Interested individuals must follow the "how to apply" link on the Geosciences E4 Doctoral Training Partnership web page: http://www.ed.ac.uk/e4-dtp/how-to-apply
Summary
The grass awn is a thin structure at the tip of floral organs. What controls awn development and how it influences the grain is not clear. Using cutting-edge techniques, you will answer this in barley.
Project background
Grasses are incredibly environmentally and economically important, growing in diverse environments across the globe and providing >50% of global calories. Understanding their development is therefore key to understanding the world around us, and for food security.
A characteristic feature of many grasses is the awn. The awn is a long, thin extension that forms at the tip of outer floral organs. It is awns that give the barley ear it’s characteristic “hairy” appearance. Although the presence of an awn influences grain yield in cereal crops depending on the environment, we do not understand how the awn is specified and we do not understand how it influences grain development, beyond providing photosynthate. In particular we do not understand how awns influence the microenvironment around the developing grain, which can impact grain quality and pathogen susceptibility, and how this function is affected by changes in the environment. Using barley, this project will tackle these key questions.
The project is split into two components. First, to assess the role of the awn in grain development you will analyse grain traits and the microenvironment formed around the maturing ear when plants are grown close together. This will involve the integration of diverse datasets including time-course infra-red imaging, shape analysis, and humidity and air flow testing. By analysing different awn mutants (e.g. awnless, multiple awns, smooth awns) in different controlled environments you will be able to assess how awn morphology affects the grain and how it affects the microenvironment in which the grain matures, potentially impacting grain quality. Second, to reveal new components of the genetic mechanism underpinning awn development, you will characterise and clone the gene responsible for a classic awn mutant using 3D imaging and next generation sequencing. Using these diverse approaches you will shed light on the regulation of awn development, and the awn’s role in regulating barley grain quality.
Research questions
- How does the awn influence the grain microenvironment in barley?
- Do different awn morphologies affect the stability of the grain microenvironment?
- How does awn morphology affect barley grain traits in different environments?
- What genes underpin awn development in barley?
Methodology
Year 1: Using wild-type barley you will establish a screen to monitor the effect of the awn on the microenvironment around the developing grain when plants are grown close together similar to field conditions (referred to as the canopy here). This will include measuring features such as air flow, temperature and humidity over time. To do this you will set up an automated imaging system using raspberry Pi, normal and infrared cameras and other sensors to monitor the environment over time, alongside characterising airflow through the canopy using a wind tunnel and high-resolution filming. You will also use 3D imaging to establish a developmental series for one of the awn mutants, and collect tissue for whole-genome sequencing (WGS) and an RNAseq experiment to clone this mutant.
Outcomes: You will establish a pipeline to assess barley canopy microenvironment features under controlled environment conditions over time. You will also collect next-generation sequencing data to clone a classic awn mutant.
Year 2: Using the monitoring pipeline you developed in Year 1, you will analyse the effect of different barley awn mutants (e.g. smooth awn, barbed awn, multiple awns, awnless), which are all in the same genetic background, on the canopy microenvironment. You will harvest the seed from each experiment and assess grain traits (e.g. grain shape, size, moisture content, germination rate) to identify the effect of awn morphology on the grain. To clone the selected awn mutant you will analyse the RNAseq and WGS data to select candidate genes, and use spatial gene expression analyses (e.g. in situ hybridisation) to confirm expression patterns.
Outcomes: You will discover how awn morphology affects the canopy environment in barley. You will identify how awn morphology affects grain traits. You will build a shortlist of candidate genes for your awn mutant of choice.
Year 3: You will investigate how stable the canopy microenvironment is in the different awn mutants when challenged with changes in the growing environment (e.g. high humidity, high temperature). You will harvest the seed from each experiment and assess grain traits to see if the different mutants are able to influence the effect of changing the growing environment on grain development. Using PCR and gene expression analyses you will confirm the candidate gene for your mutant of choice using available second alleles.
Outcomes: You will establish if awn morphology is able to mitigate the effect of different extreme growing environments on the grain and link this to their possible effects on the canopy environment. You will also confirm the causal gene underlying a classic barley awn mutant, identifying a new genetic component controlling the development of the barley awn.
Training
A comprehensive training programme will be provided comprising both specialist scientific training and generic transferable and professional skills.
You will learn specific skills in experimental design, data analyses, image analysis, crop genetics, bioinformatics and molecular biology, alongside scientific presentation and writing. This training will be provided through hands-on experience in the lab, attending training courses through the University of Edinburgh Institute of Academic Development and through attending scientific conferences and workshops.
Requirements
We are looking for an enthusiastic and self-motivated student with a passion for understanding plant growth and development, and how a plant interacts with its environment. The successful student will be keen to learn diverse techniques to address scientific questions, with a background in biology or computational image analysis. The lab is a friendly and supportive environment and we welcome applicants from all backgrounds.
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