Current projects

Awarded BARIToNE 2023 studentship

Producing more with less: adapting high-yielding barley varieties to low-input agriculture

Student: James Grieves

Principal Industrial Supervisor: Prof. Katherine Smart, Diageo, UK

Principal Academic Supervisors: Dr Tracy Valentine, The James Hutton Institute, UK

Additional Supervisors: Dr Matthew Crow, Diageo, UK, Prof. Adrian Newton, The James Hutton Institute, UK, Dr. Davide Bulgarelli, University of Dundee, UK

Agriculture is under enormous pressure to increase crop yield and quality for food, feed and other products, while reducing its’ carbon footprint. The James Hutton Institute and University of Dundee offer a 4-year fully funded PhD studentship to determine barley traits adapted to sustainable crop production. This research project will be conducted in partnership with Diageo and will offer the opportunity to undertake an extra industrially relevant qualification, alongside valuable industrial experience during a hosted placement within a Technical Division of Diageo. Barley is a critical crop for the brewing and distilling industry where Diageo is a leading player in the food & drinks sector. Barley is also an important component of animal feed.  

While high-yielding varieties selected to maximise their responses to non-renewable inputs, intense soil management and monoculture have guaranteed profitable yields over the past 60 years, it is now clear that their environmental impact will be unsustainable in 21st century agriculture. Conceptually novel varieties, tailored to the so called low-carbon agronomy are therefore needed to ensure global food security. Chief in achieving this ambitious objective will be identifying genetically determined traits, underpinning barley’s adaptation to the soil environment. We hypothesis that root traits (e.g. architecture, hairs & exudates) are associated with adaptation to low carbon systems (e.g.no-tillage) and plants’ responses are integrally linked in a feedback loop to soil characteristics (e.g. microbiota) and soil resources  (e.g. nitrogen, soil carbon)

Research will start with literature reviews (incl. meta-analysis), to extract barley genotypes and germplasm with differential responses to tillage in different soils, potential root traits of interest, soil impacts (inc. soil history, environment/climate etc.), and methodologies for rapid screens (Obj1).  Rapid variety screens will calibrate traits against key soil physical and health traits (e.g. structure, sand/loam composition, nutrient levels) using traditional and imaging technologies (Obj2). These will be followed by plot field trials under differential tillage conditions (Obj3). While, this project will focus on plant traits, soil health characteristics and soil structure will be investigated (e.g. via the Soil Health Card system, water, soil strength & structure, C & N ).  Genetic indicators of traits and effects on soil microbiome will be achieved through comparative genomics, metagenomic and transcriptomics profiles of adapted lines and rhizosphere where appropriate (Obj4).  

The outcome will be identification of barley traits associated with soil tillage adaptation and their impact on productivity and soil health under low carbon production agronomy which will be valuable for barley breeding and agronomic advice.

Barley growing systems towards the net zero economy

Student: Sophie Blenkinsopp

Principal Industrial Supervisor: Dr Richard Allan, Chivas Brothers Ltd, Paisley

Principal Academic Supervisors: Dr Steve Hoad, SRUC, Edinburgh

Additional Supervisors: Dr Tim George, The James Hutton Institute, Dundee; Prof. Bob Rees and Dr Rachael Ramsey, SRUC, Edinburgh

This project will be based at the SRUC, Edinburgh and the appointed student will register at University of Dundee as the degree awarding institution.

This four-year PhD studentship is fully funded by the BARIToNE Collaborative Training Partnership and offered (from Oct. 2023) by University of Dundee, Chivas Brothers Ltd, SRUC, and the James Hutton Institute.

Progression to the net zero carbon economy is a major driver across all UK industry sectors. In the barley supply chain – from crop breeding, farming and processing – stakeholders are seeking sector-wide reduction in carbon footprints whilst maintaining barley productivity and product quality. Taking the example of malt whisky production, emissions from barley growing account for almost 40% of the sector’s total carbon release. Whilst processes of malting and distilling, and brewing, have potential to reduce carbon emissions through renewable energy sources, barley growing systems may require several different strategies involving soil management, fertilizer use and agronomy in-order to become more efficient and carbon neutral. The aim of this project is to re-design barley growing systems to support the whole barley supply chain’s transition to the net zero economy.

Working with field experiments under a range of different weather and soil conditions, spring barley growing systems will be dissected as contributions from the genotype (G), environment (E) and management (M) to overall production efficiency and reducing the crop’s carbon footprint. Crop and soil measures based on carbon and nitrogen flow will be coupled with the ‘Agrecalc’ carbon accounting tool to allow the study to quantify G x E x M effects, including a crop’s agronomic value and potential for new management such as reduced or novel fertilizer use. This detailed analysis of the growing system will be linked to the wider barley supply chain through case studies hosted by two BARIToNE commercial partners – Chivas Bothers and Opportunity NE. The Glenlivet Estate case study hosted by Chivas Brothers along with analysis of grain supply and farm demonstration through Opportunity NE will frame outputs from the project. Throughout the research programme, the student will have opportunity to engage with a broader programme of strategic research at SRUC and JHI in agronomy, crop improvement and carbon accounting.

This project which connects farming with crop improvement and grain processing will support BARIToNE’s strategic aim to safeguard the production of local and sustainable high-quality barley. Expected outputs for barley growing systems towards the net zero economy will include guidance to farmers, connectivity in carbon accounting between grain production and end usage, and new crop growing protocols to connect barley growing to plant breeding and variety testing.

Expanding the range of barley gene editing tools

Student: Shanzay Qamar

Principal Industrial Supervisor: Dr Nicholas Pitts, Scotch Whisky Research Institute (SWRI), Edinburgh

Principal Academic Supervisors: Dr Craig Simpson, The James Hutton Institute, Dundee

Additional Supervisors: Dr Laurence Ducreux, the James Hutton Institute, Dundee;  Dr Piers Hemsley, the James Hutton Institute, Dundee; Dr Pete Hedley, the James Hutton Institute.

This project will be based at the James Hutton Institute, Invergowrie and the appointed student will register at University of Dundee as the degree awarding institution.

This four-year PhD studentship is fully funded by the BARIToNE Collaborative Training Partnership and offered (from Oct. 2023) by University of Dundee, SWRI, and the James Hutton Institute.

Do you want to become expert in plant gene editing (GE) and develop the newest range of climate ready crops? GE or precision breeding is a remarkable new tool that is fundamentally different from established conventional breeding and GM methods. Gene-editing edits the target gene directly and precisely within the genome of an elite crop line with no additional genetic material and no increase in gene number. A better understanding of gene editing tools is vitally important to support production of cereal yield, with fewer inputs in the face of a changing climate. This is a 4-year studentship that will allow you to explore and develop cutting-edge GE methods with the opportunity to adapt and develop your own methods of creating new edited changes. Changes will be made in barley that is relevant worldwide to food and drink security. GE is usually used to induce a gene mutation that knocks out the function of the targeted gene with the associated crop benefit. The aim of your studentship will be to select important gene targets, develop different GE methods and develop different methods of delivering the GE machinery to the plant cell allowing for the potential of GE to be fully realised. We have established genomic and transcriptomic datasets that will help select important gene targets. A strong background in molecular biology will help but we have people and facilities at the James Hutton Institute in Dundee that will allow you to develop your skills and identify new novel gene targets.

The effect of the barley pathogen ramularia collo-cygni on the quality of malt and the potential to control the disease through host resistance

Student: Pippa Wan

Principal Industrial Supervisor: Dr Frances Jack, Scotch Whisky Research Institute (SWRI), Edinburgh

Principal Academic Supervisors: Dr Joanne Russell, The James Hutton Institute, Dundee

Additional Supervisors: Dr Neil Havis, SRUC, Edinburgh

This project will be based at the James Hutton Institute, Invergowrie and the appointed student will register at University of Dundee as the degree awarding institution.

This four-year PhD studentship is fully funded by the BARIToNE Collaborative Training Partnership and offered (from Oct. 2023) by University of Dundee, SWRI, and the James Hutton Institute.

Across the cereals sector, there is much interest in grain health and the presence of seed borne pathogens, especially in barley for malting. One of the major economic barley diseases in Scotland is Ramularia leaf spot (RLS), caused by the dothidiomycete fungus, Ramularia collo-cygni . This fungus has been shown to reduce grain yield and quality. It also has a seed borne stage in its life cycle. This BARIToNE PhD project builds on previous research by investigating (1) the effect of R. collo-cygni presence in harvested grain on malting and sprit (2) utilising previous genome wide analysis, which identified candidate gene regions associated with field resistance, we will genetically dissect this region using multi-parent populations developed from landraces and an elite cultivar (3) the potential for these crosses to display increased resistance to the pathogen will be validated in controlled condition and field experiments. The project relates strongly to the reduced input theme as RLS control relies on fungicide sprays just before head emergence. To address these three objectives, the project will combine biochemistry, genetics, genomics and field phenotyping in the following experimental approaches:

Biochemical approaches. Micromalting of infected samples to determine malt quality (predicted spirit yield), diastatic power and wort viscosity in grain samples with varying levels of Rcc (including some lines with enhanced tolerance/resistance) . Then alcohol yield, congener profile and flavour profile of spirit produced from that malt. This will provide robust evidence on the impact of the fungus on product quality and also the impact of breeding for resistance on grain quality.

Genetics and genomic approaches. A recent genome wide association analysis has highlighted candidate genes on the barley chromosomes which are associated with disease resistance in field experiments. An analysis will be conducted on a wider panel of genotypes including landrace accessions from a legacy collection, to identify genotypes which carry the candidate genes and develop novel germplasm for validation in controlled and field studies.

Field disease phenotyping and validation approaches. i) Testing predicted resistance. The levels of resistance in the panel of genotypes analysed in part 2 will be tested in controlled conditions and field experiments to determine levels of resistance to symptom expression. ii) Resistant and susceptible lines will be tested for levels of apoplastic leakage and cuticle thickness to determine their potential influence on disease levels.

Throughout the research programme, the student will have opportunity to engage with broader strategic research on crop health and improvement.

Unlocking the potential of the soils for carbon farming to meet net zero through real time ghg predictions

Student: Happison Chakova

Principal Industrial Supervisor: Dr Ronald Daalmans, Chivas Brothers Ltd, Paisley

Principal Academic Supervisors: Dr Jagadeesh Yeluripati, The James Hutton Institute, Aberdeen

Additional Supervisors: Dr Frances Sandison, The James Hutton Institute, Aberdeen

This project will be based at the James Hutton Institute, Aberdeen and the appointed student will register at University of Dundee as the degree awarding institution.

This four-year PhD studentship is fully funded by the BARIToNE Collaborative Training Partnership and offered (from Oct. 2023) by University of Dundee, Chivas Brothers Ltd, and the James Hutton Institute.

In November 2018, the Committee on Climate Change reported that ‘fundamental reform is required to ensure that land becomes a more effective carbon store’ (CCC, 2018), and suggested land use policy must promote radically different uses of UK land to support deeper emissions reductions. Existing carbon trading or payment mechanisms have highlighted the enormous potential for economic levers to deliver Net Zero. Progress made in GHG mitigation and carbon sequestration in agriculture and land use sector is very slow and faces challenges technically due to lack of scalable alternate processes and economically lack of viable customised business models suited for local conditions.

Robust knowledge and tools are needed for policymakers and farmers to ensure future sustainable management of soils, and production of agricultural commodities to meet Net Zero goals. There is a need for credible and reliable measurement, monitoring, reporting and verification (MRV) platforms, for national reporting, emissions trading and to track progress towards Net Zero, as well as transparency and understanding of GHG emissions along the entirety of product supply chains.

The PhD student is expected to upscale technology developed in RETINA project by dealing with various stakeholders ranging from farmers to private and public sector stakeholders. The student is expected to undertake a case study on the Whisky supply chain, to create carbon footprint models to identify hotspots, potential improvements and viable business models for carbon farming and trading. This PhD will characterize the elements of successful business models, identify market failures, and outline a range of challenges to be overcome to build a commercial case for the private sector for viable carbon trading. The student will build on existing strengths within Hutton developed with recent success (~£2 million investment). This includes the NERC-RETINA project, which developed a functional digital MVR prototype by combining information from field-based sensors, remote sensing, smartphone apps and integration of models to confirm management practice effectiveness on soil carbon and GHG reductions, and the EU-SENSE project.

The project provides excellent opportunities for training in multi-disciplinary skills and techniques spanning agroecology, biogeochemical modelling, statistical analysis, training in High performance computing and knowledge translation that will be highly attractive to future employers. The project will suit candidates with an agriculture/agroecology background interested in working with stakeholders to solve sustainability challenges facing the barley industry. Placements at Chivas Brothers will provide invaluable insights into the practicalities of processing grain for malt and spirits, and an important link to barley growers supplying the whisky industry.

Barley malting – a steep learning curve

Student: Christabel Smith

Principal Industrial Supervisor: Dr Jeremy Derory, Limagrain, UK

Principal Academic Supervisor: Prof David Cook, University of Nottingham, UK

Additional Supervisors: Dr Luke Ramsay, The James Hutton Institute, Dundee

This project will be based at the University of Nottingham and the appointed student will register at University of Nottingham as the degree awarding institution.

This four-year PhD studentship is fully funded by the BARIToNE Collaborative Training Partnership and offered (from Oct. 2023) by University of Nottingham, Limagrain and the James Hutton Institute.

Malting is one of the oldest biotechnologies, but urgently requires innovative approaches to reduce energy and water consumption to deliver long-term sustainability. Steeping is the first step in the malting process and is where the barley grains are submersed in water to increase the moisture content of grains homogeneously and trigger germination. Steeping also acts to clean the grain and remove germination inhibitors. Steeping normally entails using successive wet (under water) and dry stands (‘air rests’), which ensure the grain does not ‘drown’ from continuous immersion, improves germinative vigour and the rate of water uptake overall. Two or three wet steep cycles are commonly employed, which contribute significantly to the maltings water usage (typically 2.5-6 m3/tonne). Each steep utilises around 0.8 m3/tonne (conical bottomed or Eco-steep vessels) or 1.3 m3/tonne (flat bottomed vessels). Thus, the industry is looking towards technologies, raw materials and processes which enable more water efficient steep processes using fewer steeps. Examples of this include the use of ‘pre-steep’ processes in washing screws (0.3 m3/tonne) followed by one ‘main’ steep, or the recently developed ‘Optisteep’ technology. The latter continuously circulates steep water through a 2-stage water purification and oxidation process which enables a faster and continuous 1-wet steep.

We hypothesise that malting barley varieties will react differently under these novel conditions as plant breeders will not have been selecting lines to meet these new criteria. The aim of this project is to identify the best performing lines in these new steeping regimes and to identify genetic markers that can differentiate good and bad performing lines. To achieve this goal, the project will use a diversity panel, comprising mainly spring barley lines, to identify these key loci using genome-wide association studies. The final panel will comprise both old and new varieties and will be selected from a larger set of material that has been assessed for its germination index following steeping. The screen will allow for an investigation of the physiological and genetic characteristics that enable barley lines to germinate homogeneously under these differing water regimes and whether the result of these selection pressures would have positive or negative effects on agronomic performance. The project will be able to investigate whether known QTL for germinative energy, identified in the IMPROMALT project, explain some of the genetic variation or that novel loci are important for this new malting environment.

Barley starch structure and quality for brewing: impacts of genotype, environment and crop management

Student: Nigel Muchiwanga

Principal Industrial Supervisor: Ms Tanya Henderson, AB InBEV, USA

Principal Academic Supervisor: Prof David Cook, University of Nottingham, UK

Additional Supervisors: Dr Guillermina Mendiondo, University of Nottingham, UK

This project will be based at the University of Nottingham and the appointed student will register at University of Nottingham as the degree awarding institution.

This four-year PhD studentship is fully funded by the BARIToNE Collaborative Training Partnership and offered (from Oct. 2023) by University of Nottingham and AB InBev.

Key malt processing quality parameters, like the starch gelatinization temperature, vary with barley variety and harvest year. More knowledge is required regarding the relative significance of genotype, environment and crop management practices in determining starch properties. This project will be conducted in partnership with AB InBev, the world’s largest brewing company, who manufacture one in four of all beers consumed worldwide. There will be an opportunity to gain valuable industry experience during a placement within a Technical Division of AB InBev.

In Year 1, several lines will be grown across two distinct sites to generate samples for initial characterization, training in the required techniques and to provide an initial snapshot of the significance of genotype. In subsequent years selected varieties will be grown in multiple sites both within the UK and globally under controlled conditions selected to evaluate the separate impacts of environment and crop management practices.

Barley samples will be micromalted and characterized for significant parameters related to starch breakdown during mashing, including: nitrogen content, a- and b-amylase activities, starch content, amylose to amylopectin ratio. Thermal properties of the starches will be determined using Differential Scanning Calorimetry (DSC) and Rapid Visco Analysis (RVA). Malts will be mashed using industry standard protocols and the resulting wort extract and fermentable sugars spectrum determined. Statistical analyses will determine the relative impacts of genotype, site and management practices on starch properties and function. Desirable traits and practices linked to best performance in brewing will be identified.

Machine learning based image analysis for phenotyping to speed up barley breeding

Student: Milos Micik

Principal Industrial Supervisor: Dr Jonathan Snape, James Hutton Ltd, Dundee

Principal Academic Supervisor: Dr Runxuan Zhang, The James Hutton Institute, Dundee

Additional Supervisors: Dr Sarah McKim, the James Hutton Institute, Dundee; Prof Ping Lin, University of Dundee, Dundee

This project will be based at the James Hutton Institute, Invergowrie and the appointed student will register at University of Dundee as the degree awarding institution.

This four-year PhD studentship is fully funded by the BARIToNE Collaborative Training Partnership and offered (from Oct. 2023) by University of Dundee, James Hutton Ltd, and the James Hutton Institute.

Automated image-based plant phenotyping allows high throughput quantification of plant traits by analysing images captured by sensors and cameras in controlled environments or in the fields at any defined time interval. Visible light, fluorescent, near infrared, infrared and hyperspectral image can be captured from different viewing angles allowing the construction of 2D and 3D model of plants and their components, e.g. leaves, stems, flowers and spikes etc. Morphological and structure information about the plant, such as plant height and volumetric biomass, as well as physiological changes, such as temperature, water content, as well as the stress levels of leaves thus could be inferred, allowing non-destructive plant phenotyping in a high-throughput manner. Combined with experiments studying biotic and abiotic stresses, these images taken at multiple time points and conditions will illustrate the dynamic changes of the traits providing valuable information, such as the plant growth rate, stem elongation speed and trajectories of leave angle etc, thus providing key data for finding solutions for adaptation to climate change (e.g. drought, waterlogging, pathogen) and reduce the input for agriculture (e.g. fertilizers and pesticides).

Supervised deep learning networks and segmentation algorithms, developed in Prof Lin’s lab, have been successfully applied in dentistry to segment dental scan images, identify tooth types, and measure surgical outcomes using 3D models. We aim to leverage methods, tools, and expertise in Lin’s lab to, in the controlled environment, e.g. using the image station at APGC, construct accurate 2D and 3D models for single or a small number of plants using images taken from multiple viewing angles.

Using these models, develop machine learning based automatic systems that allows the detection of different components of the plants, such as leaf, stem, flower, seeds, etc and provide accurate measurements for a list of comprehensive plant traits such as plant height, leaf size, canopy size and maturation time and derived measures such as seed weights, etc. Using the drone images and images captured by new robot from JHL, we will improve the algorithms developed for “real life” field condition, field conditions.

Initially the technology will be developed using barley plants as a model, but the algorithm would be generally applicable to other plants. The proposed system will allow more accurate phenotyping with increased resolution and significantly reduced labour costs. This technology will greatly accelerate and enhance breeding of improved crops with beneficial architectural and physiological traits.

Moving to net zero barley production

Student: Kira Lutter

Principal Industrial Supervisor: Gillian MacDonald, Glenmorangie

Principal Academic Supervisors: Dr. Roy Neilson, James Hutton Institute (JHI)

Additional Supervisors: Dr. Eric Paterson, JHI & Dr. Davide Bulgarelli, University of Dundee

This project will be based at the James Hutton Institute, Invergowrie and the appointed student will registered at the University of Dundee as the degree awarding institution. This project will be based at the James Hutton Institute, Invergowrie and the appointed student will registered at the University of Dundee as the degree awarding institution.

The Climate Emergency demands that innovative and effective mitigations are urgently developed to achieve a just transition to Net Zero. There is an increasing focus on how this can be tackled in the agricultural sector, while still maintaining production for a growing global population. This project, co-developed by academic and industry partners, will explore the potential for reducing the environmental impact of barley cultivation for the whisky industry.

Whisky is the single most valuable Food and Drink product in the UK (£5.5Bn in 2020), but the barley cultivation stage contributes approximately 50% of the carbon footprint associated with each bottle produced. In large part, this is a consequence of chemical fertiliser use (both energy costs of manufacture and GHG fluxes from soil following application). Therefore, strategies to reduce use of chemical fertilisers, while maintaining sustainable grain production are urgently needed.

The use of distillery wastes for energy production (biogas) through anaerobic digestion (AD) is already an established means of off-setting carbon costs of whisky manufacture. However, AD itself generates wastes with high-nutrient content (digestates) that have potentially deleterious environmental impacts (e.g. effluent discharges affecting water quality). Therefore, the specific aim of this project is to examine the potential value of AD wastes for use as fertiliser replacements, exploiting their high-nutrient value in barley cultivation and supporting circular economy principles through diversion from waste streams. The research will involve controlled environment and field trials to assess the fertiliser equivalence of AD wastes, quantifying growth and grain quality of malting barley, relative to chemical fertilisers. It is essential that impacts of AD wastes on soil health are neutral or positive, and the project will quantify effects of their application on soil biological diversity and functions. This will include isotopic approaches to quantify carbon and nutrient cycling processes in soils (including GHG fluxes and nutrient leaching), combined with molecular characterisation of microbial /faunal communities to determine associated impacts of AD waste application. Based on results obtained, formulations (e.g., AD effluent in combination with biochar generated from solid waste fractions) will be explored to optimise barley production and to foster long-term sustainability of soil ecosystem services in malting barley production systems.

The project provides a motivated candidate with an exceptional opportunity to contribute to a highly topical research area, and to gain invaluable experience of working in both academic and industry settings, generating research-specific and transferable skills from collaboration with each partner organisation.

Awarded BARIToNE 2022 studentship

Defining the genetic basis of barley metabolite content to improve nutrient use efficiency, crop quality and resilience with reduced inputs

Student: George Epaku

Industrial Partner: SWRI

Industrial supervisor: Barry Harrison

Academic Partner: The James Hutton Institute

Academic Supervisors: Will Allwood, Kelly Houston, Tim George

Barley is a crop of great importance with respect to both spring malting barley for the renowned Scotch whisky industry, and winter barley for animal feeds. Only high-quality barley from a limited number of varieties is taken forward to malting and distilling, therefore greatly influencing market value.

Barley is regarded as a high-input cereal and therefore contributes significantly to the overall carbon footprint of whiskies and beers. Optimum nitrogen (N) levels promote the enzymatic breakdown of starch in raw grains to sugars during malting. The current solution is the addition of N fertilisers which enhance yield and assure quality. However, the energy costs of producing N fertiliser and an unbalanced N cycle in soils which produces ghg emissions in the form NOx contribute most to the unfavourable environmental footprint. Improving N recovery and utilisation will reduce the need for inputs and reduce pollution (key to the green recovery).

The aim of the PhD will be to assess and improve our understanding of the genetic and metabolic basis of high nitrogen use efficiency and photosynthetic capacity in barley, whilst producing grains with high distilling quality.

Key to barley quality is the capacity to maintain carbon assimilation and export to developing grains under a range of conditions. This requires constant metabolic adjustment in response to environmental variation. A first step towards breeding metabolically resilient barley will be to define the genetic architecture underpinning the optimisation of metabolism. A further objective is to link an understanding of metabolic resilience to key yield and quality traits.

To achieve this, barley populations will be screened for high photosynthetic rates and efficient grain import, under reduced N inputs and with alternative fertilisers (e.g. municipal compost, distillery co- products). This data will be used in a genome wide association study (GWAS) to identify Quantitative Trait Loci (QTL) and candidate genes contributing to variation in these traits under different nitrogen conditions. Additionally, the impact of these nitrogen treatments on the metabolome will be determined. Laboratory scale micro-malting, mashing, fermentation and distillation can then be used to produce spirit and assess the impact on alcohol yield and flavour profile. Understanding the genetics and physiology underpinning these traits will provide knowledge, and genetic and metabolic QTL, to aid breeding towards reduced inputs and environmental footprint.

The project offers excellent interdisciplinary training, developing skills in plant growth and phenotyping, genomics, metabolomics, flavour chemistry, and sensory analysis, as well as statistical analysis and modelling.

Understanding the genetic control of rhizosheath and its role in tolerance to abiotic stress in barley

Student: Alex Cort

Industrial Partner: Elsoms Ackermann Barley Ltd

Industrial supervisor: Miroslav Bukan

Academic Partner: The James Hutton Institute

Academic Supervisor: Tim George

With global population set to hit nine billion by 2050 and the resources needed to sustain this population diminishing, unsustainable agronomic practices and environmental change have brought us to the point where a revolution in agricultural production is necessary to ensure future agricultural sustainability. A new generation of crops adapted to environmental change is needed and the key to breeding such crops is the identification and utilisation of genetic variation in yield in marginal environments. Of the traits responsible for this yield variation, those associated with roots are perceived to have great potential.

Temperate cereals, produce rhizosheaths of soil that stick to root hairs along main root axes and their lateral branches. Rhizosheath mass depends on both genetic and soil factors and has been associated with improved phosphate and water uptake. Rhizosheath mass has the potential to provide a rapid integrative screen for root hair production and functionality, particularly useful for breeding nutrient- and water-efficient crops that perform well in reduced-input agriculture.

Previous research has revealed that root hairs (length, density, and morphology) and root and microbial exudates play a role in rhizosheath formation. In addition, we have shown that both root hair length and rhizosheath production improve resource acquisition in drought conditions. Understanding the genetic and biophysical bases of rhizosheath mass, and how these interact to influence water and nutrient uptake is now required. Rhizosheath mass has potential as a novel functional trait that can be screened rapidly to determine the genetic and physiological controls of crop tolerance to nutrient and water deficit.

The project will take advantage of considerable genomic and genetic resources with initial focus on two row spring barley association panel assembled from national and recommended list culitvars, with access to field trials that can be run across many environments in Europe.

The project aims to understand traits and genes that control rhizosheath mass. Specifically, the candidate will

1) Undertake association studies of rhizosheath traits (root hair and exudates) to validate and extend our preliminary data on genotypic variation in rhizosheath mass and identify candidate genes.

2) Determine the physiological roles of root hair traits and exudates in rhizosheath mass and how these are influenced by environmental conditions.

3) Test the association of rhizosheath mass with plant performance under nutrient-deficit and drought in both controlled environments and in the field.

4) Develop markers for the rhizosheath trait to be tested in a prebreeding and breeding environment.

Advanced sensing technology for improving nutrient management in barley

Student: Abdulazeez Tukur

Industrial Partner: Diageo

Industrial supervisor: Katharine Smart

Academic Partner: University of Dundee

Academic Supervisor: Mark Cutler

A priority for the barley sector – from production into the whole supply chain – is to become more efficient in use of agronomic resources. This includes reducing barley’s carbon footprint whilst maintaining productivity and product quality. This BARIToNE CTP project builds on previous research by coupling field-based crop nutrition studies with remote sensing at scales that are effective for efficient management of nutrients and fertilizers. The drive towards efficient crop nutrient use relates strongly to BARIToNE’s theme on reducing inputs, as well as supporting climate resilience.

The aim is to combine remote sensing with change in crop nutrient use to improve nutrient utilization and efficiency in barley. This includes managing nitrogen fertilizer more effectively in crops destined for different markets such as malting, and to make more efficient use of soil derived nutrients, including better fertilizer recovery and less waste, by frequent monitoring of crop nutrient status. The experimental hypothesis states that remotely sensed spectral responses can detect change in crop nutrient demand with sufficient precision to improve nutrient application, resulting in better nutrient capture and reduced loss or waste.

In framing field experiments, the student will identify research questions in three key areas:

(1) scope for reducing inputs, and reducing waste and loses, (2) strategies to manage nutrients and fertilizers more efficiently and (3) working towards ‘just-in-time’ management of fertilizer, with replenishment as demanded by the crop. Links to industry and wider application include: (a) developing crop management for local growing conditions and needs, (b) advice on growing barley in more challenging, and changing environments, including marginal soils and (c) scope for use of advanced technologies and nutrient studies in crop genetic improvement.

Project resources include remote sensing and crop nutrient study at multiple sites (including JHI’s Balruddery Farm and SRUC’s barley trials in East and Mid Lothian centres, as well as controlled environment facilities), expertise in hyperspectral reflectance and fluorescence data analysis, support from recent research on advanced technology for efficient crop production, and use of Agrecalc – a tool for carbon foot-printing. Throughout the research programme, the student will have opportunity to engage with a broader programme of strategic research in advanced agronomic techniques and crop resource use, including Scottish Government funded research on crop improvement and climate change.

This research project will be conducted in partnership with Diageo and will offer the opportunity to gain valuable industrial experience during a hosted placement within a Technical Division of the company, as well as undertaking an industrially relevant qualification.

Defining barley varietal traits for climate change mitigation and adaptation with emphasis on reduced inputs and variable water

Student: Paulina Aboyadana

Industrial Partner: KWS Lochow

Industrial supervisor: Klaus Oldach

Academic Partner: The James Hutton Institute

Academic Supervisor: Luke Ramsay

Climate change and society’s reaction to it will, both directly and indirectly, push agricultural production to have to function in increasingly marginal conditions. We need to utilise the crop diversity available to generate the improved crop varieties that will be adapted to these marginal conditions while at the same time mitigating climate change by reducing N inputs. Understanding the yield architecture under reduced inputs (nitrogen and water) will be key to the future breeding of such varieties and to managing both nitrogen use efficiency (NUE) and in reducing greenhouse gas emissions from agriculture. The genetic control of nitrogen uptake and utilisation will underpin the realised NUE and resilience to abiotic stress, such as variation in water availability, will be key to adaptation.

This project will quantify a range of above and below ground traits associated with climate change mitigation and adaptation, in relevant populations of barley. This study will therefore include detailed dissection of yield architecture and partition of nitrogen as well as an overview of root system architecture.

There are a number of barley populations that are available to the project, but the focus will begin on a Nested Association Mapping (NAM) population produced by KWS using 12 donor parents including barley landraces from a range of environments with a range of inherent stress. This population has been extensively genotyped and a working population of 89 lines has been selected from 352 lines. Importantly previous field trialling has already indicated that this subset includes introgressions from the landrace/older varietal parents that have a beneficial effect on yield and yield stability over a range of environments. Initial research will focus on this core set of lines and derived material.

In the preliminary experiments the candidate will subject the NAM population to a range of reduced N and variable water availability treatments (field or CE?). Data will be used to derive QTLs for tolerance to reduced N inputs, water stress and a combination of both stresses and their association with a range of developmental and morphological traits. These initial studies will guide subsequent experimentation that will include glasshouse and field phenotyping and molecular physiological studies. The PhD candidate will have the opportunity to develop the project further in the direction of genetics/genomics, plant physiology and nitrogen use and will have the opportunity to work closely with scientists and breeders in KWS, the commercial partner.

Can we develop novel phytonutrients from whisky production to produce barley sustainably in a changing climate?

Student: David Ashworth

Industrial Partner: Chivas Brothers

Industrial supervisor: Tom Mulholland

Academic Partner: The James Hutton Institute

Academic Supervisor: Kelly Houston

The Scotch Whisky industry is committed to reaching net zero by 2040 and this year the Scotch Whisky Association launched its new Sustainability Strategy (SWA, 2021). With less than two decades to significantly reduce the environmental impact, ‘end to end’ innovative solutions are required that benefit the whole supply chain. Scotch Whisky requires high yielding and good quality malting barley, of which almost 90% is grown locally in Scotland. To maintain this requires considerable inputs, which are currently costly and unsustainable. In addition, from the production side, distillery-derived by-products require efficient and sustainable disposal. One potential solution is to use these by-products to develop new phytonutrients that can be used in the primary production of the barley crop, providing a circular sustainable growth system, reducing requirements for inputs and at the same time minimising need for disposal of waste products from distilling. Historically, seaweed and other algae have been used as a nutrient supply to grow barley on farms or crofts successfully, but to scale production to generate the quantities and quality of grain required for distilling would be impractical.

We propose to examine the effects of applying these novel by-product derived nutrients on barley growth, in comparison with standard malting regime inputs, on a range of different barley cultivars which are commonly grown for malt. We will compare yield and grain characteristics, including grain nitrogen and ultimately malting quality traits. Furthermore, we will determine the effects of these nutrients on the microbiome populations of the roots and soil rhizosphere. Combining trait data gathered from initial glasshouse-controlled experiments, with genetic data generated previously, we can begin to understand the genetic control of nutrient uptake. This will allow us to identify barley cultivars that are better suited at utilising novel sources of nutrients and define potential genetic markers that can be used in downstream breeding programmes to integrate these sustainability traits. The PhD candidate will have the opportunity to exploit the long-established genetic and genomic resources available at the James Hutton Institute, gaining experience in these essential areas, along with plant & soil physiology. Importantly, they will develop skills relating to industry, specifically malting and distilling, through the close collaboration with Chivas Brothers.

Identifying novel traits and molecular markers for improved n-use efficiency in malting barley

Industrial Partner: ABInBEV

Industrial supervisor: Alex Park

Academic Partner: University of Nottingham

First Supervisor: John Foulkes

Student: Karol Kukula

Developing cultivars with high yields and malting quality whilst minimising N inputs is a key target for the production of sustainable barley crops. High N applications are uneconomic and pose a potential threat of nitrate pollution of ground water as well as emissions of GHGs due to the release of N2O. To develop N-efficient cultivars will require improved understanding of the genetic and physiological bases of both N uptake and utilization. The project will identify novel genotypes expressing high N-uptake efficiency and N-utilization efficiency, understand the mechanisms underlying the improved N efficiency and investigate the genetic bases of these traits. The plant material phenotyped will include elite UK and European malting barley cultivars and landraces in the public domain and an elite GWAS panel from the ABI breeding programme. In years 1 and 2, a panel of ten elite cultivars and landraces will be phenotyped at a field site at Nottingham University at four fertilizer N rates ranging from sub-optimal to a supra-optimal N rates. Physiological analysis will be carried out to understand how the high N-use efficiency genotypes are explained by the different physiological components of: (i) root activity, (ii) leaf/canopy photosynthetic rate and (iii) optimized N remobilization determining the stay green trait. The field studies will utilise shovelomics or electrophysiological or penetrometer methods for quantifying root traits.

Photosynthetic traits will be quantified through analysis of multi and hyperspectral reflectance indices. In addition, biomass and N uptake and dry matter and N partitioning will be quantified at critical development stages through the growing season. Malting quality of grain samples will be assessed through analysis of grain N%, germination performance, texture and micro-malting tests (alpha amylase, moisture, protein, beta glucan, DP, FAN, extract, s/t, soluble protein, turbidity, and wort color). From these data, we will understand the bases of the improved for N-efficiency for malting barley genotypes and identify target traits for improved NUE for further genetic analysis. In year 3, a Genome Wide Association Study (GWAS) study will be carried out phenotyping target traits in a field experiment on an ABI GWAS malting barley panel utilizing a 40,000 SNP array to identify mark-trait associations. The most promising Marker Trait Associations will then be used to search for candidate genes, for which molecular markers will be established for the NUE traits for deployment in the ABI malting barley breeding program.

Strategies for control of head disease and associated mycotoxin risk in spring barley production and utilisation

Student: Dylan Penlington

Industrial Partner: MAGB

Industrial supervisor: Julian South

Academic Partner: University of Dundee

First Supervisor: Edgar Huitema

Across the cereals sector, there is renewed interest in grain health and concern about presence of toxic chemicals such as mycotoxins. This concern has been widespread in barley for malting, in wheat destined for milling and feed, and in oats for milling and processing. A project on barley head diseases would attract broad cereal sector interest and would have wide application.

This BARIToNE PhD project builds on previous and ongoing research by considering how crop management and barley cultivar influence the occurrence of major barley head diseases, including blight and ergot. The project relates strongly to the climate resilience theme, but also considers reduced and more efficient inputs. Experimental approaches will combine pathology, agronomy and physiology along with chemical analytical approaches and methods in the following main strands:

1. Agronomic management. To provide gap filling in our current knowledge and include field experiments on the impact of changing agronomic systems on ergot survival and proliferation. We know that ergot infection of adjacent grass swards and margins in getting into grain samples and that previous cropping and cultivation can affect fusarium infection. This aspect will be developed within a suite of agronomic management and risk factors to identify future threats to production. This part of the study will also include novel control measures for ergot and fusarium, such as biological control of plant disease which is a growing area of interest in more integrated approaches to crop protection. In addition, the impact of environmental conditions which favour the germination of ergot sclerotia and the expression of toxin production genes will be examined.

2. Monitoring the presence of mycotoxins. To understand the presence of soil and trash borne inoculum and ergot sclerotia and their contribution to mycotoxin and alkaloid concentrations. The monitoring of the presence of mycotoxins and alkaloids will be undertaken with wider project collaboration, including methods for their minimisation through the supply chain and subsequent processing. We also consider that any changes in agronomy that control ergot must not be to the detriment of Fusarium derived mycotoxins, of which T2/HT2 are important in barley.

Throughout the research programme, the student will have opportunity to engage with broader strategic research on crop health and improvement.