomic analyses of plant performance on, and responses to, environmental conditions affecting plant Fe nutrition.

    Qualifications needed MSC in biology or related; knowledge and practical hands-on experience in molecular physiology, RNA-seq, plant nutrition, hydroponic plant cultivation

Contact: Ute Krämer, www.rub.de/mgpp/kraemer.html

 

A10: Adaptive potential of sulfate content in Arabidopsis thaliana and Hordeum vulgare (UoC)

  • PhD project: Sulfur is an essential plant nutrient, but sulfate concentrations in soil strongly fluctuate over the life cycle of plants. This project will examine how ecologically diverse Arabidopsis thaliana and Hordeum species adjust sulfate uptake and accumulation to fluctuating sulfate concentrations and thus sustain plant performance.

    Qualifications needed: We are looking for an enthusiastic student with MSc in biology or biochemistry and experience in plant sciences.

Contact: Stanislav Kopriva, www.ag-kopriva.botanik.uni-koeln.de

 

A11: Ecological importance and genetic basis of plant-microbe associations in Brassicaceae and Hordeum species exposed to environmental challenges (UoC)

  • PhD project: In the rhizosphere microorganisms often form diverse communities of interacting species. These associations are shaped by metabolic exchanges and can provide the host with beneficial functions, such as pathogen protection and nutrient mobilization. However, the ecological forces, molecular mechanisms and plant genes that govern microbiota assembly and stability are not well understood. The ability to predict the structure and function of these complex microbial communities is critical to understanding them and harnessing their full potential. We will develop bottom-up experimental approaches and microbial synthetic communities allowing reproducible conditions and controlled perturbation of specific factors. This enables us to identify molecular and ecological mechanisms driving microbiota functions and the host genetics in barley and Arabidopsis. The 2 PhD projects will focus on the mechanistic understanding of how plant-beneficial microbe interactions contribute to host environmental adaptation using intra- and interspecific genetic variation within plant host species, molecular, biochemical and cytological approaches.

    Qualifications needed: MSc in biology or biochemistry, experience with plant eco-physiology and genetics is required

Contact: Alga Zuccaro, www.ag-zuccaro.botanik.uni-koeln.de/

 

A12: Comparative analysis of gene-specific adaptive potentials across changing environments in Arabidopsis thaliana (Uoc)

  • PhD project: Comparative analysis of gene-specific adaptive potentials across changing environments in A. thaliana:

    This project aims at determining how individual genes shape the ecological niche that a species inhabits. Combining analyses of A. thaliana natural diversity and mutant lines, the effect of single genes will be characterized in conditions of nutrient limitation and competition.

    Qualifications needed: MSc in plant biology, with skills in quantitative biology (statistics, quantitative genetics or similar)

Contact: Ute Höcker & Juliette de Meaux, www.ag-hoecker.botanik.uni-koeln.de & www.ag-demeaux.botanik.uni-koeln.de

 

B2: Adaptation of perennial Arabis alpina along a latitudinal gradient in Scandinavia (MPIPZ)

  • PhD project 1: One student will use population genetics methods to model the postglacial colonization history of Scandinavia by Arabis alpina and identify genomic regions and phenotypes associated with adaptation to high latitudes.

    Qualifications needed: Experience in population genetics, genomics, bioinformatics, plant sciences will be preferred

  • PhD project 2: The second student will study the genetics and molecular basis of a difference in flowering time detected in a Scandinavian population, and determine how widely distributed this variation is in other Scandinavian populations. The project will utilize quantitative genetics and CRISPR for reverse genetics of candidate genes.

    Qualifications needed: Knowledge of genetics, molecular biology and plant biology is preferred

Contact: George Coupland & Andrea Fulgione, www.mpipz.mpg.de/coupland & www.mpipz.mpg.de/fulgione

 

B3: Adaptation to the afroalpine environment in Brassicaceae species with contrasting ecological strategies (MPIPZ)

  • PhD project: Some of the earliest evidence of local adaptation comes from studies of eco-clines, or patterns of correlation between traits and environmental factors. This PhD project applies population genetic modeling to reconstruct demographic and adaptive history of plant populations along elevational gradients.

    Qualifications needed: priority will be given to students with training in population genetics and bioinformatics 

Contact: Angela Hancock, www.mpipz.mpg.de/hancock

 

B4: Adaptation in endangered Arabis floodplain species (UoC)

  • PhD project: The project will focus on the history of Arabis sagittata, a species that receives gene flow from the closely related species A. nemorensis. The student will apply a combination of phenotypic analyses and population genetics approaches to determine the genetic landscape of the species the impact of gene flow on its distribution.

    Qualifications needed: MSc in plant biology, with skills in ecology, population genetics or quantitative biology

Contact: Juliette de Meaux, www.ag-demeaux.botanik.uni-koeln.de

 

B5: Evolutionary signatures in gene copy-number variation in Brassicaceae (UoC)

  • PhD project: The goal of this project is to determine the adaptive role of copy number variation in plant gene families. Although copy number variation is widespread in plants and has been shown repeatedly to fuel adaptation, we lack comprehensive models to discern when copy variation evolved in response to selection. We will investigate the extent to which natural selection contributes to copy number variation within and between species in the Brassicaceae family. We will integrate empirical data, newly developed theoretical models as well as computer simulations under neutral and selective processes to model the role of copy number variation in plant adaptation.

    Qualifications needed: Ideally, the student is already familiar with quantitative methods in evolutionary biology, population genetics and/or bioinformatics. As proof of proficiency, a master's degree in a relevant subject (quantitative biology, bioinformatics, biomathematics) or other suitable documentation of equivalent skills is expected.

Contact: Thomas Wiehe & Laura Rose; www.bioinf-popgen.uni-koeln.de & www.popgen.hhu.de/en/our-team.html

 

B6: The role of polygenic adaptation and pleiotropy in the establishment of trait-syndromes (UoC)

The ecological specialization of plants generally relies on the joint adjustment of multiple traits: the so-called adaptive trait syndromes. This project will develop new theory about how multidimensional quantitative traits evolve and adapt to new environments. We will further perform simulations and test our predictions deriving our parameters from the large-scale empirical data collected in the CRC.

  • PhD project 1: The student will develop and study analytical models for the adaptation of single and multiple traits under different environmental scenarios. The mathematical framework combines an additive genotype-phenotype map with a nonlinear phenotype-fitness map displaying a unique optimal trait combination. The project is suitable for applicants with a background in theoretical population genetics, theoretical physics or mathematics.

    Qualifications needed: MSc degree in biology, physics, mathematics, computer science or related fields. Previous experience with evolutionary theory and modelling is an asset but not a requirement.

    Contact: Joachim Krug, www.thp.uni-koeln.de/krug/

  • PhD project 2: The student will employ forward-in-time simulations to study the adaptation of single and multiple traits under different environmental scenarios. We will apply these models to explicit plant populations and compare them to empirical data. The project is suitable for applicants with a background in (theoretical) population genetics, quantitative genetics or mathematics.

    Qualifications needed: MSc degree in biology, physics, mathematics, computer science or related fields. Previous experience with evolutionary theory and modelling is an asset but not a requirement.

    Contact: Markus Stetter, www.cropevolution.org/

 

B7: Adaptation in ecologically diverse Hordeum species: a comparative intra- and inter-species approach (PUM)

  • PhD project: The PhD student will study ecological and genetic variation within Hordeum murinum, a wild relative of cultivated barley. The work programme includes field sampling of the species across Europe, growing plants in the common garden and genotyping by sequencing. Basic knowledge of European flora is advantage. The position is located at the Philipps University Marburg.

    Qualifications needed: MSc in biology or related discipline; experience in plant ecology and evolution; basic knowledge of European flora is an advantage

Contact: Anna Lampei-Bucharova, www.uni-marburg.de/de/fb17/fachgebiete/naturschutz/ag-naturschutzbiologie/team/anna-lampei-bucharova