Join our international PhD program in the Plant Sciences in Cologne, Germany: The 2023 IMPRS Application Call is currently OPEN and you can find more information below.
Requirements
As a highly international program, we encourage students from all countries to apply. Successful applicants will be enrolled at a German University, which is typically the University of Cologne (UoC). The Max Planck Institute for Plant Breeding Research (MPIPZ) and the University of Cologne are equal opportunity employers.
To be considered for selection, you must hold a Master’s degree or comparable and have completed 4 to 5 years of university studies in subjects relevant to the individual projects. While it is not necessary to hold the degree at the time of application, it must be awarded before PhD projects start.
Solid knowledge of the English language is necessary to succeed in our program. We thus encourage you to support your application with the results of internationally accepted language exams such as TOEFL or IELTS, which are however not mandatory.
What we offer
The MPIPZ and the University of Cologne form an outstanding cluster for basic research in the plant sciences. Supported through the Excellence Strategy of the German federal and state governments, we offer a truly interdisciplinary training of young researchers who will work in a supportive international environment designed to harness creativity.
PhD positions are fully funded for 3 years, with possible extension, and PhD students will benefit from a structured supportive program with shared supervision and training in a wide range of transferable and applicable skills. All applicants can indicate their preference for a number of advertised projects.
7 PhD students. We look for candidates with a keen interest in experimental & computational plant biology to join us in 2023:
1- PhD Position: Coupland: Deciphering the role of the miRNA156/SPL15 module in the control of floral transition and inflorescence development in Arabidopsis
This project will be supervised by George Coupland at the Max Planck Institute for Plant Breeding Research
Abstract:
Timing reproduction is key to the evolutionary success of all organisms. In plants, diverse environmental and internal cues are integrated at the shoot apical meristem to control the timing of flowering and thus reproduction. After floral induction of Arabidopsis thaliana, the shoot apical meristem first produces small leaves with inflorescence branches in their axils, and later forms single flowers. This combination of structures generates the characteristic inflorescence morphology of this species. We showed that two genetically separable regulatory pathways act at the shoot meristem to initiate the formation of the inflorescence, and that these pathways act in different environments. One pathway promotes flowering of young plants and involves the florigen FLOWERING LOCUS T (FT) protein and its interacting transcription factor FD. The other pathway promotes flowering relatively slowly in winter conditions of low temperatures and short-day lengths and involves a regulatory module containing microRNA156 (miR156) and its target the SPL15 transcription factor.
We found that in the absence of FT, SPL15 can efficiently activate the first stage of inflorescence development and produce inflorescence branches, but that it requires FT activity to induce the second stage and form flowers. Therefore, these two pathways have separable and interacting activities. This project aims to define the gene regulatory network controlled by the miR156/SPL15 module in promoting inflorescence development, a function which appears to be widely conserved in Angiosperms and Gymnosperms, and its interaction with FT to induce floral development. It makes use of unique genetic material that we have generated and the methods of confocal imaging, RNA sequencing and CRISPR-mediated reverse genetics.
Key publication: Hyun, Y., Vincent, C., Tilmes, V., Bergonzi, S., Kiefer, C., Richter, R., Martinez-Gallegos, R., Severing, E., and Coupland, G. (2019). A regulatory circuit conferring varied flowering response to cold in annual and perennial plants. Science 363, 409-412. doi: https://doi.org/10.1126/science.aau8197
2- PhD Position: Garrido-Oter: Studying the robustness and long-term dynamics of synthetic microbial foodwebs
This project will be supervised by Ruben Garrido-Oter at the Max Planck Institute for Plant Breeding Research
Abstract:
Experimental microbial systems have long been employed to explore key questions in ecology, dating back almost a hundred years. Reductionist systems consisting of assemblages of few microbial strains have been instrumental in ecological research, providing fundamental insights such as the principle of competitive exclusion, the dynamics of predator-prey systems, or the predictability of ecological tipping points. Recently, advances in high-throughput isolation of microbial strains have enabled the reconstitution of more complex, ecologically-inspired synthetic communities from a variety of environments. One such system is based on mutualistic interactions between the green alga Chlamydomonas reinhardtii and a community of associated phycosphere bacteria. Recently, we have demonstrated the potential of this system by exploring the mechanisms driving the assembly of microbiota structures conserved between terrestrial green algae and land plants.
In this project, we will construct synthetic microbial foodwebs consisting of three groups of organisms: a primary producer (the alga C. reinhardtii), a predator (the model ciliate Tetrahymena pyriformis) and a synthetic community of phycosphere bacteria. Experiments using gnotobiotic photobioreactors will allow us to precisely measure microbial community and exo-metabolome composition in long-term experiments. These data will be analysed using state-of-the-art bioinformatic tools and machine learning approaches in order to explore the long-term behaviour of synthetic microbial foodwebs. If successful, this project has the potential to help answer fundamental questions in theoretical ecology and to make practical contributions to restoration ecology and biotechnology.
Key publication: Durán P, Flores-Uribe J, Wippel K, Zhang P, Guan R, Melkonian B, Melkonian M, Garrido-Oter R. Shared features and reciprocal complementation of the Chlamydomonas and Arabidopsis microbiota. Nat Commun. 2022 Jan 20;13(1):406.
3- PhD Position: Hay: Genetic control of polar lignin deposition
This project will be supervised by Angela Hay at the Max Planck Institute for Plant Breeding Research
Abstract:
Cardamine fruit use an explosive mechanism to disperse their seeds. This morphomechanical innovation evolved in Cardamine, and differs dramatically from the non-explosive fruit found in the model species Arabidopsis. During explosive dispersal, the two fruit valves coil rapidly, accelerating the seeds at speeds greater than 10 m/s to disperse over a large area. The goal of this project is to investigate the genetic basis of explosive seed dispersal. It builds on the key finding that an asymmetric pattern of lignin deposition in a single cell layer of the fruit valve is necessary for explosive coiling. Moreover, this lignin pattern is strictly associated with the evolutionary novelty of explosive seed dispersal in Cardamine. Therefore, this project sets out to identify the genetic basis for polar lignin deposition in explosive fruit. It takes advantage of a set of mutants in Cardamine hirsuta with disrupted lignin polarity.
A mapping-by-sequencing approach will be used to identify the genes underlying these mutant phenotypes. Developmental genetics and cell biology approaches will be used to characterize the role of these genes in localised lignin deposition. Findings from this project will be important to understand the genetic basis of polar lignin deposition and its role in explosive seed dispersal.
Key publication: Pérez-Antón M, Schneider I, Kroll P, Hofhuis H, Metzger S, Pauly M, Hay A. Explosive seed dispersal depends on SPL7 to ensure sufficient copper for localized lignin deposition via laccases. Proc Natl Acad Sci U S A. 2022 Jun 14;119(24):e2202287119. doi: https://doi.org/10.1073/pnas.2202287119
4- PhD Position: Hildebrandt/Töpfer: Understanding storage protein metabolism during germination and seedling development in the high protein crop Lupinus albus through data-integrative metabolic modelling
This project will be co-supervised by Tatjana Hildebrandt and Nadine Töpfer at the University of Cologne
Abstract:
During germination and early seedling development plants rely on their seed storage compounds to provide them with energy and precursors for the synthesis of macromolecular structures. Lupin seeds use predominantly proteins as their storage compounds (up to 35% of the seed dry weight) and do not contain starch and are thus a valuable crop for human nutrition and animal feed. However, plant metabolism is primarily geared to using carbohydrates as substrates for mitochondrial ATP production and as starting materials for the synthesis of cell walls. During carbohydrate starvation, storage proteins are used as alternative respiratory substrates and they can also be converted to glucose for cellulose synthesis. These processes potentially liberate large quantities of toxic ammonium. It is not clear how the seeding metabolically integrates amino acid and nitrogen fluxes from storage proteins.
To tackle this question, in this project the candidate will construct a time-resolved, large-scale metabolic model to analyze storage protein metabolism during germination and post-germinative seedling growth in Lupinus albus. The model will be parameterized with existing proteomics, metabolite profiling, and physiological parameters and analyzed using flux-balance approaches. Furthermore, the candidate will generate additional modelling relevant data and test model-based hypotheses. This approach will elucidate how the different metabolic processes are coordinated to meet the demands of the growing seedling. The gained knowledge will increase our understanding of metabolic adaptations required for using proteins as major seed storage compounds and will identify targets for breeding future crops with a beneficial seed protein composition.
Key publication: Moreira TB, Shaw R, Luo X, Ganguly O, Kim HS, Coelho LGF, Cheung CYM, Rhys Williams TC. A Genome-Scale Metabolic Model of Soybean (Glycine max) Highlights Metabolic Fluxes in Seedlings. Plant Physiol. 2019 Aug;180(4):1912-1929. doi: 10.1104/pp.19.00122.
5- PhD Position: Marques: Genomic differentiation in holocentric carnivorous Drosera plants
This project will be supervised by André Marques at the Max Planck Institute for Plant Breeding Research
Abstract:
Most studied and sequenced organisms have one single centromere in each chromosome, i.e. monocentric chromosomes, visible as a primary constriction during metaphase. However, several animal and plant species have evolved holocentric chromosomes, where each chromosome harbors hundreds of small centromeres distributed along their entire lengths. Thus, both genome and cell-division related adaptations are expected to be found in such holocentromere-based genomes. This project aims to address how transition from monocentric to holocentric chromosome has influenced genome organization and meiotic recombination using the carnivorous plant genus Drosera as a model system. The genus Drosera is a very exciting group to study adaptation to holocentricity because closely related monocentric and holocentric species can be found.
The selected PhD student will be mainly involved in bioinformatic analyses, including genome assemblies, scaffolding and construction of recombination maps, thus, good bioinformatic experience is desired. However, upon interest of the candidate wet-lab experiments could be also undertaken and discussed. Thus, both wet-lab and bioinformatics students may apply for this project. This study will provide a deep knowledge about the impact of transition to holocentricity on genome organization and meiotic recombination dynamics.
Key publication: Hofstatter PG, Thangavel G, Lux T, Neumann P, Vondrak T, Novak P, Zhang M, Costa L, Castellani M, Scott A, Toegelová H, Fuchs J, Mata-Sucre Y, Dias Y, Vanzela ALL, Huettel B, Almeida CCS, Šimková H, Souza G, Pedrosa-Harand A, Macas J, Mayer KFX, Houben A, Marques A. Repeat-based holocentromeres influence genome architecture and karyotype evolution. Cell. 2022 Aug 18;185(17):3153-3168.e18.
6- PhD Position: Mercier: Causes and consequences of aneuploidy
This project will be supervised by Raphael Mercier at the Max Planck Institute for Plant Breeding Research
Abstract:
Aneuploidy, the presence of one or several additional chromosomes in the karyotype, affect development in many eukaryotes, including human and plants. Meiosis is central in eukaryote reproduction, as it reduces and distributes the set of chromosomes in the gametes. Meiotic defects are a major source of aneuploidy, and in return, the presence of an extra chromosome disturbs the meiotic process. The project aims to use a high throughput approach based on genomics to detect aneuploids, understand their origin, and study their consequences on development and reproduction, in the model plant Arabidopsis thaliana. The project is organized into four complementary parts: (i) Analyze the effect of meiotic missegregation on the karyotype of progeny.
Have males and females the same propension to generate aneuploids? Have all chromosomes the same capacity to be trisomic? etc. (ii) Analyze the effect of different aneuploidies on growth and development. (iii) Analyses the effect of the presence of an extra-chromosome on meiosis, notably on chromosome pairing, recombination, and segregation, using both genetic and cytological tools; (iv) Conduct a forward genetic screen, and downstream functional studies, to decipher the mechanisms of karyotype instability.
Key publication: Durand S, Lian Q, Jing J, Ernst M, Grelon M, Zwicker D, Mercier R. Joint control of meiotic crossover patterning by the synaptonemal complex and HEI10 dosage. Nat Commun. 2022 Oct 12;13(1):5999.
7- PhD Position: Tsiantis: Investigating the genetic basis for predictability of morphological evolution of plant leaves
This project will be supervised by Miltos Tsiantis at the Max Planck Institute for Plant Breeding Research
Abstract:
Plant leaves offer attractive opportunities for studying the genetic basis for evolutionary change because (i) they show substantial heritable morphological variation and (ii) their shapes evolve in close correspondence with the environment indicating their role to physiological adaptations of plants. Recent information also suggests that mechanisms underlying diversification of leaf shape are to some degree predictable. Specifically, two classes of homeobox genes are repeatedly deployed to support evolutionary shifts in leaf form, with the pleiotropy of these genes also influencing their potential to contribute to evolutionary change. Here we propose to investigate the mechanistic basis and limits of this predictability in the Brassicaceae family.
We will ask whether two independent instances of a difference between simple and complex leaves are caused by similar gene expression signatures and whether these homeobox transcription factors promote leaf complexity by acting through the same downstream genes and protein partners in different species. The project will make use of comparative ChIP-Seq, snRNA-Seq, study of protein-protein interactions as well as interspecific gene transfers and comparative mutant analysis. We will determine to what degree equivalent morphological shifts during crucifer evolution have a similar genetic basis. This will be a key advance in understanding the genetic basis for evolutionary change in plants.
Key publication: Wang Y, Strauss S, Liu S, Pieper B, Lymbouridou R, Runions A, Tsiantis M. The cellular basis for synergy between RCO and KNOX1 homeobox genes in leaf shape diversity. Curr Biol. 2022 Sep 12;32(17):3773-3784.e5. doi: https://doi.org/10.1016/j.cub.2022.08.020
Timeline (2023 Application Call):
The final deadline for application is January 6, 2023 (23:59 CET). Please note that we will ask two referees to support your application and that the referees’ deadline to submit a reference letter is January 13, 2023. Shortlisted applicants will be invited to an online Selection Symposium that takes place from March 20 to March 23, 2023. Applicants invited to the Selection Symposium will need to give and discuss a presentation and will get to know the IMPRS through meetings with the PhD Office, current PhD students, the recruiting IMPRS Faculty and their groups. Successful applicants will be offered a position in April 2023 and they will be given the option to visit Cologne before starting the PhD. All projects should start until fall 2023.