Job Description

Background Plants are inherently plastic organisms, and this property is critical for their survival. 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\xe2\x80\x99s fitness, it\xe2\x80\x99s ability to photosynthesise, and it\xe2\x80\x99s productivity. In nature and in intensive cropping systems, plants must deal with adverse light environments for photosynthesis and plant development. It is estimated that in crops in dense canopies, shaded leaves contribute to 50% of the total canopy carbon gain, and therefore are critical for determining crop yield. This project will focus on phytochromes, a unique group of light receptors that enable plants to detect nearby vegetation and elicit adaptive responses that ensure survival in the face of competition. It builds on recent discoveries in the Toledo-Ortiz and Halliday labs, that provide new insights into the operational properties of phyA, one of the most important phytochromes. PhyA is currently thought to operate as a deep (vegetation) shade detector, in conditions which are typically dimly lit and have higher proportions of long wavelength Far-Red light. Recent data from the Halliday lab has shown phyA action is not restricted to deep shade, rather it is tuned to detect wide-ranging conditions. This indicates that phyA plays a pivotal role in a newly identified \xe2\x80\x9cshade survival response\xe2\x80\x9d (SSS). The Toledo-Ortiz lab has shown that adaptations to the photosynthetic apparatus are a critical component of phytochrome activity, including the SSS. These findings provide a new conceptual framework to understand phyA function, in the adaptation to plant growth and development under canopy environments. Aims. This PhD will seek to uncover the molecular properties that enable phyA to respond to different environments and climatic conditions. Genetic and molecular resources will be used to derive new mechanistic understanding of how phyA function changes in different light and temperature regimes, including its role in conditions that limit plant productivity such as canopy shade and low light. Methodology/Approach. The project will make use of novel optogenetic tools to track the activity of phyA and assess it\xe2\x80\x99s links to the adaptation (short, medium, long term) of Arabidopsis plants to canopy light and temperature environments. Analyses will include growth responses, production of biomass and chloroplastic functions to uncover the basis of growth and photosynthetic acclimation. The student will build core expertise in photophysiology and molecular-genetic analysis, and a range of techniques including gene editing, bioluminescence imaging, qPCR, RNAseq, chromatin immunoprecipitation, western blotting, phenotyping, photosynthetic efficiency measurements and principles of the use of theoretical approaches. Outline for 1st 12-18 Months In addition to familiarization with the phytochrome light signaling literature, initial work will focus on assessment of the activity of phyA using optogenetic tools under different canopy light and temperature regimes, including conditions that mimic neighbor perception, shade and deep shade at different time scales (short, medium and long term). These conditions will imply environments enriched in Far Red-light as well as changes in light intensity. On a second stage we will evaluate the role of variations in temperature within the range existing in canopies. Using existing mutants defective in phyA activity, we will evaluate the contribution of phyA to plant architecture, leaf development, photopigments and photosynthetic parameters. Mutants defective in phyA will be contrasted to the other phy sensing shade (phyB). These studies will map the predominant, cooperative, or antagonistic roles of these two photoreceptors to adaptation of plants to dynamic and different canopy environments. Based on the full phenotypic evaluations, conditions will be selected for the 2nd stage of the work that will include transcriptomics to identify responsive pathways and candidate genes working with phyA in the control of particular growth and photosynthetic responses, with initial emphasis in leaf morphology and photosynthesis using new APGC phenotyping facilities. These studies will likely deliver new components working with the phytochromes for acclimating photosynthesis acclimation to adverse environments and those allowing adaptation of growth responses. Following this initial characterization, the direction of the research will be determined by student interests in consultation with the supervisors. A number of potential avenues exist including deeper understanding of the signalling pathways influencing photosynthetic efficiency, those determining leaf morphology or those leading to biomass accumulation. This 4 yr PhD project is a competition jointly funded by The James Hutton Institute and the University of Edinburgh. The supervision team comprised of Dr Gabriela Toledo-Ortiz and Dr Rob Hancock of the James Hutton Institute along with Professor Karen Halliday of the University of Edinburgh.This opportunity is open to UK students and will provide funding to cover a stipend and UK level tuition. International students may apply, but must fund the difference in fee levels between UK level tuition and international tuition fees. Students must meet the eligibility criteria as outlined in the UKRI guidance on UK and international candidates. Applicants will have a first-class honours degree in a relevant subject or a 2.1 honours degree plus Masters (or equivalent).

We will not consider the use of 3rd party recruitment agencies for the sourcing of candidates for this position. The James Hutton Institute is an equal opportunity employer. We celebrate diversity and are committed to creating an inclusive environment for all employees. The James Hutton Institute is a: Stonewall Diversity Champion; Athena SWAN Bronze Status Holder; Disability Confident Committed Employer and a Living Wage Employer. The James Hutton Institute is Happy to Talk Flexible Working.