PhD Opportunities

PhD applications for October 2021 start are now closed.

.....If you are interested in applying for a PhD please contact karen.halliday@ed.ac.uk to discuss project options

Lab team work!!

PhD Opportunities - see project descriptions below

We are seeking highly motivated PhD candidates to join our team. If you are interested we are happy to assist with applications for PhD positions, and other types of funding, including scholarships.

LAB Inclusion Statement

Professor Halliday is Dean of Systematic Inclusion and is responsible for overseeing Equality, Diversity and Inclusion (EDI) strategy in the College of Science and Engineering. EDI is very much embedded in lab practice. We celebrate diversity and are proud that our lab team has minority ethnic and white members from different regions of the world and socio-economic backgrounds. Our aim is to provide a welcoming, inclusive environment where everyone can reach their full potential irrespective of background.

Our Research

Molecular signalling: Define the environment-controlled molecular mechanisms that regulate plant growth and development. (molecular-genetics, physiology)

Modelling: Build mathematical models that can predict molecular or physiological biological behaviour. (maths/physics)

Crop development for the future: Develop food crops that can withstand the climate change. (molecular-genetics, physiology)

Social Impact: Working with Social Scientists to challenge descriminatory practices and to evolve an inclusive working environment that attracts and supports diverse employees in STEM.

PhD projects are advertised each Fall, but if you think you would like to join our lab - we strongly encourage you to contact us earlier in the year

Contact: karen.halliday@ed.ac.uk, Tel. +44 +131 651 9083 (phone not active during covid pandemic)

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Descriptions of PhD positions to start in 2021, applications now closed (deadline 6th January 2021)

 

Project 1: Light control of protein translation and plant biomass

Primary supervisor, Prof. Karen Halliday; second supervisor, Dr Edward Wallace

Plants are inherently plastic organisms. Their general body plan is genetically encoded, but plant architecture can be modified to adjust to the environment that surrounds it. In this sense, external cues, such as light, have a profound effect on the way a plant grows and develops, ultimately affecting a plant’s fitness, disease resistance and productivity. Growth plasticity is particularly pronounced in leaves that are exposed to vegetation shade. Proximity of nearby plants is detected by the phyB photoreceptor, which then adjusts leaf growth and physiology to ensure survival in the face of competition.

This project builds on recent discoveries in the Halliday lab, that significantly expand our understanding of how phyB operates in the leaf. phyB is currently thought to promote leaf elongation by manipulating plant hormone pathways. Our unpublished data point to a novel role for phyB in regulating the leaf cell division machinery, ribosome biogenesis and translation, key contributors to plant biomass. Collectively, these findings provide a new conceptual framework to understand and interrogate phyB function. 

The project will focus on establishing how phyB regulates ribosome biogenesis and translation. This will be accomplished by testing our central hypothesis that phyB regulates the basic translational machinery through transcriptional and post-transcriptional mechanisms. Results from this PhD project will be highly relevant for crop research. An expected outcome will be the identification of molecular strategies to improve plant architecture and biomass in dense cropping environments (that normally reduce yield). The project will also have broad reach as it will deepen our understanding of environment-driven growth plasticity, a fundamental property that underlies the extraordinary evolutionary success of plants on earth.

Training: You will benefit from expertise in the Halliday (photochemistry, molecular signalling in plants) and Wallace (protein translation in fungi, bioinformatics) labs, which will provide training in a range of complementary cutting-edge methods.  Analysis of the transcriptional mechanism will build your expertise in a range of molecular techniques such as qPCR, chromatin immunoprecipitation (ChIP) and bioluminescence reporter analysis. This will provide a foundation for high-throughput measurement of transcription by RNA-seq and translation by ribosome profiling, and you will be trained in bioinformatic analysis of these rich data. You will also measure plant growth using quantitative 3D plant phenotyping. In addition to core training in basic research, you will be offered career mentoring, and will have opportunities to gain broader experience in networking, outreach, diversity and inclusion activities.

 

Project 2: Light control of leaf cell division

Primary supervisor, Prof. Karen Halliday; second supervisor Dr Annis Richardson

Plants are highly malleable organisms that are able to adjust their growth strategy to a changing environment. The leaf is an excellent example of a highly plastic organ, where shape and size are not predetermined, but influenced by external signals such as light. These adaptative qualities are important for survival as leaves perform critical roles in temperature regulation, gas exchange and sunlight capture for photosynthesis.

Under vegetation shade, leaf blade growth is severely restricted and carbon resources are redirected to the leaf petiole which elevates and reorientates the blade to capture sunlight. This adaptive response, which is controlled by phytochrome B (phyB), is critical for survival in vegetation rich environments. The PhD program will delineate the molecular mechanism through which phyB controls leaf blade growth. You will test two key hypotheses that emerge from recent discoveries in the lab: i) phyB operates through a principal leaf development module to regulate leaf cell division; ii) phyB regulates cell division through parallel control of the cell cycle and cytokinesis.

Training: The Halliday and lab offers a dynamic learning environment with inputs from different disciplines. During the PhD you will work alongside and learn from experts in plant physiology and phenotyping, molecular signalling and pathway modelling. Your second supervisor Dr Richardson brings important specialist knowledge in quantifying and modelling leaf shape. An important component of the program will be quantitative analysis of plant growth in different growth regimes. Here you will work with experts in 3D plant imaging to develop skills in image capture and analysis. You will also acquire a range of molecular techniques including: DNA/RNA gel electrophoresis, qRT-PCR; protein analysis e.g. western blotting, yeast-two-hybrid, chromatin immuno-precipitation and bioluminescence imaging. The program will provide training in data analysis, hypothesis-based experimentation, critical thinking and report writing. There will be opportunities for you to present your research at regular lab meetings, at national and at international conferences (online and in person when covid19 restrictions allow). The Halliday lab works closely with world-leading scientists in photobiology which will open routes for networking and future collaboration. On joining the lab you will be offered career mentoring, and will have opportunities to gain broader experience in outreach, diversity and inclusion activities.

 

Project 3: The Dual Function of Light in Controlling Plant Growth

Primary supervisor, Prof. Wayne Powell; second supervisor, Prof. Karen Halliday

With changes in population demographics, urbanisation and the declared climate emergency in Scotland there is a need to use resources more sustainably. The importance of breeding climate resilient crops has never been greater. Various approaches built around the deployment of disruptive technologies (Hickey et al 2017) have been proposed to increase the pace and precision of breeding. One such technology is speed breeding which is designed to accelerate plant development, particularly flowering time based on extended light regimes (Watson et al. 2018). Although the concept is empirically well advanced the underpinning biology and potential disruption of the circadian rhythm (biological clock) is poorly understood. Plant breeders regularly manipulate light and temperature to reduce generation time and hasten the breeding cycle through the adoption of single seed descent approaches. This approach may have introduced unconscious selection for speed-breeding responsive types. Preliminary data obtained at SRUC have confirmed that there are genetic differences between modern barley varieties developed through accelerated breeding and older varieties and land races in their response to speed breeding regimes. These observations provide the experimental framework to identify the key genetic determinants of speed breeding and the consequences of selection on circadian-clock genes and genomic plasticity in an economically important crop, barley. Furthermore, unravelling the genetics of plasticity to speed breeding brings the opportunity to deliver step changes in the breeding of climate resilient crops.

We propose to identify key determinants of speed-breeding plasticity. We will use barley as a model for ecological adaptation and an important crop for Scotland. Modern elite barley germplasm along with older varieties that are less likely to have undergone unconscious selection from rapid cycling breeder interventions will be screened for speed breeding plasticity. This will be measured by reversion to normal growth after exposure to a speed breeding environment. Our preliminary data indicate that variation in plant responses ranging from continued rapid development to reversion to normal rates of developmental will be detected. This plasticity will be mapped by methods such as next generation sequencing of the extreme bulks. Additionally, network modelling of the genetic mapping results (Chew et al. 2017) will be deployed to provide further and deeper understanding of the response to speed breeding. Overall, we aim to move our understanding of speed breeding from an empirical approach to a predictive enabling technology that can be directly applied in pre-breeding where little is known about the consequences of selection on genome plasticity.

This project will provide interdisciplinary student training in modern plant breeding mathematical and systems biology. Training in plant breeding and quantitative genetics will be provided through our group in SRUC, and training in systems biology and mathematical modelling will be available through our project partner, Prof. Andrew Millar, University of Edinburgh, further enhancing the training of the student.