EpiSeedLink: From seed to seedling: Epigenetic mechanisms of priming to design strategies for crop improvement: Marie Skłdowska-Curie Doctoral Network: High profile joint research & training network that will improve career prospects in academia & private sector, Keywords: Seed priming, Arabidopsis, Oilseed rape, Epigenetics, Epigenomics, Biostimulants, Abiotic stress, Climate change.
Summary: EpiSeedLink’s mission is to train 11 predoctoral researchers in the epigenetic regulation of seed priming mechanisms and to translate scientific knowledge and skills into innovation and applications. Crop performance is threatened by climate change and hence EpiSeedLink focuses on training a new generation of scientists with a broad range of scientific and transferable (e.g. communication and entrepreneurship) skills to tackle main agricultural challenges, and to enhance their career perspectives in both academic and non-academic environments. Through its doctoral training programme, the network will provide international, multidisciplinary, and inter-sectorial training in experimental and computational biology, and will generate an in depth understanding of the molecular mechanisms underlying ‘epigenome priming’ at the genetic and molecular level.
The programme combines the unique know-how of academic experts and seed companies in seed biology, crop breeding, epigenetics, biochemistry and biostimulants to synergise research and knowledge transfer between a model plant (Arabidopsis thaliana) and the premium crop oilseed rape (Brassica napus). EpiSeedLink will hence not only contribute to excellent research, but also address urgent societal and agricultural needs by contributing to the development of a sustainable bioeconomy and meeting climate targets.
Position 1: Plant Proteostasis and Epigenome Dynamics:
PhD position in Plant Proteostasis and Epigenome Dynamics under the supervision of Vicente Rubio at Centro Nacional de Biotecnología (CNB-CSIC) in Madrid, Spain.
What are you going to do?
Novel histone modifications promoting seed priming and drought tolerance
You will characterise the role of acetylation of H2B (H2Bac), an orphan-of-function histone posttranslational modification, during the seed-to-seedling transition and drought tolerance in both Arabidopsis and oilseed rape. The project involves identification of H2Bac-targeted genes to be used as markers for optimal seed priming and seed quality, as well as the enzymes; H2B acetyltransferases (HATs) and deacetylases (HDAs) that modulate H2Bac deposition in response to stresses.
The project will allow the unveiling of new molecular connections between environmental signaling pathways, chromatin remodeling and proteostatic machineries that trigger precise gene expression programmes that allow increased tolerance of crops to climate change associated stresses, particularly favoring enhanced seed vigour.
Your aim will be to get insights on the functions of H2Bac in plants, by 1) generating databases for H2Bac profiles and gene sets regulated/targeted by this mark; 2) identifying HATs and HDAs controlling H2Bac deposition and chromatin dynamics during seed-to-seedling transition and drought; 3) isolating chemicals that modulate H2Bac-dependent gene expression and associated traits; and 4) identifying H2Bac-targeted genes to be used as markers for optimal seed priming and seed quality.
For this, a multidisciplinary approach will be undertaken; integrating phenotypic, molecular, proteomics and epigenomic information from both Arabidopsis and oilseed rape plants grown under control and stress conditions.
You will actively collaborate with partners at the University of Clermont Auvergne (France), at the company Deutsche Saatveredelung AG (DSV, Germany) and at the IBMCP-CSIC in Valencia (Spain). You will also benefit from training in plant phenotyping and bioinformatics by the DSV and Sequentia companies.
What do you have to offer?
- MSc in Molecular Biology, Plant Science, or related biological sciences.
- Strong interest in deciphering how plant adapt to changing environmental conditions,
with a specific emphasis on abiotic stresses. - Conceptual background in epigenetics and gene expression.
- Knowledge in molecular biology techniques.
It is a preference if you also have experience in data analysis and motivation for training in bioinformatics.
Our offer
The appointment will be on a temporary basis for a period of three years. The appointment will be according to the employment rules of Spain and should lead to a dissertation (PhD thesis). A Personal Career Development Plan will be drafted that includes the attendance to EpiSeedLink courses and meetings.
The gross monthly salary will be according to the MSCA programme, taking into account the country-specific correction coefficient. Besides the salary, you will obtain a mobility allowance.
Any questions?
Do you have any questions, or do you require additional information? Please contact: Dr Vicente Rubio; vrubio@cnb.csic.es, phone: +34 680635275.
About us
The National Centre for Biotechnology (CNB) is a research centre of the CSIC, Spain’s most important public scientific institution. The CNB opened in 1992 at the Campus of the UAM, Madrid, to lead in developing modern biotechnology in Spain. Our principal objectives are to:
– Acquire knowledge and develop new technologies in the areas of human and animal health, agriculture and the environment
– Promote knowledge and technology transfer for the benefit of society
– Train future generations of researchers and technologists
– Engage and inform society about advances and the benefits of biotechnology
The CNB is distinguished by its versatile interdisciplinary research that combines molecular biology methods with the latest technology in the fields of functional and structural biology. We are a team of more than 600 professionals committed to research excellence. The CNB has been recognised repeatedly by an international committee of experts as one of the Severo Ochoa Centres of Excellence in Medicine and Life Sciences.
Position 2: Hormonal Regulation of Transcriptional Dynamics:
PhD position in Hormonal Regulation of Transcriptional Dynamics under the supervision of Drs David Alabadí and Javier Gallego-Bartolomé at the Instituto de Biología Molecular y Celular de Plantas (IBMCP), Valencia, Spain.
What are you going to do?
DELLA-dependent chromatin features during seedling adaptation to drought
You will work in a project about the transcriptional mechanisms by which DELLA proteins contribute to plant adaptation to drought. DELLAs are transcriptional regulators that are degraded in response to the hormone gibberellin (GA) and regulate different actors during transcription by physical interaction, e.g. transcription factors or transcription elongation factors. DELLAs have proven to be useful in agriculture, since the varieties responsible for the Green Revolution that took place in the 60s and 70s of the last century carried alleles with enhanced DELLA activity.. These alleles help the plant to cope with harsh environments, e.g. drought, however, the underlying molecular mechanisms are mostly unknown.
Your aim will be to identify the physiological, transcriptomic, epigenomic, and interactomic traits triggered by drought that are dependent on DELLAs. You will use Arabidopsis and oilseed rape plants, except for the identification of the drought-dependent DELLA interactome, which will be determined in Arabidopsis. To modulate DELLA levels in both species, you will use treatments with GAs and with the GA biosynthesis inhibitor paclobutrazol, and also GA/DELLA mutants in Arabidopsis. The experimental approaches will include RNA-seq to determine transcriptomic changes; Chromatin Immunoprecipitation coupled to sequencing (ChIP-seq) to determine the genomic distribution of DELLA, RNAPII, and selected epigenetic marks; ATAC-/MOA-seq to infer chromatin accessibility; and AP/MS to define DELLA protein networks. You will infer the underlying mechanisms of DELLA action by performing meta-analyses that integrate the phenotypic, transcriptomic, epigenomic, and interactomic data.
To achieve this goal, you will actively collaborate with academic partners at CBGP-CSIC (Madrid), University of Amsterdam, University of Regensburg and ENS (Paris) to get not only specific training in molecular approaches, but also intellectual input that will be valuable to the progress of your project. You will also receive training on the phenotyping of oilseed rape traits at the facilities of one of the industrial partners, DSV.
What do you have to offer?
- MSc in Molecular Biology, Plant Science, or any related science.
- Knowledge in molecular biology.
- Background in epigenetics and/or transcription.
- Knowledge or motivation for training in bioinformatics will be valued.
Our offer
The appointment will be on a temporary basis for a period of three years according to the employment rules of Spain and should lead to a dissertation (PhD thesis). It will, in line with the duration of the PhD studies in the Universidad Politécnica de Valencia (UPV), be extended for an additional year according to the employment rules of the Consejo Superior de Investigaciones Científicas (CSIC). A Personal Career Development Plan will be drafted that includes the attendance to EpiSeedLink courses and meetings. The gross monthly salary will be according to the MSCA programme, taking into account the country-specific correction coefficient. Besides the salary, the PhD student will obtain a mobility allowance. Positions are aimed at being full-time, but by exception, if needed for family reasons, part-time appointments are possible.
Any questions?
Do you have any questions, or do you require additional information? Please contact: Drs David Alabadí; dalabadi@ibmcp.upv.es, phone: +34 963877723 ext 77723 and Javier Gallego-Bartolomé; jagalbar@ibmcp.upv.es, phone: +34 963877856 ext 78675.
About us
The Institute of Molecular and Cellular Biology of Plants (IBMCP) established in 1992, is a joint research center of the CSIC, the largest research institution in Spain, and the UPV. It is located in the Campus of the UPV in Valencia, very close to sea shore. Its main activity is to carry out cutting-edge and quality scientific research about key processes driving plant growth and development and their ability to adapt to the environment. More than 200 students of many different nationalities have obtained the doctorate degree in our institute. It currently houses 29 research groups, with 41 senior researchers, 10 career track fellows, 50 postdocs and 66 predocs.
Position 3: Seed Adaptation to Warm Ambient Temperature:
PhD position in Plant Molecular (Epi)genetics at the group of Dr Manuel Piñeiro and José A. Jarillo at the Centro de Biotecnología y Genómica de Plantas (CBGP) (UPM – INIA, CSIC) in Madrid, Spain.
What are you going to do?
Molecular mechanisms underlying seed adaptation to warm temperature
You will work on a PhD project addressing the plant genetic and non-genetic mechanisms underlying the effect of maternal exposure to warm temperature on seed germination and seedling establishment using the premium oil crop oilseed rape (Brassica napus) and the related model species Arabidopsis thaliana. Warm ambient temperature experienced by maternal plants can influence the germination behavior of their offspring, but the molecular mechanisms responsible for this transgenerational seed response conditioning crop establishment remains largely unknown. A deeper knowledge of this process will facilitate the development of strategies that improve crop adaptation to the current scenario of global warming that is threatening agricultural production.
Your aim will be to investigate global epigenetic changes triggered in the seeds following the exposure of mother plants to warm temperature at different stages of development. Warm temperature-induced modifications in epigenomic features will be correlated with transcriptomic alterations and changes in seed vigour. This will be a highly multidisciplinary project in which you will perform phenotypic analyses of seed traits, transcriptomic profiling using Next Generation Sequencing approaches (RNA-seq), as well as epigenetic and epigenomic analysis by Chromatin Immunoprecipitation (ChIP) and ChIP coupled to sequencing (ChIP-seq) as well as accessibility techniques in oilseed rape and Arabidopsis. You will also get familiar with bioinformatic analysis of massive sequencing data.
You will be actively collaborating with partners in the University of Amsterdam, and will receive training on phenotyping of oilseed rape seeds at DSV (Germany) and on bioinformatic analysis of next generation sequencing data at the company Sequentia. Additional collaborations within the consortium will be possible.
What do you have to offer?
- MSc in Molecular Biology, Plant Biotechnology, Plant Science, or related topics
- Knowledge and experience in Molecular Biology or Molecular Genetics
- Familiar with Epigenetics
Some background in bioinformatic data analysis is preferable.
Our offer
The appointment will be on a temporary basis for a period of three years. The appointment will be according to the employment rules of Spain and should lead to a dissertation (PhD thesis). A Personal Career Development Plan will be drafted that includes the attendance to EpiSeedLink courses and meetings. The gross monthly salary will be according to the MSCA programme, taking into account the country-specific correction coefficient. Besides the salary, the PhD student will obtain a mobility allowance . Positions are aimed at being full-time, but by exception, if needed for family reasons, part-time appointments are possible.
Any questions?
Do you have any questions or do you require additional information? Please contact: Dr. Manuel Piñeiro; pineiro@inia.csic.es, phone: +34 910679175 or Dr. José A. Jarillo; jarillo@inia.csic.es, phone: +34 910679173.
About us
Our laboratory is based at the Plant Biotechnology and Genomics Centre (CBGP), a joint centre involving INIA, CSIC (the largest public research institution in Spain), and the Polytechnical University of Madrid (UPM), located in the Montegancedo Campus, awarded as Spanish Campus of International Excellence. The CBGP has been awarded twice with “Severo Ochoa Programme for Centres of Excellence in R&D”, and hosts state-of-the-art laboratories working on both model plant and crop species.
Position 4: Plant Photobiology and Epigenome Dynamics:
PhD position in Plant Photobiology and Epigenome Dynamics under the supervision of Fredy Barneche at Institut de Biologie de l’Ecole Normale Supérieure (IBENS) in Paris, France.
What are you going to do?
Non-genetic phenotypic plasticity induced by light acclimation
You will work in a project about short-term priming and transgenerational acclimation to light stress. The host laboratory identified that gene induction during Arabidopsis photomorphogenesis is enhanced by a prior, short and transient, exposure to light. The physiological relevance and molecular mechanisms underlying light-induced plant priming have not been addressed, nor its links to other priming mechanisms. The process could significantly favour seedling vigour in agriculture under extreme light conditions (heat waves, high altitude, low latitude).
Your aim will be to contrast and compare epigenome and transcriptome/epitranscriptome changes induced by short-term priming in Arabidopsis and oilseed rape plants. In parallel, you will characterise gene regulatory pathways impacting light-induced priming and transgenerational effects of high light acclimation. In these analyses, you will use Arabidopsis chromatin and photoperception mutant lines and benefit from a unique collection of Arabidopsis wild type and mutant lines with different life histories of light environment for five successive generations. This will be a highly multidisciplinary project in which you will integrate phenotypic, molecular and epigenomic information, including transcriptome/epitranscriptome time-series (RNA-seq), chromatin marks and accessibility, transcription factors and DELLA protein profiles of Arabidopsis and oilseed rape plants in the selected conditions.
You will actively collaborate with partners at the University of Amsterdam (Netherlands), Regensburg (Germany), CSIC in Madrid and Valencia (Spain). You will also benefit from training in plant phenotyping and bioinformatics by the DSV and Sequentia companies.
What do you have to offer?
- MSc in Molecular Biology, Plant Science or related biological sciences
- Strong interest in deciphering how plant adapt to changing environmental conditions
with a specific emphasis on light - Conceptual background in epigenetics and gene expression
- Knowledge in molecular biology techniques
It is a preference if you also have experience in data analysis and motivation for training in
bioinformatics.
Our offer
The appointment will be on a temporary basis for a period of three years. The appointment will be according to the employment rules of CNRS and should lead to a dissertation (PhD thesis). A Personal Career Development Plan will be drafted that includes the attendance to EpiSeedLink courses and meetings.
The gross monthly salary will be according to the MSCA programme, taking into account the country-specific correction coefficient. Besides the salary, you will obtain a mobility allowance
Any questions?
Do you have any questions, or do you require additional information? Please contact: Dr Fredy Barneche; Barneche@bio.ens.psl.eu, phone: +33 144323531.
About us
Ecole Normale Supérieure is a small and historical French institution located in the centre of Paris. ENS is dedicated to training through research with a multidisciplinary and international perspective with 300 foreign researchers and 650 PhD students. ENS is a founding member of Paris Sciences Lettres (PSL) University, ranked among the top 5 young universities under 50 years of age in the THE (Times Higher Education) and QS (Quacquarelli Symonds) rankings (2019-2021), and the 38th best university according to the 2021 Shanghai ranking.
Position 5: Nuclear Dynamics during Seed Priming:
PhD position in Developmental Epigenetics at the group of Dr Sara Farrona in the Centre for Plant and Agricultural Biosciences-Ryan Institute at the University of Galway, Galway, Ireland.
What are you going to do?
Epigenetic mechanisms of the memory to seed osmopriming
You will work in a project about the molecular memory triggered by seed priming (SP) in response to osmotic stress. SP has been used in agriculture for many years as a means to increase seed vigour, which is a key agricultural trait to secure successful germination and establishment of the new plant. SP may trigger a molecular memory that can persist throughout plant development. Thus, it has been hypothesised that epigenetic mechanisms, which contribute to generate stable transcriptional patterns, may be essential for generating a SP memory. In addition, it is still unknown which particular plant cells may be the depository of such a memory. Shoot apical meristematic (SAM) cells, present during the whole life of the plant, are obvious candidates to act as SP memory reservoirs.
Your aim will be to identify transcriptomic and epigenomic changes associated to SP by performing cell-specific analyses both in Arabidopsis and oilseed rape. In addition, my group has identified a SP memory candidate gene that is well conserved in Brassicaceae. Focusing on this gene, your goal will be to identify cis-regulatory sequences associated to SP. This will be a highly multidisciplinary project in which you will apply approaches for cell sorting (e.g. INTACT) and perform RNA-seq and ChIP-seq/BS-seq in Arabidopsis. Furthermore, you will carry out phylogenetic analyses of the promoter of the candidate gene in different Brassicaceae species and molecular approaches for their characterisation (e.g. mutagenesis, expression analyses). You will study if transcriptomic/epigenomic changes are conserved in oilseed rape by ChIP/BS-qPCR and RT-qPCR.
To develop this project, you will actively collaborate with partners at the University of Amsterdam, ENS, CSIC-CBGP and BioAtlantis. You will also benefit from training in plant phenotyping, oilseed rape transformation, analysis of cis-regulatory elements and bioinformatics by various partners and associated partners.
What do you have to offer?
- MSc in Molecular Biology, Plant Science or any related science
- Knowledge in molecular biology
- Background in epigenetics and/or gene expression
It is a preference if you also have experience in cytology and data analysis techniques.
Our offer
The appointment will be on a temporary basis for a period of three years. If required, there is the possibility to extend it for an additional year in which fees will be waived by NUI Galway. The appointment will be according to the employment rules of Ireland and should lead to a dissertation (PhD thesis). A Personal Career Development Plan will be drafted that includes the attendance to EpiSeedLink courses and meetings.
The gross monthly salary will be according to the MSCA programme, taking into account the country-specific correction coefficient. Besides the salary, the PhD student will obtain a mobility allowance. The position is aimed at being full-time, but by exception, if needed for family reasons, a part-time appointment is possible.
You will enroll in the structured PhD programme in Plant and AgriBiosciences offered within the School of Biological and Chemical Sciences in collaboration with Teagasc, the Irish agricultural and food development authority, and other partner organisations. This PhD programme will prepare you for a career and future research opportunities in plant & agribioscience areas. As a NUI Galway student you will be well supported by the Graduate Office and the Career Development Centre which aim is to empower you as a student in our university and to make successful transitions towards fulfilling your career.
Any questions?
Do you have any questions, or do you require additional information? Please contact: Dr Sara Farrona; sara.farrona@nuigalway.ie, phone: +353 91 492683.
About us
National University of Ireland Galway
National University of Ireland Galway (NUI Galway) is a research and top-quality teaching university that attracts over 18,000 students and has a large international community from more than hundred different countries. The university is located in Galway, Ireland’s third largest city and regarded as the cultural capital of the country. NUI Galway is also a hub for research in Western Ireland and hosts diverse research centres focused on specific scientific disciplines. Want to know more about NUI Galway?
Our lab belongs to the Ryan Institute, NUI Galway’s largest research institute and an inter-disciplinary research cluster focused on sustainability and innovation, contributing to main Sustainable Development Goals. NUI Galway is part of the most international city in Ireland and is home to almost 4,000 international students. Galway is a highly diverse city with a strong tradition of reaching out to the world. Under the Third Level Graduate Scheme, non-EU/EEA students who have completed a PhD will be able to remain in Ireland for 24 months while seeking employment or acquiring another form of work permit or green card.
Position 6: Regulation of Transcriptional Elongation:
PhD position on the Regulation of RNA Polymerase II Transcriptional Elongation in the group of Prof Klaus Grasser at the Biochemistry Center, University of Regensburg in the Department of Cell Biology and Plant Biochemistry, Regensburg, Germany.
What are you going to do?
RNA polymerase II transcriptional elongation at changing conditions
You will work on a project addressing the role of RNA polymerase II (RNAPII) transcriptional elongation on plant responses to environmental conditions and seed priming with emphasis on seed dormancy/germination and seedling establishment. Focus will be on so-called transcript elongation factors (TEFs) that comprise histone chaperones, modulators of histone modifications and regulators of RNAPII activity. Currently it is unknown to which extent the association of TEFs with elongating RNAPII is affected by altered ambient conditions, possibly resulting in distinct versions of the active RNAPII elongation complex. This may result in modified genomic distribution of RNAPII/TEFs and changed chromatin accessibility, ultimately entailing adjusted gene transcription patterns.
Your aim will be to study the composition of RNAPII elongation complexes, TEF-dependent genomic distribution of RNAPII, chromatin accessibility and transcriptional output under the above-mentioned conditions. The majority of experiments will be performed using the Arabidopsis model, but some assays will be also implemented in oilseed rape. In the course of the project, you will employ a variety of approaches including affinity-purification of protein complexes in combination with mass spectrometry, chromatin immunoprecipitation followed by high throughput sequencing, micrococcal nuclease digestion assays as well as transcript profiling. Moreover, molecular and phenotypic analyses of wildtype and mutant plants will represent a central part of your work.
As an integral part of the project you will actively collaborate with partners at other institutions such as CSIC-CNB (Madrid, Spain), DSV (Lippstadt, Germany) and CSIC-IBMCP (Valencia, Spain).
What do you have to offer?
- MSc in Molecular Biology, Biochemistry or any related subject
- Knowledge in molecular biology and/or biochemistry
- Background in genetics and/or gene expression
Experience in bioinformatics and data analysis is beneficial.
Our offer
The appointment will be on a temporary basis for a period of three years (potentially prolongable). The appointment will be according to the employment rules of the University of Regensburg and should lead to a dissertation (PhD thesis). A Personal Career Development Plan will be drafted that includes the attendance to EpiSeedLink courses and meetings.
The gross monthly salary will be according to the MSCA programme, considering the country-specific correction coefficient. Besides the salary, the PhD student will obtain a mobility allowance . The position is aimed at being full-time, but by exception, if needed for family reasons, a part-time appointment is possible.
Any questions?
Do you have any questions, or do you require additional information? Please contact: Klaus Grasser; klaus.grasser@ur.de.
About us
University of Regensburg
More than 20,000 students are enrolled at the University of Regensburg, which is a modern university campus comprising 12 faculties. The city of Regensburg is located in Bavaria in the south-east of Germany approximately 100 km from Munich in an attractive environment. Our lab belongs to the Department of Cell Biology & Plant Biochemistry as well as to the Regensburg Center for Biochemistry. Here, a stimulating atmosphere for research is offered as well as advanced facilities for protein analyses, imaging and systems biology. You will become member of the Regensburg International Graduate School of Life Sciences (RIGeL) offering a well-structured PhD program and additional benefits.
Position 7: Chromatin Dynamics during Germination:
PhD position in chromatin dynamics during germination under the supervision of Dr Aline Probst at the Institute of Genetics, Reproduction and Development (iGReD) in Clermont-Ferrand, France.
What are you going to do?
Role of chromatin dynamics in seed germination
You will work on a project aiming to understand the mechanisms and biological role of chromatin reorganisation during seed germination. Histone variants affect nucleosome stability and deposition of epigenetic marks on histones, and contribute to gene expression control. Specific histone variants and modifications characterise chromatin organisation in the dry seed embryos and are hypothesised to be key players in the rapid transcriptome reprogramming during seed germination.
Your aim will be as a first step to characterise chromatin organisation in dry seeds focusing on histone variants and histones modifications. Then, you will investigate how chromatin organisation is remodelled during seed germination and early seedling development under optimal and stress conditions. Finally, you will investigate the promising action of plant biostimulants that prepare seeds for critical stress periods (priming) by studying how they modify chromatin organisation during seed germination. You will work on two plant species: the model species Arabidopsis thaliana and the cultivated species Brassica napus (oilseed rape). You will take advantage of available Arabidopsis mutant collections and transgenic lines carrying tagged histone variants to dissect mechanistically chromatin dynamics in the germinating seed and translate your discoveries to Brassica napus, for which plant material with different germination efficiency will be made available by the DSV company.
You will actively collaborate with partners at the CSIC in Madrid (Spain) for mass spectrometry and oilseed rape transformation, at the ENS (France) for epigenomics, and at the DSV Company (Germany) for plant phenotyping. This will provide a multi-disciplinary training ranging from fundamental knowledge in epigenomics, mass-spectrometry and bio-imaging to a more applied experience in plant phenotyping in a breeding company.
What do you have to offer?
- MSc in Molecular Biology, Plant Science or related biological sciences.
- Knowledge in molecular biology.
- Background in genetics and epigenetics.
- Strong interest in multi-disciplinary approaches centred on genetics.
It is a preference if you are also motivated to learn and apply bioinformatics approaches.
Our offer
The appointment will be on a temporary basis for a period of three years. The appointment will be according to the employment rules of France and should lead to a dissertation (PhD thesis). A Personal Career Development Plan will be drafted that includes the attendance to EpiSeedLink courses and meetings.
The gross monthly salary will be according to the MSCA programme, taking into account the country-specific correction coefficient. Besides the salary, you will obtain a mobility allowance.
Any questions?
Do you have any questions, or do you require additional information? Please contact: Dr Aline PROBST; aline.probst@uca.fr.
About us
University Clermont Auvergne (UCA) is a multidisciplinary higher education institution composed of 39 research laboratories working in the fields of fundamental and engineering sciences, life and health sciences as well as law, human and social sciences. Our lab belongs to the Genetics, Reproduction and Development institute (iGReD), which is located in a modern building, inaugurated in 2017, and comprises state of the art facilities in microscopy and image analysis, molecular biology, bioinformatics and high computing capacities and brand new plant growth facilities. The iGReD is composed of 16 research teams working on various model species and provides a stimulating research environment with many PhD students and postdocs, weekly seminars and a dedicated group of 7 teams working on chromatin and epigenetics in drosophila, mouse and plants.
Position 8: Cis-Regulatory Elements of Drought Resistance:
PhD position in Gene Regulation and Epigenetics in the group of Dr Maike Stam at the Swammerdam Institute for Life Sciences at the University of Amsterdam, Amsterdam, Netherlands.
What are you going to do?
Identification of oilseed rape cis-regulatory elements involved in drought resistance
You will be working on a project about the cis-regulatory code playing a role in drought resistance in oilseed rape. One of the biggest challenges of your generation is to find solutions to the threats of the changing climate. EpiSeedLink will explore the mechanisms underlying seed priming to improve crop performance under stress conditions such as drought, heat and high light. The response to such stresses is largely accomplished through the activation and repression of cis-regulatory DNA sequences at the correct moment in time and space. Your project will focus on identifying and characterising genes and their cis-regulatory sequences (CRSs) involved in drought resistance in oilseed rape by seed priming. This project promises new targets for informed breeding in oilseed rape.
Your aim will be to make use of different oilseed rape accessions to correlate drought responses to differential epigenomic and transcriptomic data, and nucleotide polymorphisms, to pinpoint genes and CRSs involved in the drought responses. Hereto you will generate and integrate phenotypic, transcriptomic, transcription factor binding, DNA methylation and histone modification profiles of a set of oilseed rape accessions that respond differently to priming and/or drought. You will characterise promising genes and CRSs in more detail by testing their activity and function in transient assays and by genome editing, respectively.
You will actively collaborate with partners at the NUI Galway (Ireland), DSV (Germany) and UZH (Switzerland) and others. You will also benefit from training in plant phenotyping, differential transcription factor binding assays, DNA methylation analyses, oilseed rape transformation and bioinformatics by various partners and associated partners.
What do you have to offer?
- MSc in Molecular Biology and/or Biochemistry
- Experience in molecular biology and/or biochemistry laboratory techniques
- Strong interest in epigenetics and gene regulation
- You are a teamplayer and have excellent communication skills
It is a preference if you feel comfortable performing experimental lab work and have experience with/affinity for bioinformatic data analysis.
Our offer
The duration of the appointment as an MSCA fellow will be for a maximum period of 3 years and will, in line with the duration of a PhD study in the Netherlands, be extended another year according to the employment rules of the University of Amsterdam. The initial contract will be for a period of 18 months and after satisfactory evaluation it will be extended for a total duration of 4 years. The appointment should lead to a dissertation (PhD thesis). A Personal Career Development Plan will be drafted that includes attendance to EpiSeedLink training events and meetings. We also expect you to assist in teaching undergraduates and master students.
The gross monthly salary will be according to the MSCA programme, taking into account the country-specific correction coefficient. Besides the salary, the PhD student will obtain a mobility allowance for the duration of the MSCA programme . For the one-year extension after the MSCA project, the gross monthly salary will be according to the salary scales of the University of Amsterdam. Positions are aimed at being full-time (38 hours per week), but by exception, if needed for family reasons, part-time appointments are possible.
Besides the salary and a vibrant and challenging environment at Science Park, we offer you multiple benefits:
- 232 holiday hours per year (based on fulltime)
- multiple courses to follow from our Teaching and Learning Centre;
- multiple courses on topics such as time management, handling stress and an online learning platform with 100+ different courses;
- 7 weeks birth leave (partner leave) with 100% salary;
- partly paid parental leave;
- the possibility to set up a workplace at home;
- a pension at ABP for which UvA pays two third part of the contribution;
- the possibility to follow courses to learn Dutch;
- help with housing for a studio or small apartment when you’re moving from abroad.
Any questions?
Do you have any questions or do you require additional information? Please contact: Dr Maike Stam; m.e.stam@uva.nl, phone: +31205257655.
About us
The University of Amsterdam is the Netherlands’ largest university, offering the widest range of academic programmes. At the UvA, 30,000 students, 6,000 staff members and 3,000 PhD candidates study and work in a diverse range of fields, connected by a culture of curiosity. The Faculty of Science has a student body of around 8,000, as well as 1,800 members of staff working in education, research or support services. Researchers and students at the Faculty of Science are fascinated by every aspect of how the world works, be it elementary particles, the birth of the universe or the functioning of the brain.
The Swammerdam Institute for Life Sciences (SILS) is one of the Faculty of Science’s largest institutes. Its approximately 240 scientists and staff members work in 16 research groups that perform excellent research centred on four themes: Neurosciences, Cell & Systems Biology, Green Life Sciences (GLS) and Microbiology. The position offered here is embedded within GLS.
Position 9: Biostimulant-based Seed Priming:
PhD position in Biostimulant based seed priming technologies under the supervision of Dr Sujeeth Neerakkal, BioAtlantis Ltd. and Dr Sara Farrona, Centre for Plant and Agricultural Biosciences-Ryan Institute at the University of Galway (NUI Galway), Galway, Ireland.
What are you going to do?
Biostimulant-based seed priming for improved crop growth and stress tolerance
You will work on a project to develop a novel, adaptive and sustainable seed priming technology for the seed industry and crop growers. Certain chemical and biological seed treatments can elicit ‘priming memory’ at the epigenetic level leading to enhanced survival of crops under adverse environmental conditions. The hosting institute, BioAtlantis Ltd., has recently identified naturally-derived bioactive molecules that can prime crops and act as plant oxidative stress inhibitors. This novel priming technology is proven to protect crops from adverse weather induced damages (abiotic stress) for a period of 10-14 days post application, leading to better crop yield and quality.
Your aim will be to assess the efficacy of hydro/osmopriming and seed coating techniques in the presence of natural compounds isolated from macro and microalgae, plant extracts, small organic molecules and essential trace elements. Germination, vigour, emergence-tests and field trials will be undertaken, producing phenotyping and physiological data from different species (B. napus, tomato) under control and stress conditions. You will elucidate seed priming mechanisms by working with experts in molecular priming and epigenetics in crop plants. An in-depth understanding of seed priming and germination mechanisms will be obtained via OMICs approaches (transcriptomics and epigenomics – ChIP-seq/BS-seq). The outcomes will be (a) a greater scientific understanding of molecular mechanisms of seed priming, (b) new products to enhance agricultural sustainability in the face of climate change, and (c) novel tools for efficient priming against abiotic stress. You will develop unique skill sets encompassing plant physiology, genetics, bioinformatics and biostatistics, preparing yourself for a successful career in both academia and industry.
You will actively collaborate with and will be enrolled for a Doctoral degree at NUI Galway and will also undertake research in the industrial settings at BioAtlantis Ltd, Ireland. You will perform B. napus phenotyping (DSV, Germany), ChIP-seq profiling (ENS, France) and BS-seq training and data analysis (UZH, Switzerland).
What do you have to offer?
- MSc in Molecular Biology, Plant Science or related biological sciences.
- Experience in molecular biology techniques and conceptual background in epigenetics and gene expression.
- Experience in statistical analysis of datasets from plant trials.
- Organizational skills to create and manage complex datasets.
It is a preference if you also have experience in data analysis and motivation for training in bioinformatics.
Our offer
The appointment will be on a temporary basis for a period of three years. The appointment will be according to the employment rules of Ireland and should lead to a dissertation (PhD thesis). A Personal Career Development Plan will be drafted that includes the attendance to EpiSeedLink courses and meetings.
The gross monthly salary will be according to the MSCA programme, taking into account the country-specific correction coefficient. Besides the salary, you will obtain a mobility allowance
Any questions?
Do you have any questions, or do you require additional information? Please contact: Dr Sujeeth Neerakkal; plant.research@bioatlantis.com, phone: +353 66 711 8477.
About us
BioAtlantis commenced in 2004, and entered the crop biostimulant market in 2007. BioAtlantis provides novel biostimulant based technologies to induce stress-protective mechanisms and help crops reach their genetic potential. The company has pioneered an innovative technology to prime and protect crops from oxidative stress and improve fruit-set. As a testament to its growth, BioAtlantis commissioned a new seaweed extraction and production facility in 2019, the largest in the north western Europe. Over 85 peer reviewed publications have been published to date on BioAtlantis’ products and formulations. We have a proven track record in scientific leadership, involved in a number of EU FP7 and H2020 projects and are currently collaborating with >40 universities worldwide.
Over 85 peer reviewed publications have been published to date on BioAtlantis’ products and formulations. BioAtlantis’s vision is to become a global brand leader in plant biostimulant and nutraceutical technology, exporting innovative products to global markets and providing sustainable solutions to climate change-associated stresses.
Position 10: Genetic Dissection of Seed Priming:
PhD position in Dissection of seed priming by Genome-Wide Association Mapping in Brassica napus under the supervision of Ulf Feuerstein at Deutsche Saatveredelung AG (DSV), Breeding Station Hof Steimke, Germany, and in cooperation with Prof. Stefan Scholten, University of Goettingen, Division of Crop Plant Genetics.
What are you going to do?
Dissection of seed priming in Brassica napus
You will work in DSV’s Seed Technology Team in the Centre for Phenotyping in Asendorf, Lower Saxony. Seed and seedling vigour are key agricultural traits impacting seed germination and seedling emergence, but also highly complex and challenging to achieve. In DSV we are interested in how seed priming treatments boost the vigour of seeds and seedlings especially under stress conditions. We know that priming effects are highly variable depending on diverse factors such as the plant genotype. Your project will focus on understanding how seed and seedling vigour are controlled at the genetic level in response to seed priming that is aimed to overcome drought stress. Using a collection of Brassica napus varieties you will identify genetic markers linked to seed/seedling vigour-related traits that will help us to tailor oilseed rape breeding.
You will carry out seed vigour and seedling emergence tests in a Brassica napus genotype collection of unprimed vs osmoprimed seeds. You will identify SNPs across the different accessions by transcriptomic analysis (i.e. RNA-seq). You will integrate phenotyping and genotyping data to identify seed priming quantitative trait loci (QTLs) and predict seed priming candidate genes. You will examine the phenotypic response of selected varieties to biostimulants from BioAtlantis.
Your aim will be to uncover candidate genes involved in triggering enhanced seed and seedling vigour in response to priming treatments by applying a GWAS approach under control and drought conditions. Hereto, you will phenotype a diversity set of annual B. napus genotypes from different origins taking advantage of DSV’s high-throughput seed phenotyping platform. You will also perform RNA-seq analyses and integrate your phenotyping and transcriptomic data to identify candidate genes that are key for the control of seed and seedling vigour traits induced by seed osmopriming.
You will actively collaborate with partners at the NUI Galway in Ireland and NuSpec in UK to process samples, produce RNA-seq data, and start data analysis, and with BioAtlantis, to evaluate the effect of seed priming using different chemical treatments on a subset of annual B. napus lines.
What do you have to offer?
- MSc in Molecular Biology, Plant Science or related biological sciences
- Strong interest in deciphering how plants respond to seed priming and adapt to the environment
- Conceptual background in epigenetics and gene expression
- Knowledge in molecular biology techniques
Experience in data analysis and motivation for training in bioinformatics are a plus.
Our offer
The appointment will be on a temporary basis for a period of three years. The appointment will be according to the employment rules of Germany and should lead to a dissertation (PhD thesis). A Personal Career Development Plan will be drafted that includes the attendance to EpiSeedLink courses and meetings.
The gross monthly salary will be according to the MSCA programme, taking into account the country-specific correction coefficient. Besides the salary, you will obtain a mobility allowance
Any questions?
Do you have any questions, or do you require additional information? Please contact: Dr Ulf Feuerstein, Ulf.Feuerstein@dsv-saaten.de, phone: +49 (4253) 9311 11.
About us
Deutsche Saatveredelung AG (DSV)
DSV exists for almost 100 years and is one of the leading plant breeding and seed companies in Germany, with its head office in Lippstadt. DSV provides services in research, breeding, production, processing and seed distribution and is, besides in Germany, present in Poland, France, Great Britain, Ukraine, the Netherlands, Denmark and Argentina. More than 700 employees work for the company. DSV has a broad range of scientific experience. At its Seed Technology Facilities DSV has the possibility to have a close look at seed and seedling vigour, their speed of emergence and early root growth under laboratory and field conditions.
Position 11: Plant Reproductive Genetics and Epigenetics:
PhD position in plant reproductive genetics and epigenetics at the group of Prof. Dr. Ueli Grossniklaus at the Department of Plant and Microbial Biology (IPMB) of the University of Zurich, Switzerland.
What are you going to do?
Transcriptomic and epigenomic effects of seed priming on seedling establishment during drought
Your project will focus on how molecular priming, e.g., treating seeds with diverse agents, can protect plants against stress later during development. How a memory of the priming treatment can be maintained over time and how it affects gene expression is not well understood. You will address this important question. First, you will screen different priming agents for their effectiveness in protecting seedlings from drought if applied to Arabidopsis seeds in collaboration with BioAtlantis Ltd in Ireland. Second, you will use the most effective priming agents to assess genome-wide changes in the transcriptome and methylome over time to identify key factors that underly priming memory. Third, selected factors will be functionally assessed by testing the priming response in corresponding Arabidopsis mutants by high-throughput phenotyping in collaboration with DSV in Germany, and the CSIC-CNB in Spain.
In your PhD project, you will address a challenging question and will have to set-up high-throughput protocols for transcriptome, methylome, and phenotypic analyses. You will identify priming agents and their targets in Arabidopsis, which can serve as breeding targets in the long-term. You will perform wet-lab experiments in the fields of genetics, genomics, and molecular biology, as well as bioinformatic analyses in a stimulating network of peers and benefit from international experiences in training and research.
As the project relies heavily on collaborations with other partners of the EpiSeedLink consortium, you will experience the research environment in different countries and sectors, benefit from the diverse expertise of your supervisors, and develop a wide scientific network.
What do you have to offer?
- MSc in Molecular Biology, Plant Science, or related biological sciences
- Interest and a conceptual background in epigenetics and gene expression
- Knowledge in molecular biology techniques and, preferably, bioinformatics
It is a preference if you also have experience in data analysis and motivation for training in bioinformatics.
Our offer
The appointment will be on a temporary basis for a period of three years, with the possibility to extend to four years. The appointment will be according to the employment rules of the University of Zurich and the Swiss National Science Foundation, and it should lead to a dissertation (PhD thesis). A Personal Career Development Plan will be drafted that includes the attendance to EpiSeedLink courses, workshops, and meetings.
The gross monthly salary will be in Swiss Francs according to the MSCA programme. Besides the salary, the PhD student will obtain a mobility allowance. Positions are aimed at being full-time, but by exception, if needed for family reasons, part-time appointments are possible.
Any questions?
Do you have any questions or do you require additional information? Please contact Prof. Dr. Ueli Grossniklaus (grossnik@botinst.uzh.ch, +41 44 634 82 40).
About us
With over 26,000 students and 690 professors, the University of Zurich (UZH) is by far the largest university in Switzerland, offering a broad range of courses. In the Shanghai Ranking 2021 for the best universities worldwide, UZH ranked on place 54, exemplifying that UZH is one of the top institutions for education and research.
Together with the Swiss Federal Institute of Technology (ETHZ), the Zurich region constitutes a highly attractive area for students and researchers from all over the world. Consequently, the proportion of foreign students and professors is very high, especially in the area of Life Sciences and Agriculture, which ranks even better in the Shanghai Ranking (rank 25 in 2016) than UZH as a whole. With 10 professors and a highly international scientific staff of roughly 180 people, the Department of Plant and Microbial Biology (IPMB) is one of the larger institutes of UZH’s Faculty of Science. IPMB specialises mainly, but not exclusively, in the investigation of molecular aspects of plant physiology, plant development, plant-pathogen and plant-soil interactions, microbiology, limnology, and evolutionary ecology.
The Grossniklaus laboratory investigates the molecular basis of plant reproduction, with an emphasis on cell specification, signalling processes, and epigenetic gene regulation. In particular, the group is highly international and has played a leading role in the study of maternal effects through epigenetic mechanisms such as genomic imprinting and Polycomb-based gene repression. Moreover, the group is interested in the biomechanics of cellular morphogenesis, and investigates the ecological and evolutionary role of epigenetic variation.
How to apply:
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Aplication deadline: October 1st, 12 p.m.