Staff

The International Barley Hub is backed by decades of excellent research carried out at several academic institutions in Scotland, the UK and beyond.

Researchers associated with the International Barley Hub

Dr Will Allwood

Dr Will Allwood
Senior research scientist and mass spectrometry technologist,
Environmental and Biochemical Sciences group,
James Hutton Institute, Dundee
01382 568745
will.allwood@hutton.ac.uk

Research Interests

For over 19 years Will has made major contributions in the field of metabolomics and metabolite profiling. He is interested in the study and development of chromatography – linked – mass spectrometry (LC and GC) for a range of applications in the fields of plant-physiology, pathology and insect interactions, as well as natural product discovery. Will was a core researcher within the two teams who were first recognised for applying metabolomics approaches to the study of plant disease and insect interactions. Will has previously run and provided metabolic profiling services within the Universities of Manchester and Birmingham across many plant science, microbiological and clinical, studies.  Will is currently responsible for the LC-MS metabolomics services at James Hutton Institute – Dundee, where he serves as both an LC-MS technologist and a research scientist. Will also serves as the current deputy leader of the Plant Biochemistry and Food Quality (PBFQ) programme. Will collaborates within a large international network (e.g. Max Plank Institute for molecular plant physiology – Golm, Plant Research International – Wageningen University, and INRAe Bordeaux), he has a strong track record of producing high impact publication outputs (H index 29, i10 index 55 (09/12/21)).  Dr Allwood currently serves as the chair of the Scottish Metabolomics Network as well as being a member of the Springer Metabolomics journal editorial board.

Current Research Projects

2020-2023:  Scottish Government.  Endophyte grasses: assessing the risk to Scotland (EndoScot). Total value £117,457 (Co-I)

2020-2021: IN-U-Bar: Improving nitrogen utilisation in barley for the Scottish distilling and brewing industry. Hutton Seedcorn. Total Value £25K (Lead-I)

2016-2021. Scottish Government Strategic Research Programme, Theme 3 – Food, health and Wellbeing, WP 3.1 – Improving Food and Drink Production

2016-2020. H2020: GOODBERRY – Improving the Stability of High-Quality Traits of Berry in Different Environments and Cultivation Systems for the Benefit of European Farmers and Consumers. EU, £3.5M (Co-I)

2018-2019. Feasibility of developing a novel breeding methodology to improve berry flavour. Innovate UK, Co-I. £210.5K (Co-I)

2016-2018. Strategies to reduce waste due to greening in potato tubers. Innovate UK, £237K (Co-I)

Some Recent Publications

Allwood, J.W., Martinez-Martin, P., Xu, Y., …., Goodacre, R., Marshall, A., Stewart, D., Howarth, C. (2021). Assessing the impact of nitrogen supplementation in oats across multiple growth locations and years with targeted phenotyping and high-resolution metabolite profiling approaches, Food Chem. 355: 129585. doi.org/10.1016/j.foodchem.2021.129585

Allwood, J.W., Williams, A., Uthe, H., van Dam, N.M., Mur, L.A.J., Grant, M.R., Pétriacq, P. (2021). Unravelling Plant Responses to Stress—The Importance of Targeted and Untargeted Metabolomics. Metabolites 11(8): 558. https://doi.org/10.3390/metabo11080558

Allwood, J.W., Gibon, Y., Osorio, S., Araújo, W.L., Vallarino, J.G., Pétriacq, P., Moing, A. (2021). Chapter One – Developmental metabolomics to decipher and improve fleshy fruit quality. In Advances in Botanical Research, vol 98: 3-34. Editors: Pétriacq, P., Bouchereau, A.  https://doi.org/10.1016/bs.abr.2020.09.016

Moing, A., Allwood, J.W., Aharoni, A., …., Hall, R.D.; Schaffer, A.A. (2020). Comparative Metabolomics and Molecular Phylogenetics of Melon (Cucumis melo, Cucurbitaceae) Biodiversity. Metabolites 10: 121. https://doi.org/10.3390/metabo10030121

Matos, S.M.*, Anastacio, J.D.*, Allwood, J.W.*, …., Stewart, D., Nunes dos Santos, C. (2020). Assessing the intestinal permeability and anti-inflammatory potential of sesquiterpene lactones from chicory, Nutrients 12: 3547. https://doi.org/10.3390/nu12113547

Okamoto, H., Ducreux, L.J.M., Allwood, J.W., Hedley, P., Gururajan, V., Wright, A., Terry, J.M. Taylor, M.A. (2020). Light regulation of chlorophyll and glycoalkaloid biosynthesis during tuber greening of potato S. tuberosum. Frontiers in Plant Science 11: 753. https://doi.org/10.3389/fpls.2020.00753

Mori, K., Beauvoit, B., Biais, B., Chabane, M., Allwood, J.W., Deborde, C., Maucourt, M., Goodacre, R., Cabasson, C., Moing, A., Rolin, D., Gibon, Y. (2019). Central metabolism is tuned to the availability of oxygen in developing melon fruit. Frontiers in Plant Science 10: 594. https://doi.org/10.3389/fpls.2019.00594

Allwood, J.W., Xu, Y., Martinez-Martin, P., Palau, R., Cowan, A., Goodacre, R., Marshall, A., Stewart, D., Howarth, C. (2019). Rapid UHPLC-MS metabolite profiling and phenotypic assays reveal genotypic impacts of nitrogen supplementation in oats. Metabolomics 15: 42. Special collection: Feeding a healthier world: metabolomics for food and nutrition. Editors: Allwood, J.W., Hall, R., Fitzgerald, M. https://doi.org/10.1007/s11306-019-1501-x

Allwood, J.W., Woznicki, T., Xu, Y., Foito, A., Aaby, K., Sungurtas, J., Freitag, S., Goodacre, R., Stewart, D., Remberg, S.F., Heide, O.M., Sønsteby, A. (2019). Application of HPLC-PDA-MS metabolite profiling to investigate the effect of growth temperature and day length on blackcurrant fruit. Metabolomics 15: 12. Special collection: Feeding a healthier world: metabolomics for food and nutrition. Editors: Allwood, J.W., Hall, R., Fitzgerald, M. https:/doi.org/10.1007/s11306-018-1462-5

Kallscheuer, N., Menezes, R., Foito, A., da Silva, M.H., Braga, A., Dekker, W., Méndez Sevillano, D., Rosado-Ramos, R., Jardim, C., Oliveira, J., Ferreira, P., Rocha, I., Silva, A.R., Sousa, M., Allwood, J.W., Bott, M., Faria, N., Stewart, D., Ottens, M., Naesby, M., Nunes dos Santos, C., Marienhagen, J. (2019). Identification of microbial production of the raspberry phenol salidroside that is active against Huntington’s disease. Plant Phys. 179: 969-985. https://doi.org/10.1104/pp.18.01074

Jarret, D.A., Morris, J., Cullen, D.W., Gordon, S.L., Verrall, S.R., Milne, L., Hedley, P.E., Allwood, J.W., Brennan, R.M., Hancock, R.D. (2018). A transcript and metabolite atlas of blackcurrant fruit development highlights hormonal regulation and reveal the role of transcription factors. Frontiers in Plant Science 9: 1235. https://doi.org/10.3389/fpls.2018.01235

* Equal contributing authorship

For a complete list of publications see:  https://scholar.google.com/citations?user=fgW6rV8AAAAJ&hl=en

Dr Will Allwood | Environmental and Biochemical Sciences | The James Hutton Institute

Dr Martin BalcerowiczDr Martin Balcerowicz
Royal Society University Research Fellow and Independent Investigator,
The University of Dundee (from January 2022)
martin.balcerowicz@slcu.cam.ac.uk

Research Interests

Martin is a plant molecular biologist interested in how plant growth and development is affected by the environment, in particular by light and temperature. He has revealed multiple mechanisms by which these two signals are perceived and transduced at the molecular level, how they are integrated into internal signalling networks and how they shape the transcriptional and translational landscape in the model plant Arabidopsis thaliana. As a newly appointed Royal Society University Research Fellow, he will continue to investigate how high temperature affects transcriptional and translational processes in plants, but also how these molecular mechanisms can be turned into genetic tools to alter temperature responses. He will expand his research to investigate how high temperatures affect growth and yield of the UK’s staple crop barley, drawing on the extensive resources and expertise of the International Barley Hub, with the ultimate goal to render barley plants more resilient towards the challenging temperature environments brought about by climate change.

Current Research Projects

Royal Society University Research Fellowship URF\R1\211672 “Control of temperature-dependent plant development through RNA thermoswitches” (£547,125) (PI)

Publications

For a complete list of publications see

https://scholar.google.de/citations?user=hhy7-oQAAAAJ&hl=en&oi=ao

Dr Martin Balcerowicz | Sainsbury Laboratory

Dr Micha Bayer
Bioinformatics Specialist,
International Barley Hub (IBH)
micha.bayer@hutton.ac.uk

Research Interests

I am a bioinformatics specialist with a focus on second and third-generation sequence analysis and 14 years of experience in barley genomics, variomics and transcriptomics. My post was created at the start of the next-generation sequencing era and I am one of the early pioneers of applying these technologies to barley. I was part of the consortia for the barley genome projects in 2012 and 2017 and a co-author on several high-impact publications revolving around the analysis of genetic variation in barley. I was also the lead bioinformatician for the last two barley genotyping platforms, the Illumina iSelect 9k and 50k genotyping chips. I have been involved in the two barley reference transcriptome projects, leading to high-quality barley reference transcript datasets (BART1 and BART2). Other projects I have been involved in include the identification of Rhynchosporium resistance genes, candidate genes for diastatic power and diagnostic markers for epiheterodendrin (EPH).

Recent Research Projects

BBSRC European Partnership Award “The exploitation and sharing of barley resources” 2021-2025 (Co-I)

BBSRC Responsive mode “The Generation Gap – Mechanisms of maternal control on grain” 2021-2024 (Co-PI)

BBSRC Responsive mode “R-EVOLVE” 2021-2025 (subcontract)

BBSRC Responsive mode “Developing nutrient-enriched cereal grains with large embryos” 2019-2022 (named researcher)

BBSRC BBR “A Reference Transcript Dataset for improved analysis of RNA-seq data from barley” 2018-2020 (subcontract)

ERA-CAPS network “BARley yield associated Network (BARN)” 2018-2021 (subcontract)

BBSRC Responsive mode “Mechanisms underlying variation in barley hull adhesion” 2018-2021 (subcontract)

Innovate UK “EPH Elimination from Malting Barley for Scotch Whisky Production” 2017-2018 (Co-I)

TSB/BBSRC AgriTech Catalyst “Breeding Targets for Durable Resistance to Rhynchosporium  (DRRUM)” 2016-2019 (Co-I)

HGCA/AHDB “A genome wide analysis of key genes controlling diastatic power activity in UK barley” 2015-2017 (Co-I)

BBSRC Crop Improvement Research Club (CIRC) “Fungal effectors as activators of novel resistances in cereals.” 2012-2016 (Researcher Co-I)

BBSRC Responsive mode “The diversity and evolution of the gene component of barley peri-centromeric heterochromatin” 2011-2014 (named researcher)

Publications

For a complete list of publications see:

Micha Bayer (0000-0003-0041-3115) (orcid.org)

Dr Micha Bayer | Information and Computational Sciences | The James Hutton Institute

Prof Rob BrookerProfessor Rob Brooker
Head of Ecological Sciences
James Hutton Institute
rob.brooker@hutton.ac.uk
tel:  01224 395 176

Research Interests

Rob is a plant ecologist with over 25 years’ experience in ecological research. He has extensive knowledge of ecology in a wide range of environments, including arctic, montane, alpine, semi-arid and agricultural ecosystems, and currently undertakes research at sites across Scotland. His main research areas are the role of plant-plant interactions in determining species diversity, the consequences of this for ecosystem functions, and the way in which these impacts are regulated by environmental drivers such as climate and land management.

A central focus of Rob’s research has been facilitative (i.e. beneficial) plant-plant interactions, and his work has contributed to current understanding that beneficial plant-plant interactions occur, and are often important, in virtually all ecosystems containing vascular plants. Underlying all Rob’s work is a strong focus on fundamental ecological theory. Building on initial studies in arctic and alpine environments, he has continued to pursue these fundamental questions through studies based in Scottish ecosystems including Scottish agricultural landscapes. This work has given him a broad understanding of the problems of food security, the challenges of biodiversity conservation in Scotland, and the potential to further link fundamental ecological knowledge to issues of sustainable food production and biodiversity conservation.

Rob has also been heavily involved in linking ecological research to policy making. He has led substantial policy-driven research projects, including reviews of the impacts of climate change on biodiversity for both the Scottish Government and Defra. This work has benefited from his genuine interest in communicating the outcome of biodiversity research to relevant stakeholders, including in the policy arena. He is now a member of the Advisory Group to the Scottish Biodiversity Programme, and Honorary Secretary for the British Ecological Society.

Recent Research Projects

  • 2019-2023: Esmée Fairbairn Foundation. Sustainability in Education and Agriculture using Mixtures (SEAMS); Brooker, Karley, Newton, Neilson, Pakeman. Hutton value £214,849.
  • 2017-2021: EU H2020. Designing innovative plant teams for ecosystem resilience and agricultural sustainability (DIVERSIFY); Karley, Newton, Iannetta, Brooker, Pakeman, Shaw. Hutton value £588,992.
  • 2018: SG – Policy Advice with Supporting Analysis (PAWSA). Grouse moors impacts review Phase 1. Brooker, Hester, Matthews, Miller, Newey, Pakeman. Hutton value £42,503.
  • 2009-2015: Scottish Natural Heritage. Feasibility study: translocation of species in northern or montane environments. Britton, Brooker, Gimona, Lennon, Littlewood, Mitchell, Pakeman. Hutton value £80,000

Selected Publications

Schob, C., et al. (2018). “Evolution of facilitation requires diverse communities.” Nature Ecology & Evolution 2(9): 1381-1385.

Schofield, E. J., et al. (2018). “Temporal Dynamism of Resource Capture: A Missing Factor in Ecology?” Trends in Ecology & Evolution 33(4): 277-286.

Brooker, R. W., et al. (2017). “Crop presence, but not genetic diversity, impacts on the rare arable plant Valerianella rimosa.” Plant Ecology & Diversity 10(5-6): 495-507.

Brooker, R. W., et al. (2016). “Facilitation and sustainable agriculture: a mechanistic approach to reconciling crop production and conservation.” Functional Ecology 30(1): 98-107.

Brooker, R. W., et al. (2015). “Improving intercropping: a synthesis of research in agronomy, plant physiology and ecology.” New Phytologist 206(1): 107-117.

Butterfield, B. J., et al. (2013). “Alpine cushion plants inhibit the loss of phylogenetic diversity in severe environments.” Ecology Letters 16(4): 478-486.

Brooker, R. W., et al. (2008). “Facilitation in plant communities: the past, the present, and the future.” Journal of Ecology 96(1): 18-34.

Prof Rob Brooker | Ecological Sciences | The James Hutton Institute

Dr Davide Bulgarelli
Senior Lecturer (Teaching and Research), University of Dundee at the James Hutton Institute, Invergowrie
Tel: 01382 568934
https://www.lifesci.dundee.ac.uk/people/davide-bulgarelli
d.bulgarelli@dundee.ac.uk

Research Interests

Davide Bulgarelli was trained in molecular plant-microbe interactions in his native Italy prior completing a post-doctoral project at the Max Planck Institute for plant breeding research in Germany.  In 2013 Davide relocated to Scotland and established his group at the University of Dundee. Davide’s lab aims at elucidating the molecular interactions between plants and the microbial communities populating the root soil interface, the so-called rhizosphere microbiota.  Akin to the microbiota populating the digestive track of vertebrates, the rhizosphere microbiota can positively impact on to plant’s performance, for instance by enhancing mineral uptake and pathogen protection. As the plant genome is a driver for these communities, identifying plant genes shaping the microbiota will pave the way for the development of innovative crops decoupling profitable yield from non-renewable inputs in the environments. One of the research foci of Davide’s lab is indeed the identification of these genes using a multidisciplinary approach encompassing plant genetics, microbial ecology and computational biology. The experimental models in Davide’s lab are crop plants, predominantly the global cereal barley. To bridge the gap between the lab and the field, Davide’s lab is also part of the International Phytobiome Alliance, an industry-academia collaborative initiative aimed at accelerating microbiota applications for agriculture.

Current Research Projects

European Commission Horizon 2020-Innovation Action 818290 ‘CIRCLES’ (Lead: University of Bologna, Italy) 2018-2024 (€10M) (WP leader, DB awarded €754,000)

BBSRC Response Mode BB/S002871/1 ‘Rhizosphere microbiota’ 2018-2022 (£761,544) (PI)

Publications

For a complete list of publications see:

https://orcid.org/0000-0002-2020-6642

Dr Davide Bulgarelli | University of Dundee

Dr Tim GeorgeDr Tim George
Rhizosphere Scientist,
The James Hutton Institute
Dundee
03449285428
tim.george@hutton.ac.uk

Tim is a plant physiologist/soil scientist and has worked on the dynamics of nutrients in the rhizosphere of plants and variation in root traits for the last 24 years.

Understanding how plants react to and alter their external environment is key to optimising their nutrition and therefore the sustainability of agriculture and natural ecosystems. He is specifically interested in understanding the physiology of and genetic controls on plant responses to P-deficiency and drought. He has specific expertise in understanding how the external environment mitigates plant physiological and genetic responses to a lack of phosphorus in the rhizosphere. In addition, he is interested in how plants interact with the soil chemical, biological and physical environment to impact nutrient cycles. His recent research includes work on the ability of Bere barley to cope with extreme micronutrient deficiency, the role of root exuded enzymes and mycorrhizae in making organic P available and the impact of root hairs on the ability of barley to acquire soil resources.

The direction of his research is moving towards investigating the use of barley diversity for climate change mitigation and adaptation. The aim is to discover genes and traits to both optimize rhizosphere N and P cycles, promote C sequestration to soils and help adapt crops to abiotic stress associated with climate change. Understanding the rhizosphere processes involved in the N, P and C cycle and how these are affected by genotypic variation in root exudate composition will be key to managing both fertilizer use efficiency and in reducing greenhouse gas emissions from agriculture.

Current Research Projects

  1. “RADIANT: Realising dynamic value chains for underutilised crops” EU H2020 [2021-2026 €6000000]
  2. “SolACE: Solutions improving agroecosystem & crop efficiency” EU H2020 [2017-2022 €5688000]
  3. “Sensing soil processes for N bioavailability (SENSOILS)” EU ERC [2016-2021 £1700000]

Publications

For a complete list of publications see Timothy S. George (0000-0003-3231-2159) (orcid.org)

Dr Tim George | Ecological Sciences | The James Hutton Institute

Dr Maddy GilesDr Maddy Giles
Research Scientist, Ecological sciences
01382 568797
maddy.giles@hutton.ac.uk

Research Interests

Maddy is a soil microbial ecologist and biogeochemist whose research focuses on the ecology of the C and N cycles. Her interests lie in relating how changes in soil functional communities can affect nutrient cycling and the production of greenhouse gases in agricultural systems. In particular, she’s interested in using next-generation sequencing techniques to characterise the soil microbiome in order to understand how microbial community dynamics can be affected by crop selection and can impact retention of N in soils and the production of greenhouse gases.

Publications

For a complete list of publications see: https://scholar.google.com/citations?user=fXm5uSoAAAAJ&hl=en

Dr Maddy Giles | Ecological Sciences | The James Hutton Institute

Dr Wenbin Guo
Bioinformatician, Information and Computational Sciences, The James Hutton Institute.
+44 (0)344 928 5428
wenbin.guo@hutton.ac.uk

Research Interests

Wenbin is a Bioinformatician, and his work focuses on developing computational and mathematical models for high-throughput experimental data analysis. He has developed several easy-to-use tools and novel pipelines for accurate transcriptomics data analysis, including RTDBox for reference transcript data (RTD) construction with Illumina short read sequencing and high-resolution single molecule long read sequencing data, Splice Junction  Usage Score (SJUS) for RTD assembly quality evaluation, 3D RNA-seq App for differential expression and differential alternative splicing analysis, and RLowPC for co-expression regulatory network construction. These tools have been applied in a wide range of projects, such as RTD constructions and data analyses in barley (BART1, BART2 and pan transcriptome studies of 20 barley genotypes), Arabidopsis (AtRTD1, AtRTD2, and AtRTD3), rice, potato, raspberry, lettuce, pumpkin as well as animal and human disease data. The 3D RNA-seq App he developed has over 6,000 users and won the Best Innovation Award in the School of Life Sciences at the University of Dundee as it is a real game-changer that allows biologists to conquer complex RNA-seq analysis in a couple of hours. The outputs of his work have engaged various opportunities for research commercialisation, internal and external collaborations with excellent research groups.

Current Research Projects

  • BBSRC BBR BB/S020160/1 “PlantRTD” 2019-2022 (£391,401) (Leading researcher)
  • FAPESP 2019/13158-8 “Heat-induced alternative splicing in rice” 2021-2026 (R$766,868) (Co-I)
  • FAPESP 2021/00394-5 “Camara growth house for plant” 2021-2026 (U$73,276) (Co-I)
  • Serrapilheira R-2011-37880 “Rice temperature memory” 2021-2024 (R$650,000) (Co-I)

Publications

For a complete list of publications see: https://scholar.google.com/citations?user=MpSTI_QAAAAJ&hl=en

Dr Wenbin Guo | Information and Computational Sciences | The James Hutton Institute

Dr Rob HancockDr Robert Hancock FRSB
Senior Crop Physiologist/Biochemist
Cell & Molecular Sciences
Scientific Lead, Advanced Plant Growth Centre
01382 568779
rob.hancock@hutton.ac.uk

Research Interests

Robert Hancock is a senior biochemist and plant physiologist with 25 years post-qualification experience. His primary interests are concerned with the biochemical determinants and impact of biotic and abiotic stress on crop quality and how crop management and management systems can influence yield and quality. He works in soft fruits, potatoes and cereals where he has extensive industry links across the production and retail chain. His laboratory uses a range of physiological, biochemical, analytical and molecular techniques to understand the impact of stress on crop quality at a systems level. This research is supported by links with bioinformaticians working within Biomathematics and Statistics Scotland (BioSS), co-located at the James Hutton Institute.  Fundamental work is complemented by more applied aspects of research which are facilitated through close interactions with colleagues working in the area of molecular breeding as well as extensive interactions and joint research projects with industrial partners.

Current Research Projects

Innovate UK Strawberry molecular breeding 10015546 2022-2025 (£298,987) (PI)

BBSRC GCRF ZIRON Pulse BB/T008865/1 2020 – 2023 (£1M) (Co-I)

Some Recent Publications

Barrera-Gavira, J.M., Pont, S.D.A., Morris, J.A., Hedley, P.E., Stewart, D., Taylor, M.A. and Hancock, R.D. (2021) Senescent sweetening in potato (Solanum tuberosum) tubers is associated with a reduction in plastidial glucose-6-phosphate/phosphate translocator transcripts. Postharvest Biology and Technology 181, 111637.

Petridis, A., van der Kaay, J., Sungurtas, J., Verrall, S.R., McCallum, S., Graham, J. and Hancock, R.D. (2020) Photosynthetic plasticity allows blueberry (Vaccinium corymbosum L.) plants to maintain yield under conditions of high sink demand. Environmental and Experimental Botany 174, 104031.

Demirel, U., Morris, W.L., Ducreux, L.J.M., Yavuz, C., Asim, A., Tindas, I., Campbell, R., Morris, J.A., Verrall, S.R., Hedley, P.E., Gocke, Z.N.O., Caliskan, S., Aksoy, E., Caliskan, M.E., Taylor, M.A. and Hancock, R.D. (2020) Physiological, biochemical and transcriptional responses to single and combined abiotic stress in stress-tolerant and stress-sensitive potato genotypes. Frontiers in Plant Science 11, 169

Foyer, C.H., Kyndt, T. and Hancock, R.D. (2020) Vitamin C in plants: novel concepts, new perspectives and outstanding issues. Antioxidants and Redox Signaling 32, 463-485.

Jia, Y., Burbidge, C.A., Sweetman, C., Schutz, E., Soole, K., Jenkins, C., Hancock, R.D., Bruning, J.B., and Ford, C.M. (2019) An aldo-keto reductase with 2-keto-L-gulonate reductase activity functions in L-tartaric acid biosynthesis from vitamin C in Vitis vinifera. Journal of Biological Chemistry 294, 15932-15946.

Trapero-Mozos, A., Morris, W.L., Ducreux, L.J.M., McLean, K., Stephens, J., Torrance, L., Bryan, G.J., Hancock, R.D. and Taylor, M.A. (2018) Engineering heat tolerance in potato by temperature-dependent expression of a specific allele of HEAT SHOCK COGNATE 70. Plant Biotechnology Journal 16, 197-207

Correia, B., Hancock, R.D., Amaral, J., Gomez-Cadenas, A., Valledor L. and Pinto, G.C. (2018) Combined heat and drought activates protective responses in Eucalyptus globulus that are not activated when subjected to heat or drought stress alone. Frontiers in Plant Science 9, 819

Petridis, A., van der Kaay, J., Chrysanthou, E., McCallum, S., Graham, J. and Hancock, R.D. (2018) Photosynthetic limitations drive yield instability in blueberries grown in a Northern European environment. Journal of Experimental Botany 69, 3069-3080.

Karpinska, B., Zhang, K., Rasool, B., Pastok, D., Morris, J., Verrall, S.R., Hedley, P.E., Hancock, R.D. and Foyer, C.H. (2017) The redox state of the apoplast influences the acclimation of photosynthesis and leaf metabolism to changing irradiance. Plant, Cell and Environment 41, 1083-1097.

Comadira, G., Rasool, B., Karpinska, B. Márquez García, B., Morris, J., Verrall, S.R., Bayer, M., Hedley, P.E., Hancock, R.D. and Foyer, C.H. (2015) WHIRLY1 functions in the control of responses to N-deficiency but not aphid infestation in barley (Hordeum vulgare). Plant Physiology 168, 1140-1151.

Comadira, G., Rasool, B., Karpinska, B., Morris, J., Verrall, S.R., Hedley, P.E., Foyer, C.H. and Hancock, R.D. (2015) Nitrogen deficiency in barley (Hordeum vulgare) seedlings induces molecular and metabolic adjustments that trigger aphid resistance. Journal of Experimental Botany 66, 3639-3655.

For a complete list of publications see: https://orcid.org/0000-0001-5465-3814

Dr Robert Hancock | Cell and Molecular Sciences | The James Hutton Institute

Dr Pete HedleyDr Pete Hedley
Head of Core Technologies, James Hutton Institute
01382 568773
pete.hedley@hutton.ac.uk

Research Interests

Pete oversees the primary research facilities group, Core Technologies, at the James Hutton Institute. This includes the Genomics, Imaging and Biotechnology labs, each enabling and providing access for Hutton and collaborative groups to state-of-the-art sequencing, microscopy and transformation technologies. Specifically, he has extensive experience in developing and utilising high-throughput genomics resources in barley, including reference genome sequences, transcriptomics and high-throughput genotyping. Pete also works with many other research groups at the Hutton, and internationally, to help develop and exploit genomics tools in other major crop species, potato & soft fruit, their associated pathogens, and in environmental samples, including soil and rhizosphere microbiota.

In the last decade, ‘big’ sequencing data has helped drive identification of candidate genes and their variants for agronomically important traits. The Genomics facility exploits Next Generation Sequencing using Illumina platforms, a MiSeq and newly acquired NextSeq 2000, long-read sequencing is provided using Oxford Nanopore Technologies, and routine DNA extraction and Sanger sequencing services are also available. In conjunction with barley geneticists and computational biologists at the Hutton, we can generate and utilise these large genomics datasets, enabling high-throughput variant discovery and gene expression analysis, essential for prioritising gene targets.

Publications

For a complete list of publications see:  https://scholar.google.co.uk/citations?hl=en&pli=1&user=Jc_X1cQAAAAJ

Dr Pete Hedley | Cell and Molecular Sciences | The James Hutton Institute

Dr Kelly HoustonDr Kelly Houston
Barley Geneticist
The James Hutton Institute
01382 568960
kelly.houston@hutton.ac.uk

Research Interests

Kelly is a geneticist who has worked in barley genetics research since completing her PhD.  Much of her research has been on two main aspects of grain composition, the plant cell wall (including (1,3;1,4)-β- glucan, arabinoxylan and phenolic acids), and micronutrient content. She identifies and characterizes genes responsible for these traits using a powerful combination of high-density marker sets to carry out statistical genetic analysis and genetic resources (including natural germplasm, mutants and CRISPR-Cas9 gene edited lines) to learn more about how these genes ultimately influence the trait of interest. Recently, Kelly has become interested in utilizing georeferenced datasets to understand more about genetic adaptation to a range of environmental conditions and how this can be applied to facilitate the development of germplasm suitable for future predicted climates.

Current Research Projects

BBSRC Response mode Developing nutrient-enriched cereal grains with large embryos. 2019-2023 (Co-I).

ARC ‘Discovery’ Determining how the soluble dietary fibre (1,3;1,4)-β-glucan is made in cereals. 2021-2024 (PI)

RESAS Improving barley quality for malt and as a health food. 2016-2022 (PI)

Publications

For a complete list of publications see: https://scholar.google.com/citations?hl=en&user=wCiHek0AAAAJ&sortby=pubdate&view_op=list_works

Dr Kelly Houston | Cell and Molecular Sciences | The James Hutton Institute

Doctor Pietro (Pete) Iannetta
Head of Ecological Food Systems
Agroecology Group
Dept. of Ecological Sciences
07736307189
pete.iannetta@huttopn.ac.uk

Research Interests

Pete is a plant biologist and ecologist, who studies the complex interactions which determine the sustainability of food- and feed-systems, including those of the brewing, distilling and aquaculture industries. He delivers key research programmes to support the Scottish Government’s strategic research program, and by securing layered funding builds international research and development networks and programmes. Pete is also an Honorary Lecturer at the University of Dundee, and his research is strongly focused on legume-supported cropped systems, from production to consumption. This includes developing the use of underutilised crops and novel cropped systems, plus the implementation of additional innovations beyond the farm-gate that encourage greater resource use efficiency, improved ecosystem functions, and realisation of circular economies. To facilitate this, Pete develops and exploits various system-function and -accounting tools from the genetics and genomics of plant growth promoting microbes and the soil microbiome, to tools which are ‘data driven’ – such as agri-food system modelling, including Life Cycle Analysis. He works very closely with a wide range of industry and applied-science stakeholders, and provides extension services to value-chain actors, including policymakers.

Current Research Projects

EU-H2020 ‘RADIANT’, Catholic Uni. Porto leading, 2021-25, €6M, PI/Deputy-Coordinator.

EU-H2020 ‘FRAMEwork’, James Hutton Institute leading, 2021-25, €9M, Co-I.

UKRI, ‘Food and Nutrition Security-COVID19, James Hutton Institute leading, 2020-21, £342k, Co-I.

Scot. Ent., ‘SAFE’ (SustaiAble Faba bEan), W.N. Lindsay leading, 2019-21, £241k, PI.

COOP, DiverBeans, World Food System Centre (ETH Zürich) leading, 2019-21, £234k, PI.

EU-H2020 ‘TRUE’, James Hutton Institute leading, 2017-21, €5M, PI/Coordinator.

EU-H2020 DIVERSify, James Hutton Institute leading, 2017-21, €5M, Co-I.

EU-H2020 TomRes James Hutton Institute leading, 2017-21, €6M, PI.

For a complete list of publications see:  ‪Pietro P M Iannetta – ‪Google Scholar

Dr Pietro Iannetta | Ecological Sciences | The James Hutton Institute

Dr Alison Karley
Agroecologist
Ecological Sciences Department, The James Hutton Institute
01382 568820
alison.karley@hutton.ac.uk

Research Interests

As pressure mounts to reduce dependence on agri-inputs, accompanied by uncertainty about the effects of climate change on crop production, the importance of diversifying agroecosystems for future sustainability is increasingly being realised. Ali’s research tests alternative cropping practices and pest control strategies to reduce reliance on external inputs and increase resilience to environmental stress. Her recent research has shaped current concepts about, and provided supporting evidence for, the design, management and ecological benefits of diversified agricultural systems and how to select crop types that optimise system functions. As co-ordinator of DIVERSify (EU Horizon 2020: 2017-2021), she led a consortium of 25 EU and international partner organisations to understand and demonstrate the benefits of mixed species cropping and identify crop species and cultivars that perform optimally when intercropped. Ali was one of the founding members of the ‘Crop Diversification Cluster’ of six EU projects (www.cropdiversification.eu/), aiming to increase research impact through sustained uptake of diversification measures by farmers in Europe.

Ali’s research includes identifying traits that allow crops to perform optimally with reduced nutrient and pesticide inputs. This area is developed though co-innovation projects with industry partners to identify desirable crop traits and to apply new imaging tools to phenotype plant responses to biotic and abiotic stress. For crop mixtures, Ali collaborates with crop scientists and breeders to pioneer an ‘ecological approach’ for crop improvement, focusing on trait combinations that optimize the benefits of intercropping. Ali uses participatory research to trial agroecological practices with farmers and other agricultural stakeholders, and she works closely with knowledge transfer organisations to develop open science methods and tools for making results accessible to different end users.

Current Research Projects

Darwin Partnership Award ‘Malawi-AgroBio’ 2021-2022 (£10K) (PI)

Scottish Government ‘EndoScot’ 2020-2023 (£66.5K) (Co-I)

EU Horizon 2020 ‘FRAMEwork’ 2020-2025 (€1.4M) (Co-I)

AHDB ‘Soft Fruit IPM’ 2020-2022 (£444K) (Co-I)

GCRF ‘ClimateSmart’ 2020-2022 (£50K) (Co-I)

Mains of Loirston ‘NOVELLA’ 2019-2023 (£47K) (Co-I)

Esmée Fairburn Foundation ‘SEAMS’ 2019-2023 (£400K) (Co-I)

Innovate UK ‘CherryBerry’ 2018-2021 (£734K) (Co-I)

EU Horizon 2020 ‘MiRA’ 2017-2021 (€3.65M) (Co-I)

Publications

For a complete list of publications see: https://orcid.org/0000-0002-0252-2086

Dr Alison Karley | Ecological Sciences | The James Hutton Institute

Dr Sarah McKimDr Sarah McKim
Senior Lecturer and Principal Investigator, Division of Plant Sciences, University of Dundee
01382 568916
smckim@dundee.ac.uk

Research Interests

Sarah is a development biologist who for the past eight years has led a research team exploring how barley plants grow and develop. Her research has revealed the genes and mechanisms which control architectural traits important to yield, such as stem elongation, spike density, row type and grain size and shape. Her recent research investigates interactions between development and resiliency, epidermal surfaces and grain quality as well as different tissues in the grain. Sarah aims to advance our mechanistic understanding of cereal development and exploit these findings for crop improvement.

Current Research Projects

BBSRC Response Mode BB/W003074/1 ‘Generation Gap’ 2022-2025 (£613,746744,015) (PI)

BBSRC Response Mode BB/R010315/1 ‘Skinning‘ 2017-2022 (£613,746) (PI)

BBSRC Australia Partnership Award BB/V018299/1 ‘International Pooling for Advanced Cereal Science’’ (£47,765) (PI)

Scottish Funding Council’s Global Challenges Research Fund, ’Genetic networks for crop resilience’ (£68,467) (PI)

 

Some Recent Publications

Dixon LE, van Esse W, Hirsz D, Willemsen V and McKim SM* (2021) Cereal Architecture and its Manipulation. Invited Annual Plant Reviews Online. Accepted 28/10/2021

Shoesmith J, Solomon C, Yang X, Wilkinson LG, Sheldrick S, van Eijden E, Couwenberg S, Pugh L, Eskan M, Stephens J, Barakate A, Drea S, Houston K, Tucker M, McKim SM* (2021) APETALA2 functions as a temporal factor to control flower and grain development in barley. Development 148 (5): dev194894.

McKim SM (2019) Moving on up – controlling internode growth. New Phytologist 226, 672-678.

Paulo Rapazote-Flores P, Brown JWS, Zhang R, Stephen G, Schreiber M, Barakate A, Casao MC, Zwirek M, McKim SM, Kam J, Halpin C, Morris J, Hedley PE, Guo W, Fuller J, Mayer C-D, Milne L, Bayer M, Waugh R, Simpson CG (2019) BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq. BMC Genomics 20, 968 (2019)

Patil V, McDermott HI, McAllister T, Cummins M, Silva JC, Mollison E, Meikle R, Morris J, Hedley PE, Waugh R, Dockter C, Hansson M, and McKim SM (2019) APETALA2 control of barley internode elongation. Development 146: dev170373

Zwirek M, Waugh R and McKim SM (2018) Interaction between row-type genes in barley controls meristem determinacy and reveals novel routes to improved grain. New Phytologist. 221(4): 1950-1965.

McKim SM*, Koppulu R and Schnurbusch T (2018) Barley Inflorescence Architecture. Pp.171-208 in The Barley Genome, ed. Nils Stein and Gary Muehlbauer. *corresponding

Bull H, Casao MC, Zwirek M, Flavell A, Thomas W, Guo W, Zhang R, Rapazote-Flores P, Kyriakidis S, Russell J, Druka A, McKim SM* and Waugh R* (2017) Barley SIX-ROWED SPIKE3 encodes a putative Jumonji C-type H3K9me2/me3 demethylase that represses lateral spikelet fertility” Nature Comms 8: 936.*co-corresponding.

Houston K§, McKim SM§, Comadran J, Bonar N, Druka I, Uzrek N, Cirillo E, Guzy-Wobelska J, Collins N, Druka A, , Halpin C, Hansson M, Dockter C, Druka A, and Waugh R (2013) Variation in the interaction between alleles of HvAPETALA2 and microRNA172 determines the density of grains on the barley inflorescence. P.N.A.S. U.S.A. 110(41): 16675–16680. §Co-first authors

For a complete list of publications see: https://orcid.org/0000-0002-8893-9498

Dr Sarah McKim | University of Dundee

Professor Adrian C Newton
Senior Research Leader, Cereal Pathology / Agroecology, James Hutton Institute
Visiting Professor in Cereal Pathology, SRUC, Edinburgh
01382 568824
adrian.newton@hutton.ac.uk

Research Interests

Adrian is an agroecologist and barley / cereal pathologist with over 40 years of research experience. Initially his interests were in cereal pathogen populations and their response to cereal crop variety deployment. Deployment of diversity within cereal crops, referred to as cereal variety mixtures or blends, became a major interest in terms of disease control and resource use efficiency as measured by yield and quality outcomes. His recent focus has been on broader plant diversity interactions in the field from genotypes to species including intercropping, and variety/genotype interactions with soil tillage and crop sequence. Another parallel research interest has been induced resistance, whether through pathogens or application of resistance elicitors, and this now includes the induction mediated by soil microbial communities in soils differentially affected by cultivation and previous crops. These interests feed into current work in the broad area of regenerative agriculture including pasture diversity.

Current Research Projects

Scottish Government Strategic Research Programme Theme 2 – Productive and Sustainable Land Management and Rural Economies. Research objectives in IPM, Novel Crops, Sustainable Soil and Water Management, Integrated Management Systems, 2016-2022

Esmee Fairbairn: Crop Mixtures for Sustainable Agriculture, 2019-2023

Mains of Loirston Trust: Tillage-agronomy interaction in direct drill and conventional cultivation, 2019-2023

UKRI ‘Food Security during and after the Covid-19 Pandemic’, 2020-2021

Scottish Government: The Effects of Grass Seed Intentionally containing Endophytes on the Environment, 2020-2022

Mains of Loirston Trust: Novel winter legume-cereal mixtures for Scotland, 2019-2022

SSCR: ‘Cereal variety adaptation ranking changes in CSC conventional and integrated management treatments’, 2021-2022

EU 2020: SFS-2-2016 DIVERSify ‘Designing InnoVative plant teams for Ecosystem Resilience and agricultural Sustainability’, 2017-2021

EU 2020: SFS-26-2016 TRUE ‘Transition paths to sustainable legume-based systems in Europe’, 2017-2021

Publications

For a complete list of publications see:

https://scholar.google.com/citations?hl=en&user=a9TJ89AAAAAJ&view_op=list_works&sortby=pubdate or https://www.hutton.ac.uk/webfm_send/783

Prof Adrian Newton | Cell and Molecular Sciences | The James Hutton Institute

Dr Roy NeilsonDr Roy Neilson
Group Leader, Plant-Soil Interactions, The James Hutton Institute
Invergowrie, Dundee, DD2 5DA
01382 568814
roy.neilson@hutton.ac.uk

Research Interests

Roy is a soil ecologist, and his expertise lies in understanding functional interactions mediated by soil faunal groups in the context of food security and sustainable production. His research focusses on the interactions between soil fauna, plants, environment, and land management. He is a strong advocate of strengthening the evidence base to support informed decision-making, practice, and uptake of sustainable land management to minimization degradation and loss of soils, and to ensure the benefits delivered from soil are maintained. He has a significant track record of collaborating with industrial partners to deliver solutions for early adoption and deployment based on stakeholder need. Throughout his career, he has developed several tools for the benefit of the agricultural sector. including DNA diagnostics for soil-borne nematode mediated disease, and for monitoring soil health. His research interests also include developing integrated pest management (IPM) strategies to mitigate the impacts of soil-borne disease on cropping systems in the UK and the use of agricultural waste and co-products as a proxy fertiliser. The outputs of his research have included new understanding of the ecology and biology of soil fauna, especially free-living nematodes and earthworms and their functional role in soils. Roy has strong engagement with national and international policymakers and, for example, has recently led or contributed to reports providing underpinning knowledge on soil indicators and future research and innovation required to deliver resilient production ecosystems that support a just transition to net-zero emissions. He maintains productive relationships with the international soils research community, is an invited member to several national and international committees, and has published extensively in scientific and industrial domains.

Current Research Projects

EU H2020 101000339 ‘IPMWORKS’ 2021-2026 (£210.951) (Co-I)

BBSRC BPD-CT/BB/T010657/1 ‘DES-BL’ 2020-2023 (£900,062) (Co-I)

ESMEE FAIRBURN FOUNDATION ‘SEAMS’ 2019-2023 (£286,481) (Co-I)

EU NSR INTERREG ‘SOILCOM’ 2019-2023 (£271,518) (Co-I)

SCOTTISH GOVERNMENT ‘ENDOSCOT’ 2020-2022 (£100,000) (Co-I)

Publications

For a complete list of publications see:  https://scholar.google.com/citations?user=IdgGnzoAAAAJ&hl=en

Dr Roy Neilson | Ecological Sciences | The James Hutton Institute

Dr Eric PatersonDr Eric Paterson
Principal Scientist, Plant-Soil Interactions
The James Hutton Institute, Ecological Sciences
+44 (0)344 928 5428
eric.paterson@hutton.ac.uk

Research Interests

Eric has more than 25 years’ experience working on plant-soil interactions in the context of sustainable crop production systems, soil health and mitigation of environmental impacts. His group have developed novel stable isotope approaches that allow quantification of plant-mediated impacts on soil C and N cycling processes, identifying the importance of these interactions in the contexts of soil GHG exchanges and nutrient supply in semi-natural and agroecosystems. Most recently he has applied these approaches to study interactions between plant genotype, management and environment (G x M x E) in UK, European and African agricultural systems, to optimise of crop production, while fostering the sustainability of the soil resource. He is a Subject Editor for the journals Plant & Soil and Soil Biology & Biochemistry, and has more than 90 ISI listed publications (WoK h-index = 34). His research has been supported by Scottish Government, BBSRC, NERC, British Council, EU and industry. He currently co-ordinates Soils research within the Scottish Government Strategic Research Programme, is a board member of the NERC Soils Training and Research Studentships CDP (STARS) and has served as a review panel member for NERC, BBSRC and international research funders.

Current Research Projects

BBSRC GCRF Foundation Award BB/P022936/1 (2017-2021): Exploiting the potential of genotype microbiome interactions to promote sustainable soil health in southern Africa. (£532k, Hutton PI).

BBSRC GCRF Sustainable Agriculture for Sub-Saharan Africa BBR020590/1 (2018-2022): Science-driven Evaluation of Legume Choice for Transformed livelihoods (£1.8M; Hutton PI).

BBSRC GCRF BB/T012552/1 (2020-2022): Africa SOIL: Soil Organic matter Improves Livelihoods (£250k, Hutton PI).

NERC CDP NE/M009106/1 (2017-2022): Soils Training and Research Studentships (£2.3M, Co-I)

PhD project, Walsh Foundation (2018-2022) Linking microbially mediated soil organic matter turnover to N availability in agricultural soils.

PhD project, Gatsby Foundation (2018-2022) Impacts of maize-legume intercropping on rhizosphere C:N:P stoichiometry and nutrient availability.

PhD project, Joint Studentship Programme (2019-2023) The interactions of plant, microbial and physico-chemical controls on carbon and nutrient cycling in the rhizosphere.

Publications

For a complete list of publications see: Web of Science Researcher ID

Dr Eric Paterson | Ecological Sciences | The James Hutton Institute

Dr Luke RamsayDr Luke Ramsay
Barley Geneticist
James Hutton Institute
01382 568 736
luke.ramsay@hutton.ac.uk

Research Interests

My research interests are centred on the development of genetics tools and genomics resources for barley and their application to breeding.  This underpins an interest in association genetics for agronomically important traits that has involved the development of high-throughput SNP genotyping capabilities.  This work has fostered closer ties with industry in particular breeding companies with UK-based programmes.  Interactions on dissection of genetic control of economic traits and the development of pre-breeding material will form the basis of much future work as will the possibilities that an ability to influence distribution and frequency of recombination would bring to longer-term breeding goals.

Current Research Projects

BBSRC Response Mode ‘R-Evolve’ BB/V016938/1 2021-2025 (£657,162)(Co-I)

BBSRC Response Mode BB/R010315/1 ‘Skinning’ 2017-2022 (£585,468) (Co-I)

EU H2020 101000622 RADIANT ReAlising DynamIc vAlue NeTworks for underutilised crops  (Co-I)

BBSRC Response Mode BB/T002905/1 ‘Developing nutrient-enriched cereal grains with large embryos’ (Co-I)

FACCE-JPI DEFRA CH0213 ‘Barista’ 2019-2022 (£60,000) (C0-I)

Some Recent Publications

Arrieta M, Macaulay M, Colas I, Schreiber M, Shaw PD, Waugh R and Ramsay L (2021) An Induced Mutation in HvRECQL4 Increases the Overall Recombination and Restores Fertility in a Barley HvMLH3 Mutant Background. Front. Plant Sci. 12:706560. https://doi.org/10.3389/fpls.2021.706560

Sharma, R., Cockram, J., Gardner, K.A. et al. Trends of genetic changes uncovered by Env- and Eigen-GWAS in wheat and barley. Theor Appl Genet (2021). https://doi.org/10.1007/s00122-021-03991-z

Lewandowska et al The proteome of developing barley anthers during meiotic prophase I. (2021)   Journal of Experimental Botany, erab494 https://doi.org/10.1093/jxb/erab494

Barakate A, Arrieta M, Macaulay M, Vivera S, Davidson D, Stephens J, Orr J, Schreiber M, Ramsay L, Halpin C and Waugh R (2021) Downregulation of Barley Regulator of Telomere Elongation Helicase 1 Alters the Distribution of Meiotic Crossovers. Front. Plant Sci. 12:745070. https://doi.org/10.3389/fpls.2021.745070

Barakate A, Orr J, Schreiber M, Colas I, Lewandowska D, McCallum N, et al.  Time-resolved transcriptome of barley anthers and meiocytes reveals robust and largely stable gene expression changes at meiosis entry (2021) Front. Plant Sci. https://doi.org/10.3389/fpls.2020.619404

Arrieta, M; Willems, G; DePessemier, G; Colas, I; Burkholz, A, et al.  The effect of heat stress on sugar beet recombination (2021) Theoretical and Applied Genetics, 134, 81-93 https://doi.org/10.1007/s00122-020-03683-0

Looseley, M.E.; Ramsay, L.; Bull, H.; Swanston, J.S.; Shaw, P.D.; Macaulay, M.; Booth, A.; Russell, J.R.; Waugh, R.; Thomas, W.T.B. (2020) Association mapping of malting quality traits in UK spring and winter barley cultivar collections, Theoretical and Applied Genetics, 133, 2567-2582.

Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, et al. A chromosome conformation capture ordered sequence of the barley genome. Nature. 2017;544(7651):427  https://doi.org/10.1038/nature22043

For an updated list of publications see https://orcid.org/0000-0003-2209-2308

Dr Luke Ramsay | Cell and Molecular Sciences | The James Hutton Institute

Dr Mike RivingtonDr Mike Rivington
Senior Scientist
The James Hutton Institute
0344 9285428
mike.rivington@hutton.ac.uk

Research Interests

Mike is a senior scientist at the James Hutton Institute and has researched land use and climate change issues for 22 years. He studied Ecological Science (Bsc), Natural Resource Management (MSc) and a PhD at Edinburgh University. His main research interests are in understanding how climate change impacts land use and ecosystems, in Scotland and globally, and how mitigation and adaptation options can be developed. He uses a range of research approaches including: use of crop simulation models applied spatially at a high resolution to estimate barley growth under future climate conditions for the whole of Scotland; mapping agro-meteorological indicators spatially to assess risks and opportunities for land management. Particular attention is paid to understand future soil water conditions. He is an inter- and trans-disciplinary scientist, for example he is currently Principal Investigator on an ESRC funded project ‘UK food and nutrition security during and after the COVID-19 pandemic’. His other interests include ecosystem management and ecosystem services, particularly for climate change mitigation and adaptation. He has written policy briefs for UNEP on ecosystem-based adaptation, contributed to the US National Climate Assessment chapter on agriculture, and was a member of a UK-US tasks force on extreme weather and resilience of the global food system.

Current Research Projects

  • Team Leader: Scottish Government Strategic Research Programme – spatial barley modelling and mapping, simulating barley growth in arable areas of Scotland under current and future climates; mapping spatial agro-meteorological indicators, observed trends and climate change projections.
  • PI: Land Capability for Agriculture and Forestry classification systems under climate change. Developing a new digital platform to understand land capability under future climate projections.

Some Recent Publications

Rivington, M., King, R., Duckett, D., Iannetta, P., Benton, T.G., Burgess, P., Hawes, C., Wellesley, L., Polhill, J.G., Aitkenhead, M., Lozada‐Ellison, L.‐M., Begg, G., Williams, A.G., Newton, A., Lorenzo‐Arribas, A., Neilson, R., Watts, C., Harris, J., Loades, K., Stewart, D., Wardell‐Johnson, D., Gandossi, G., Udugbezi, E., Hannam, J. and Keay, C. (2021). UK food and nutrition security during and after the COVID‐19 pandemic. Nutr Bull, 46: 88-97. https://doi.org/10.1111/nbu.12485

Cammarano, D. Hawes, C. Squire, G. Holland, J. Rivington M, et al (2019) Rainfall and temperature impacts on barley (Hordeum vulgare L.) yield and malting quality in Scotland. Field Crop Research, 241, Article No. 107559

Cammarano, D., Rivington, M., Matthews, K.B., Miller, D.G. & Bellocchi, G. (2017). Implications of climate model biases and downscaling on crop model simulated climate change impacts. European Journal of Agronomy 88, 63-75.

Bailey, R … Rivington, M et al (2015) Extreme weather and resilience of the global food system. Prepared for the UK-US Taskforce on extreme weather and global food system resilience. Report to the Foreign and Commonwealth Office in conjunction with the Global Food Security Programme, May 2015.

Dr Mike Rivington | Information and Computational Sciences | The James Hutton Institute

Dr Joanne RussellDr Joanne Russell
Barley Geneticist
Cell and Molecular Sciences
James Hutton Institute
Dundee, UK
01382568857
joanne.russell@hutton.ac.uk

Research Interests

Research over the past 27 years has focused on developing genetic markers to explore and understand diversity within the extensive assembled collections of barley germplasm, including cultivars, globally distributed landraces and wild progenitors. Following technological advances our emphasis has shifted from cataloguing diversity to recognition of the genetic value of these resources for sustainable and resilient barley production. Because of these advances in genomics my focus is now on addressing more challenging aspects of diversity, such as adaptation to changing climate.

Current Research Projects

BBSRC Response Mode ‘Rapid Evolution of wild barley: R-Evolve’ 2021-2025 (£657,162) (PI)

BBSRC ERA-CAPS ‘BARley yield associated Network: BARN’ 2018-2022 (£649,658) (Co-I)

FACCE-JPI DEFRA CH0213 ‘Advanced tools for breeding Barley for intensive and sustainable agriculture under climate change scenarios: Barista’ 2019-2022 (£60,000) (Co-I)

EU H2020 ‘Ancient genetics: Capturing signatures of nutrient stress tolerance from extant landraces to unlock the production potential of marginal lands (AGENT)’ 2020-2022 (£195,552) (Co-PI)(Marie curie Fellow, Dr Sidsel Birkelund Schmidt)

BBSRC Response mode ‘Developing nutrient-enriched cereal grains with large embryos’ 2019-2023 (£87,675) (Co-PI) (Lead PI Dr Kay Trafford, NIAB)

Royal Society ‘Nutrient management, next generation sequencing technology and breeding for improving grain yield and nutritional quality in Thai local fragrant rice’ 2018-2022 (£12,000) (PI) (Mobility awarded to Dr Tonapha Pusadee, University Chiang Mai, Thailand)

EU H2020 ‘ReAlising DynamIc vAlue NeTworks for underutilised crops:RADIANT’  2021-2025 (£603,527)(Co-I)

Some Recent Publications

Cope JE, Russell J, Norton JG, George TS and Newton AC. (2020) Assessing the variation in manganese use efficiency traits in Scottish barley landrace Bere (Hordeum vulgare L.), Annals of Botany, 126: 289–300, https://doi.org/10.1093/aob/mcaa079

Bustos-Korts D, Dawson IK, Russell J. et al. (2019) Exome sequences and multi-environment field trials elucidate the genetic basis of adaptation in barley. The Plant Journal 99, 1172-1191. https://doi.org/10.1111/tpj.14414

Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, et al. (2017) A chromosome conformation capture ordered sequence of the barley genome. Nature. 2017;544(7651):427.  https://doi.org/10.1038/nature22043

Russell J, Mascher M, Dawson IK. et al. (2016) Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. Nat Genet, 48, 1024-1030. https://doi/10.1038/ng.3612. Epub 2016 Jul 18. PMID: 27428750.

For a complete list of publications see: https://scholar.google.com/citations?user=iCI4-dAAAAAJ&hl=en

Dr Joanne Russell | Cell and Molecular Sciences | The James Hutton Institute

Dr Paul ShawDr Paul D. Shaw
Senior Research Scientist Bioinformatics/Information Systems, International Barley Hub / The James Hutton Institute
01382 568864
paul.shaw@hutton.ac.uk

Research Interests

Paul focuses on software development for plant genetic resources, genetics and plant breeding. He leads several projects where his research contributes towards making experimental data including plant passport, pedigree, phenotypic and genotypic data available to collaborators, research and breeding communities using a suite of database and visualization tools that his team develops. He is particularly interested in biological visualization and how data can be effectively presented, explored and accessed in logical, digestible chunks in order to gain maximum impact and insight. He is also interested in how biological entities, such as plant accessions in pedigrees, and samples in plant breeding and genetics experiments, can be visualized and modelled using graphs.

The main software his group develops and maintains include the informatics platforms Germinate (https://germinateplatform.github.io/get-germinate) for the storage of experimental data resulting from plant germplasm collections and Helium (https://ics.hutton.ac.uk/helium) for the visualization of complex plant pedigrees. His group is also active in the development of innovative mobile applications for the efficient collection of experimental data (https://cropgeeks.github.io/gridscore) and tools to help with general informatics requirements of genotyping platforms such as the barley 50K SNP platform and maintaining Hutton’s seed store and Underpinning Capacity collections.

He maintains regular interactions with the international plant genetic resources community both through research interests, collaborations and involvement in international groups such as the International Network (https://divseekintl.org).

Current Research Projects

  • The Global Crop Diversity Trust/Norwegian Government ‘BOLD’ Biodiversity for Opportunities, Livelihoods and Development 2022-2032 (PI)
  • BBSRC International Partnering Award ‘BarleyEUNetwork’ BB/V018906/1 2021-2024 (Co-I)
  • EU Horizon 2020 ‘BreedingValue’ ID:101000747” 2021-2025 (Co-I)
  • Templeton World Charity Foundation/Global Crop Diversity Trust ‘Safeguarding crop diversity for food security: Pre-breeding complemented with Innovative Finance’ ID TWCF0400 2019-2022 (PI)
  • INNOVATE UK ‘CherryBerry’ ID:104624 2019-2021 (Co-I)
  • Global Crop Diversity Trust/Norwegian Government ‘Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives’ GS17010 2017-2021 (PI)

Publications

For a complete list of publications see: https://scholar.google.com/citations?user=kwK7rKsAAAAJ

https://orcid.org/0000-0002-0202-1150

Dr Paul Shaw | Information and Computational Sciences | The James Hutton Institute

Dr Craig SimpsonDr Craig Simpson
Senior Research Scientist
Director of The James Hutton Institute Postgraduate School
+44 1382 568774
craig.simpson@hutton.ac.uk
ORCID: 0000-0002-1723-1492

Research Interests

Craig’s research focus is transcriptional and post-transcriptional processes that regulate plant development and environmental response pathways in crop and model plants. He established the first high-resolution method that monitors dynamic transcriptional diversity in hundreds of genes. This was used to determine alternative splicing responses in a range of plant tissues, experimental conditions and Arabidopsis mutants, which led to multiple collaborations and high impact publications. Craig is now utilising RNA-seq methods to identify the range of genes and gene transcripts that respond to different abiotic and biotic stresses. To achieve this he has established, with colleagues, reference transcript datasets for barley and raspberry that allow fast and accurate quantification of expressed gene transcripts. This allows him to identify differentially expressed genes that respond significantly to developmental and environmental changes. Gene expression values were used to produce a high-quality Barley Expression Database (EORNA) that holds multiple gene and transcript abundance values for many different RNA-seq experiments. The gene transcript expression values were used to create a visualisation tool that displays comparative gene and transcript abundance data on demand across all samples and all the genes. Craig’s experience in transcriptomics has been used successfully to develop several genetic and transcriptomic data resources for raspberry.

Current Research Projects

Transcriptional dynamics that underlie adaptive processes of barley.

Development of a pan-transcriptome.

EoRNA2, community access to barley RNA-seq data.

RSE Joint Projects. Regulation of transcript switching in response to temperature changes in barley and rice. 2022-2023 (£11,440) (Lead)

Innovate UK – 48163. Raspberry Auxin Soil/Substrate Protectant (RASP). 2020-2022 (£227,512) (Co-I).

Publications

For a complete list of publications see: https://orcid.org/0000-0002-1723-1492

Dr Craig Simpson | Cell and Molecular Sciences | The James Hutton Institute

Dr Tracy ValentineDr Tracy Valentine
Root Biologist, Ecological Sciences, James Hutton Institute
+44 (0)344 928 5428
tracy.valentine@hutton.ac.uk

Research Interests

Tracy works at the interface between plant roots and soil (biological and physical). She explores the impact of variation in plants and soil on this relationship and the impact on plant performance via applied and underpinning research.   Latterly this has particularly involved developing methods for understanding the impact of soil management (including in agricultural rotations) on soil structure and the impact on root development, and crop performance.  This is set in the context of the variability of baseline and responses of root traits due to genetic variation and how this impacts on the root:soil relationship, and downstream ecosystem function.
Her research is based on an understanding of the effects of genetic variation, and plant responses to biological (e.g. disease)  and physical constraints (e.g. Tillage/Compaction) in ex-situ and agricultural systems. She has developing methods (including image analysis) for exploring plant root trait responses at the scale of root tips and seedlings, through to measurement of responses of mature plants including cereals to different nutrient and physical conditions.

Current Research Projects

AHDB (Lead: NIAB) ‘Management of Rotations’ 2016-2021 (£1.8M) (PI/Co-I)

Publications

For a complete list of publications see:

https://scholar.google.co.uk/citations?hl=en&user=XUGoLTMAAAAJ&view_op=list_works&sortby=pubdate

Dr Tracy Valentine | Ecological Sciences | The James Hutton Institute

Prof Robbie WaughProfessor Robbie Waugh FRSE FRSB
Scientific Director, International Barley Hub
Professor in Plant Genomics, The University of Dundee
01382 568734
robbie.waugh@hutton.ac.uk

Research Interests

Robbie has made major contributions to the development and exploitation of enabling technologies and accompanying genetic resources that have promoted barley as both a ‘crop and model’ for the research and commercial sectors.  He developed a range of practical tools and informational resources that now pervade barley genetics research in both the global academic and commercial sectors (e.g SNP genotyping platforms, genome sequences, reference transcriptomes etc.).  Over his career he has exploited these platforms for genetic analyses, gene isolation and functional characterisation.  His research is based largely on understanding and using biodiversity, particularly through the development and application of genetic approaches for trait dissection.  He established a powerful platform for efficiently exploiting mutants for gene identification and functional validation by both forward and reverse genetics strategies.  The outputs of his research have provided new understanding of the genetic control of inflorescence architecture, culm branching, pigmentation, lignin content, meiosis, growth habit and heading date.  He maintains productive relationships with the international cereals research community and despite the more ‘translational’ nature of his research that has been exclusively conducted on crops he has published extensively and is highly cited.

Current Research Projects

BBSRC Collaborative Training Partnership (Lead: SWRI) ‘BARIToNE’ 2022-2028 (£3.6M) (PI/Co-I)

BBSRC Response Mode ‘R-Evolve’ BB/V016938/1 2021-2025 (£657,162)(Co-I)

BBSRC International Partnering Award ‘BarleyEUNetwork’ BB/V018906/1 2021-2024 (£30,000) (Co-I)

ARC ‘Discovery’ ‘Accelerated Domestication’ DP210103744 2021-2026 (Au$635,000) (Co-I)

NCRIS ‘OzBarley’ 2021-2023 (Au$400,000) (Co-PI)

BBSRC BBR BB/S020160/1 ‘PlantRTD’ 2019-2022 (£391,401) (Co-I)

BBSRC Response Mode BB/S002871/1 ‘Root microbiota’ 2018-2022 (761,544) (Co-I)

BBSRC Response Mode BB/R010315/1 ‘Skinning’ 2017-2022 (£585,468) (Co-I)

BBSRC ERA-CAPS BB/S004610/1 ‘BARN’ 2018-2022 (£649,658) (PI)

FACCE-JPI DEFRA CH0213 ‘Barista’ 2019-2022 (£60,000) (PI)

BBSRC BB/N023455/1 ‘MAXBIO’ 2017-2022 (£1,544,929) (Co-I)

Publications

For a complete list of publications see:  https://scholar.google.com/citations?hl=en&user=SfcO540AAAAJ&view_op=list_works

Prof Robbie Waugh | Cell and Molecular Sciences | The James Hutton Institute

Dr Runxuan ZhangDr Runxuan Zhang
Computational Biologist
01382 568886
runxuan.zhang@hutton.ac.uk

Research Interests

My research group focuses on the development of novel and cutting-edge computational methods for analysing high throughput experimental data. I pioneered the development of methods for accurately measuring gene expression from plant RNA-seq experiments by developing the quality control pipelines that were essential for constructing a comprehensive Reference Transcript Dataset in Arabidopsis (AtRTD2). AtRTD2 allows rapid and accurate quantification of differential expression and alternative splicing (AS) analysis. This method has been translated into barley, potato and other plant species. My group also developed novel analytical tools for time-series RNA-seq data that capture the dynamics of expression and AS changes, including the first tool (R package TSIS) for characterising transcript isoform switches in a time series. These methods have now been incorporated into an easy-to-use tool for rapid and accurate RNA-seq and alternative splicing analysis (3D RNA-seq) which has been taken up by >6,000 users from ~60 countries. My group recently developed Protview which optimizes the enzyme scheme to increase the protein coverage for proteomics experiments.

Current Research Projects

BBSRC BBR BB/S020160/1 ‘PlantRTD’ 2019-2022 (£391,401) (PI)

BBSRC Response Mode ‘The Generation Gap – Mechanisms of maternal control on grain’ BB/W002590/1 2022-2025 (£744,015) (Co-I)

BBSRC International Partnering Award ‘BarleyEUNetwork’ BB/V018906/1 2021-2024 (£30,000) (Co-I)

BBSRC International Partnering Award ‘UK Australia’ BB/V018299/1 2021-2024 (£30,000) (Co-I)

BBSRC ERA-CAPS BB/S004610/1 ‘BARN’ 2018-2022 (£649,658) (Co-I)

Some Recent Publications

Guo, W., Tzioutziou, N., Stephen, G., Milne, I., Calixto, C., Waugh, R., Brown, J.W.S. and Zhang, R. (2020)  “3D RNA-seq – a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists”, RNA Biology, https://doi.org/10.1080/15476286.2020.1858253.

Calixto, C.P.G., Guo, W., James, A., Tzioutziou, N., Entizne, J., Panter, P., Knight, H., Nimmo, H., Zhang, R., and Brown, J. (2018) “Rapid and dynamic alternative splicing impacts the Arabidopsis cold response transcriptome”, The Plant Cell, 30: 1424–1444

Zhang, R., Calixto, C.P.G., Marquez, Y., Venhuizen, P., Tzioutziou, N.A., Guo, W., Spensley, M., Entizne, J.C., Lewandowska, D., ten Have, S., dit Frey, N.F., Hirt, H., James, A.B., Nimmo, H.G., Barta, A., Kalyna, M. and Brown, J.W.S. (2017) A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing”, Nucleic Acid Research, 45(9): 5061-5073

For a complete list of publications see: https://scholar.google.com/citations?user=dTzeLGkAAAAJ&hl=en&oi=ao

Dr Runxuan Zhang | Information and Computational Sciences | The James Hutton Institute