Professor Robbie Waugh FRSE FRSB

Cell and Molecular Sciences, JHI, and Professor, Div. Plant Sciences, University of Dundee.

01382 568734
robbie.waugh@hutton.ac.uk

Research Interests

Robbie has made major contributions to the development and exploitation of barley as both a cereal crop and model for the Triticeae research and commercial sectors.  An early adopter of genomics and informatics technologies he has developed tools and resources that pervade global basic and applied barley genetics research, with reach to other temperate cereals.  He exploits these platforms for high resolution genetic analyses focused on the isolation and characterization of genes and pathways determining variation in plant morphology and developmental aspects of natural diversity and adaptive traits. He plays a leading role in the barley genetics/genomics community.  He has recently developed an initiative to ‘galvanise’ the International barley genetic community by organising online seminars every fortnight and posting the seminars online on the IBH website. 

Awards and Commissions of trust

Fellow of the Royal Society of Edinburgh (2013)

Fellow of the Royal Society of Biology (2014)

Education

BSc (Hons), Strathclyde University (1981)

PhD, University of Dundee (1987)

Current Research Funding

BBSRC Follow on Fund INCREACR (2023-2025)(£240K) (Co-PI)

EU Horizon program BEST-CROP Grant Agreement No 101082091 (2023-2028)(€400K)(Co-PI)

Scottish Government SRP ‘BARGAIN’ JHI-B1-2 (2022- 2028) (~£6M)(Co-PI)

BBSRC Collab. Training Partnership ‘BARIToNE’ BB/W009382/1 (2022-2028)(£4M)(Co-PI)

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

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

ARC ‘Discovery’ DP220102271 ‘Grain Retention’ 2022-2025 (Au$417,200) (Melbourne.: Co-I)

ARC ‘Discovery’ DP210102225 ‘Beta Glucan’ 2021-2024 (Au$491,691) (LaTrobe: Co-I)

Publications

Orr, J. et al (2023) “Loss of E3 ligase HvST1 function substantially increases recombination” PNAS USA (under review) (bioRxiv, 2023.05. 19.541444 https://doi.org/10.1101/2023.05.19.541444)

Bernad V. et al (2023) High-throughput phenotyping of the core European Heritage Collection (ExHIBiT) under waterlogging Authorea https://doi.org/0.22541/au.166733722.21198616/v1

Hu, H. et al, (2023) Genomic signatures of barley breeding for environmental adaptation to the new continents Plant Biotechnology Journal 27th July 2023 https://doi.org/10.1111/pbi.14077

Wonneberger et al (2023) “Major chromosome 5H haplotype switch structures the European two-rowed spring barley germplasm of the past 190 years” Theor. Appl. Genet. 136 (8) 174 https://doi.org/10.1007/s00122-023-04418-7

Schreiber, M., et al (2023) “Genomic resources for a historical collection of cultivated two-row European spring barley genotypes”. Scientific Data (in press) (bioRxiv, 2023.03. 06.531259 – https://doi.org/10.1101/2023.03.06.531259

Houston, K., et al. (2023). “The p-coumaroyl arabinoxylan transferase HvAT10 underlies natural variation in whole-grain cell wall phenolic acids in cultivated barley”. Frontiers in Plant Sciences 14 – 1095862 https://doi.org/10.3389/fpls.2023.1095862

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 Martin Balcerowicz

Royal Society University Research Fellow and Independent Investigator, University of Dundee

MBalcerowicz001@dundee.ac.uk

Research Interests

Martin is a plant molecular biologist interested in how plant growth and development are 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 | University of Dundee

Professor Rob Brooker

Executive Director of Science

01224 395 176
rob.brooker@hutton.ac.uk

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 Micha Bayer

Bioinformatics Specialist,
Dept of Information and Computational Sciences, James Hutton Institute

micha.bayer@hutton.ac.uk

Research Interests

I am a bioinformatics specialist with a focus on second and third generation sequence analysis and 15 years of experience in barley genomics, variomics and transcriptomics. My post was created at the start of the next generation sequencing era and I was one of the early pioneers of applying the new technologies in 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). Currently I am part of the ongoing efforts to produce a barley pan-transcriptome and a second iteration of the barley pan-genome.

Recent Research Projects

• Scottish Government – RESAS project JHI-B1-2: Exploring Barley Diversity for resilience and sustainability (BARGAIN)
• BBSRC European Partnership Award: The exploitation and sharing of barley resources
• BBSRC Responsive mode: The Generation Gap – Mechanisms of maternal control on grain
• BBSRC Responsive mode: R-EVOLVE
• BBRSC BBR: Opening gene expression data to the research community
• Norwegian Government via Crop Trust: Biodiversity for Opportunities, Livelihoods and Development (BOLD)
• International barley pan-transcriptome consortium
• International barley pan-genome consortium

Publications

Bayer, M.M., et al. Development and Evaluation of a Barley 50k iSelect SNP Array. Frontiers in Plant Science 2017;8(1792).

Bayer, M., et al. Exome Capture for Variant Discovery and Analysis in Barley. In: Harwood, W.A., editor, Barley: Methods and Protocols. New York, NY: Springer New York; 2019. p. 283-310.

Chen, Y.-Y., et al. The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication. The Plant Journal 2022;111(6):1580-1594.

Comadran, J., et al. Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley. Nature genetics 2012;44(12):1388-1392.

Coulter, M., et al. BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification. The Plant Journal 2022;111(4):1183-1202.

Liu, L., et al. Conserved signalling components coordinate epidermal patterning and cuticle deposition in barley. Nature Communications 2022;13(1):6050.

Mascher, M., et al. A chromosome conformation capture ordered sequence of the barley genome. Nature 2017;544(7651):427-433.

Milne, I., et al. Tablet–next generation sequence assembly visualization. Bioinformatics 2010;26(3):401-402.

Milne, L., et al. EORNA, a barley gene and transcript abundance database. Scientific Data 2021;8(1):90.

Rapazote-Flores, P., et al. BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq. BMC Genomics 2019;20(1):968.

Russell, J., et al. Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. Nature genetics 2016;48(9):1024-1030.

Full list of publications available at https://orcid.org/0000-0003-0041-3115

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

Dr Jorunn Bos

Cell and Molecular Sciences

Royal Society Fellow

jorunn.bos@hutton.ac.uk

+44 (0)344 928 5428 (*)

Research Interests

My research is aimed at understanding how aphids modify their host plants at the molecular level to enable successful infestations. Aphids are devastating plant sap-feeding insects. These insects cause direct feeding damage and transmit the majority of plant viruses, resulting in significant yield losses, particularly in staple food crops.

Aphid control relies on insecticides that are damaging to the environment and to which aphids can become resistant. To develop new control strategies we need to understand how these insects interact with plants at the cellular and molecular level.

Key questions herein are: Which plant cellular processes are perturbed by aphids and how does that enable infestation? What do aphids “inject” into host plants to establish successful infestations? Can we generate crops with durable aphid resistance while reducing insecticide usage?

Recent work suggests that aphids, like plant pathogens, secrete effectors into their host plants to manipulate host cell processes and impact the ability to infest plants. These effectors are produced in the aphid salivary glands and secreted into the host during aphid feeding.

My lab aims to identify and characterise these effectors from the aphid species Myzus persicae (green peach aphid) to understand how they perturb plant cellular processes and promote host plant infestation.

Past research

October 2010 – Present: Independent Research Fellow, The James Hutton Institute – Royal Society of Edinburgh/Scottish Government Marie Curie Personal Research Fellowship 2010-2015.
Manipulation of plant host cell processes by aphid saliva proteins.

November 2008 – October 2010: Post-doc, The John Innes Centre, Norwich, UK
Supervisor: Dr S. Hogenhout
Functional genomics and proteomics approaches to identify candidate effectors from the aphid species Myzus persicae.

October 2007 – November 2008: Post-doc, The Sainsbury Laboratory, Norwich, UK
Supervisor: Dr S. Kamoun
Investigation of the molecular basis of INF1 cell death suppression by Phytophthora infestans RXLR effector AVR3a

September 2003 – August 2007: PhD, The Ohio State University, Wooster OH, USA
Supervisor: Dr S. Kamoun
Function, structure and evolution of the RXLR effector AVR3a of Phytophthora infestans.

Dr Davide Bulgarelli

Senior Lecturer (Teaching and Research), University of Dundee at the James Hutton Institute, Invergowrie

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 Isabelle Colas

Plant Molecular Geneticist at the James Hutton Institute, Invergowrie

+44 (0) 1382 568962

Isabelle.Colas@hutton.ac.uk

Research Interests

Breeding programmes rely on meiotic recombination to develop new varieties, however, in barley, large part of the chromosomes exhibits very low genetic recombination. To understand barley meiosis, she characterized a number of barley mutants (bowman isoline), aiming at modulating the distribution of recombination across the genome. Moreover, the use of 3D-SIM microscopy highlighted specific organization of the barley genome and crossover regulation when compared to Arabidopsis studies. A breakthrough for her lab is the discovery that the absence of the barley E3 ubiquitin ligase HvST1 increases recombination by 50%. With no obvious orthologues in Arabidopsis nor mammals, the presence of this new gene suggests that barley has additional pathways to control recombination, which may explain some of the differences between cereals and other systems. Her current research focuses on understanding and utilizing HvST1 and other meiotic genes to modulate recombination in barley to increase gene diversity.

Dr Isabelle Colas completed her molecular biology training in France and began her career in the private sector at Agrogene SA, a company specialized in agricultural DNA analyses and GMO detection. She conducted a PhD and a postdoc at the John Innes Centre, and worked on the wheat Ph1 locus project where she developed her interest in plant meiosis and published a number of quality publication. She moved to the James Hutton Institute in 2010 where she established her lab as a world reference for plant super resolution microscopy (1st Prize GE Healthcare Image Competition 2015). Her main interest is on barley meiosis with the goal to be able to modulate recombination to increase biodiversity.

Recent Funding

2020-2023: BBSRC New Investigator – (BB/T008636/1) HvST1: A novel suppressor of recombination in barley – Total Value £505,746 (PI)

2021-2025: BBSRC International Partnering Awards – (BB/V018906/1) Create new opportunities to exploit barley resources and accelerate breeding – Total Value £34,698.60 (PI)

2022-2023: BBSRC 21ALERT Mid-range equipment Initiative – (BB/W019752/1) A low-light 3D-STED confocal microscope: super-resolution imaging of nanoscale functions in plants and other organisms – Total Value £1,223,219 (Co-I)

2022-2024: The Wolfson Foundation – Hutton Molecular Phenotyping Centre – Total Value £1,000,000 (Co-I)

2023-2025: BBSRC Follow on Fund – (APP2456) Increased Recombination for Cereal Breeding – Total Value £220,848 (Co-I)

Publications

For a complete list of publications see:

https://orcid.org/0000-0001-6980-9906

Dr Tim George

Director of the International Barley Hub

03449285428
tim.george@hutton.ac.uk

Tim is a plant physiologist/soil scientist and has worked on rhizosphere processes for the last three decades.

Understanding how plants react to and alter their external environment is key to optimising their resource use, adaptation to stress and resilience 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 nutrient 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. 2023-2028 EU Horizon Europe “COUSINS: Crop Wild Relatives Utilization and Conservation for Sustainable Agriculture”. Co-I (Hutton lead) Total Value €6000000
2. 2022-2027 EU Horizon Europe “Root2Res: Root phenotyping and genetic improvement for rotational crops resilient to environmental change”. Coordinator,  Total  value €6999998
3. 2021-2025 EU H2020 “ReAlising DynamIc vAlue chaiNs for underuTilised crops- RADIANT”. Co-I, Total value €5999715

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 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

Honorary Associate

+44 (0)344 928 5428
wenbin.guo@hutton.ac.uk

Research Interests

Wenbin is a pioneering Bioinformatician driving the advancement of tailored computational and mathematical models for high-throughput experimental data analysis. His expertise has led to the creation of user-friendly tools and innovative pipelines that empower precise 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 impactful tools have been seamlessly integrated into a diverse array of projects, spanning RTD constructions and data analyses in a wide range of organisms including barley (BART1, BART2, and pan transcriptome studies of 20 barley genotypes), Arabidopsis (AtRTD1, AtRTD2, and AtRTD3), rice, potato, raspberry, lettuce, pumpkin, and even extending to animal and human disease data. The 3D RNA-seq App, bearing over 15,800 users globally, earned distinction with the Best Innovation Award from the School of Life Sciences at the University of Dundee, as an unparalleled tool enabling biologists to master intricate RNA-seq analysis within hours. He also won £360,000 in funding to create a spin-out company to drive the App’s commercialization. The outputs of his work have engaged various opportunities for research commercialisation, and internal and external collaborations with excellent research groups.

Current Research Projects

• Leading researcher, Development of barley Pan-transcriptome.
• PI, Innovate UK ICURE Explore “SHARP Genomic” 2023 (£35,000).
• Co-I, BBSRC follow-on fund “RNA-seq platform” 2023-2025 (£250,000).
• Co-I, Scottish Enterprise high growth spin-out programme “SHARP Genomic Analytics” 2023 (£75,000).
• Co-I, 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)

Publications

For a complete list of publications see: 

https://scholar.google.com/citations?user=MpSTI_QAAAAJ&hl=en

Dr Rob Hancock

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 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 Ingo Hein

Head of Potato Genetics

ingo.hein@hutton.ac.uk

+44 (0)344 928 5428 (*)

Research Interests

Ingo Hein is the Head of Potato Research at the Hutton. His research is focused on the identification, mobilisation, and cloning of durable resistances against major potato pathogens. At the core of his research lies the exploration of the Commonwealth Potato Collection, where he applies genomics and genetics to discover novel resistances. By closely collaborating with breeders, stakeholders, and industry partners, his fundamental research into disease resistance seamlessly translates into practical applications.

Current projects:

• Identification and cloning of new genetic variations in Solanum species to confer resistance against Phytophthora infestans, Potato Cyst Nematodes, and Viruses.
• Employing Association genetics (SMRT-AgRenSeq-d) to identify resistances in tetraploid potato cultivars and breeding clones.
• Development and utilisation of diploid, homozygous potatoes for trait discovery.
• Facilitating the integration of resistances into breeding programs through the development of highly transferrable markers.

By pursuing these avenues, Ingo aims to enhance the effectiveness and longevity of disease resistance in potato cultivation, contributing to the sustainable growth of the industry and ensuring food security

Past research

• 2020 – Present    Reader, University of Dundee (20% FTE)
• 2023 – Present    Head of Potato Research, The James Hutton Institute (80% FTE)
• 2020 – 2023        Band G, Associate potato group leader, The James Hutton Institute (80% FTE)
• 2017 – 2020        Principal Investigator, University of Dundee (20% FTE)
• 2012 – 2020        Band F, Principal Investigator, Individual merit-based promotion, James Hutton Institute
• 2006 – 2012        Band E, Project Leader, Individual merit-based promotion, Scottish Crop Research Institute
• 2003 – 2006        Band D, Postdoctoral Researcher, Genetics department, Scottish Crop Research Institute

Dr Rob Hancock

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 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

Dr Edgar Huitema

Cell and Molecular Sciences

Principal Investigator

edgar.huitema@hutton.ac.uk

+44 (0)344 928 5428 (*)

Research Interests

My current research is aimed at understanding the mechanisms by which Phytophthora sp., cause epidemics on crop plants. More specifically, work in my group focuses on the functions of the Crinklers, a novel class of cytoplasmic effectors from Phytophthora. In addition, we are interested in the events that couple signaling cues to developmental transitions during pathogen ingress. We hypothesise that these processes are critical for disease establishment and form a possible basis for regulation of effector secretion and delivery.

Collaborators

Professor Paul Birch – Division of Plant Sciences, University of Dundee at The James Hutton Institute, Dundee
Professor Kurt H. Lamour – Department of Entomology and Plant Pathology, University of Tenessee
Professor Sophien Kamoun – The Sainsbury Laboratory, Norwich 

Recent Publications

• See Edgar Huitema’s recent publications on PubMed.

Dr 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

Head of Department of
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 McKim

Senior Lecturer and Principal Investigator, Division of Plant Sciences, University of Dundee

01382 568916
smckim@dundee.ac.uk

Research Interests

Sarah is a developmental biologist who leads a research team using barley as a powerful experimental model. We want to identify and understand genes regulating cereal growth and development. My team has discovered genes and mechanisms controlling several traits important for cereal yield, such as stem elongation, branching and grain size and shape. Our recent research explores protective layers on the surface of plants, developmental genes improving stress resiliency, and grain development and quality.  

Current Research Projects

2023 – 2025: BB/Y001850/1 – BBSRC Standard Response Mode, PI: Facing Forwards – “Understanding epidermal development in cereals” £1,164,671

2022- 2025: BB/X001423/1 – BBSRC Standard Response Mode, co-PI: “Testing a cytokinin dilution model of floral duration in barley” £621,745

2022 – 2025: BB/W003074/1 – BBSRC Standard Response Mode, PI: “Generation Gap: Mechanisms of maternal control on grain” £744,015      

2022 – 2025: BB/V018299/1 – BBSRC Australia Partnership Award, PI: “International pooling for advanced cereal science – IPAC” £47,765

Some Recent Publications

Linsan L, SB Jose, Campoli C, Bayer MM, Sánchez-Diaz MA, McAllister T, Zhou Y, Eskan M, Milne L, Schreiber M, Batstone T, Bull ID, Ramsay L, von Wettstein-Knowles P, Waugh R, Hetherington AM, McKim SM*(2022) A conserved signaling cascade controls epidermal patterning and cuticle deposition in barley. Nat Commun 13, 6050. https://doi.org/10.1038/s41467-022-33300-1

McAllister T, Campoli C, Eskan M, Liu L, McKim SM* (2022) A gene encoding a SHINE1/WAX INDUCER1 transcription factor controls cuticular wax in barley. Agronomy. 12 (5): 1088.

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.

Parry G, Benitez-Alfonso Y, Gibbs DJ, Grant M, Harper A, Harrison CJ, Kaiserli E, Leonelli S, May S, McKim S, Spoel S, Turnbull C, van der Hoorn RAL, Murray J (2020) How to build an effective research network: lessons from two decades of the GARNet plant science community, Journal of Experimental Botany, eraa397.

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

Mr Dan Langford

Business Development Manager

International Barley Hub

+44 (0) 7735 230639
dan.langford@hutton.ac.uk

Research Interests

Mr Dan Langford | International Barley Hub | The James Hutton Institute

Dr 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 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 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 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

• PI: UKRI / ESRC Food and Nutrition Security during and after the COVID-19 pandemic. Rapid response project with Chatham House and Cranfield University. COVID-19 Food and nutrition security | The James Hutton Institute

• 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 Russell

Barley Geneticist
Cell and Molecular Sciences
James Hutton Institute
Dundee, UK

01382568857
joanne.russell@hutton.ac.uk

Research Interests

Research 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

EU HORIZON ‘Root2Resilience: Root phenotyping and genetic improvement for rotational crops resilient to environmental change’ 2022-2027(£645,000)(Co-I)

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

Schmidt SB, Brown, LK, Booth, A, Wishart J, Hedley PE, Martin P, Husted S, George TS, Russell, J. (2023) Heritage genetics for adaptation to marginal soils in barley. Trends in Plant Science 28, 544-551.

Chen, Yun‐Yu, et al. (2022) The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication. The Plant Journal 111, 1580-1594

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 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)
• Horizon Europe. Crop Wild Relatives utilisation and conservation for sustainable agriculture (COUSIN) 2024-2028 (Co-I)
• Horizon Europe/UKRI. Boosting Photosynthesis to deliver novel Crops for the circular bioeconomy (BEST-CROP). 2023-2027(Co-I)

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 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

Dr Sébastien Bélanger

Principal Investigator, Cell and Molecular Sciences, The James Hutton Institute and Barley International Hub

sebastien.belanger@hutton.ac.uk

Research Interests

Sébastien’s focus is on plant development and RNA research, particularly in the field of reproductive biology studying the role and function of small RNAs (sRNA). He has authored first-author publications, covering diverse topics such as gametic embryogenesis and doubled haploid production, sRNA’s involvement in anther development, phylogenetics of protein families involved in sRNA pathways, as well as the evolution and function of sRNAs in other systems.

Before joining the Barley International Hub, Sébastien postdoctoral works focused on reproductive phased sRNA (phasiRNA) of developing anthers in wheat and barley. He discovered novel stage-specific 24-nt phasiRNAs crucial for male fertility that are only present in wheat, barley, and their close relatives, but not in rice or maize. Moreover, he identified that the dicer-like 5 mutant in wheat was depleted in 24-nt phasiRNA and showed a temperature-sensitive male-sterile phenotype. He is developing his lab with the primary focus to understand male reproductive development in barley and other crops in the Triticeae tribe, in order to control the production of pollen for hybrid seed production.

The direction of Sébastien research is gradually moving towards investigating the use of barley morphological diversity for flower developmental studies. The aim is to discover genes and traits to optimize the morphology of the inbreeding flower architecture toward an outbreeding flower for hybrid production in barley.

Selected Publications

Bélanger S, Kramer MC, Payne HA, Hui AY, Slotkin RK, Meyers BC, Staub JM (2023a) Plastid double-stranded RNA transgenes trigger phased small RNA-based gene silencing of nuclear-encoded genes. Plant Cell. doi: 10.1093/plcell/koad165.

Bélanger S, Zhan J, Meyers BC (2023b) Phylogenetic analyses of seven protein families refine the evolution of small RNA pathways in green plants. Plant Physiol. doi: 10.1093/plphys/kiad141.

Bélanger S, Berensmann H, Baena V, Duncan K, Meyers BC, Narayan K, Czymmek KJ (2022) A versatile enhanced freeze-substitution protocol for volume electron microscopy. Frontiers Cell Dev Biology. 10:933376. doi: 10.3389/fcell.2022.933376.

Baldrich P, Bélanger S, Kong S, Pokhrel S, Tamim S, Teng C, Schiebout C, Gurazada SGR, Gupta P, Patel P, Razifard H,  Nakano M,  Dusia A,  Meyers BC,  Frank MH (2022) The evolutionary history of small RNAs in Solanaceae. Plant Physiol. 189:644–665. doi: 10.1093/plphys/kiac089css

Bélanger S, Pokhrel S, Czymmek KJ, Meyers BC (2020a) Pre-meiotic, 24-nt reproductive phasiRNAs are abundant in anthers of wheat and barley but not rice and maize. Plant Physiol. Pp.00816.2020. doi: 10.1104/pp.20.00816.

Bélanger S, Baldrich P, Lemay M, Marchand S, Esteves P, Meyers BC, Belzile F (2020b) The commitment of barley microspores into embryogenesis correlates with miRNA‐directed regulation of members of the SPL, GRF and HD‐ZIPIII transcription factor families. Plant Direct. doi: 10.1002/pld3.289.

Bélanger S, Marchand S, Jacques P-É, Meyers B, Belzile F (2018a) Differential Expression Profiling of Microspores During the Early Stages of Isolated Microspore Culture Using the Responsive Barley Cultivar Gobernadora. G3 Genes Genomes Genetics. 8:1603–1614. doi: 10.1534/g3.118.200208. 

Bélanger S, Paquet-Marceau S, Lago JED, Belzile F (2018b) QTL mapping uncovers a semi-dwarf 1 (sdw1) allele in the barley (Hordeum vulgare) ND23049 line. Genome 61:429–436. doi: 10.1139/gen-2017-021.

Bélanger S, Clermont I, Esteves P, Belzile F (2016a) Extent and overlap of segregation distortion regions in 12 barley crosses determined via a Pool-GBS approach. Theor Appl Genet 129:1393–1404. doi: 10.1007/s00122-016-2711-5. 

Bélanger S, Esteves P, Clermont I, Jean M, Belzile F (2016b) Genotyping‐by‐Sequencing on Pooled Samples and its Use in Measuring Segregation Bias during the Course of Androgenesis in Barley. Plant Genome. doi: 10.3835/plantgenome2014.10.0073.

Bélanger S, Gauthier M, Jean M, Sato K, Belzile F (2014) Genomic characterization of the Hordeum vulgare DEP1 (HvDEP1) gene and its diversity in a collection of barley accessions. Euphytica. 198:29–41. doi: 10.1007/s10681-014-1089-1. 

Dr Linda Milne

Bioinformatics specialist, Information and Computing Sciences, The James Hutton Institute

Research Interests

Linda’s focus is analysis of NGS sequence data primarily from barley, raspberry and blackcurrant and has constructed and annotated the genomes of both these soft fruits.  She also creates databases of plant genetic data and interactive websites and visualizations to deliver that data to a world-wide market.  Websites include the EORNA database which explores the gene expression of barley cultivars (https://ics.hutton.ac.uk/eorna/index.html). Other skills include developing strategies for comparing large datasets of sequences (both within and between species) and writing software for automating and streamlining the processing of large quantities of sequence data.

Current Research Projects

2023-2025 BBSRC/BBR “Opening gene expression data to the research community” (Co-I). Grant BB/X018636/1

2021-2025 EU Horizon 2020 ‘BreedingValue’ ID:101000747

Some Recent Publications

Full list of publications at https://orcid.org/0000-0002-1798-8022

Linsan Liu; Sarah Jose; Chiara Campoli; Micha Bayer; Miguel Sánchez-Diaz; Trisha McAllister; Yichun Zhou; Mhmoud Eskan; Linda Milne; Miriam Schreiber et al. Conserved signalling components coordinate epidermal patterning and cuticle deposition in barley. Nature Communications 2022 doi: 10.1038/s41467-022-33300-1

Milne L, Bayer M, Rapazote-Flores P, Mayer CD, Waugh R, Simpson CG. EORNA, a barley gene and transcript abundance database. Sci Data. 2021 Mar 25;8(1):90. doi: 10.1038/s41597-021-00872-4.

Zhang R; Kuo R; Coulter M; Calixto CPG; Entizne JC; Guo W; Marquez Y; Milne L; Riegler S; Matsui A et al. A high resolution single molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biol. 2022 Jul 7;23(1):149. doi: 10.1186/s13059-022-02711-0.

Max Coulter; Juan Carlos Entizne; Wenbin Guo; Micha Bayer; Ronja Wonneberger; Linda Milne; Miriam Schreiber; Allison Haaning; Gary Muehlbauer; Nicola McCallum et al. BaRTv2: A highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification. Plant J. 2022 Aug;111(4): 1183-1202

Schreiber, M.; Mascher, M.; Wright, J.; Padmarasu, S.; Himmelbach, A.; Heavens, D.; Milne, L.; Clavijo, B.J.; Stein, N.; Waugh, R. A genome assembly of the barley ‘transformation reference’ cultivar golden promise. G3 Genes|Genomes|Genetics 2020, 10(6):1823–1827

Dreissig S, Maurer A, Sharma R, Milne L, Flavell AJ, Schmutzer T, Pillen K. Natural variation in meiotic recombination rate shapes introgression patterns in intraspecific hybrids between wild and domesticated barley. New Phytol. 2020 Dec;228(6):1852-1863. doi: 10.1111/nph.16810. Epub 2020 Aug 9.

Schreiber M, Mascher M, Wright J, Padmarasu S, Himmelbach A, Heavens D, Milne L, Clavijo BJ, Stein N, Waugh R. A Genome Assembly of the Barley ‘Transformation Reference’ Cultivar Golden Promise. G3 (Bethesda). 2020 Jun 1;10(6):1823-1827. doi: 10.1534/g3.119.401010.

Rapazote-Flores P, Bayer M, Milne L, Mayer CD, Fuller J, Guo W, Hedley PE, Morris J, Halpin C, Kam J, McKim SM, Zwirek M, Casao MC, Barakate A, Schreiber M, Stephen G, Zhang R, Brown JWS, Waugh R, Simpson CG. BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq. BMC Genomics. 2019 Dec 11;20(1):968. doi: 10.1186/s12864-019-6243-7.

Simpson CG, Fuller J, Rapazote-Flores P, Mayer CD, Calixto CPG, Milne L, Hedley PE, Booth C, Waugh R, Brown JWS. High-Resolution RT-PCR Analysis of Alternative Barley Transcripts. Methods Mol Biol. 2019;1900:269-281. doi: 10.1007/978-1-4939-8944-7_17.

Jarret DA, Morris J, Cullen DW, Gordon SL, Verrall SR, Milne L, Hedley PE, Allwood JW, Brennan RM, Hancock RD. A Transcript and Metabolite Atlas of Blackcurrant Fruit Development Highlights Hormonal Regulation and Reveals the Role of Key Transcription Factors. Front Plant Sci. 2018 Aug 24;9:1235. doi: 10.3389/fpls.2018.01235.

Hackett CA, Milne L, Smith K, Hedley P, Morris J, Simpson CG, Preedy K, Graham J. Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening. BMC Genet. 2018 Aug 15;19(1):59. doi: 10.1186/s12863-018-0666-z.

Herzig P, Maurer A, Draba V, Sharma R, Draicchio F, Bull H, Milne L, Thomas WTB, Flavell AJ, Pillen K. Contrasting genetic regulation of plant development in wild barley grown in two European environments revealed by nested association mapping. J Exp Bot. 2018 Mar 24;69(7):1517-1531. doi: 10.1093/jxb/ery002.

Dr Miriam Schreiber

Computational Biologist in crop research, Information and Computational Science group, James Hutton Institute, Dundee

Miriam.schreiber@hutton.ac.uk

Research Interests

Miriam is a computational biologist working mostly on barley sequencing data. Miriam’s last work involved the combination of phenotypic, genotypic and expression data in a big association study on spring barley cultivars. Previous work included barley genome assemblies, working with exome capture data and whole genome shotgun sequencing of barley mutants to identify causal genes. Or using RNA-sequencing data to identify genes expressed during meiosis, by contributing to the generation of the barley transcriptome datasets but also looking at the biological changes happening during the development of anthers.

Some Recent Publications

Schreiber, M., Wonneberger, R., Haaning, A.M., Coulter, M., Russell, J., Himmelbach, A., et al. (2023). Genomic resources for a historical collection of cultivated two-row European spring barley genotypes. bioRxiv, 2023.2003.2006.531259. doi: 10.1101/2023.03.06.531259.

Wonneberger, R., Schreiber, M., Haaning, A., Muehlbauer, G.J., Waugh, R., and Stein, N. (2023). Major chromosome 5H haplotype switch structures the European two-rowed spring barley germplasm of the past 190 years. Theor Appl Genet 136(8), 174. doi: 10.1007/s00122-023-04418-7.

Chen, Y.Y., Schreiber, M., Bayer, M.M., Dawson, I.K., Hedley, P.E., Lei, L., et al. (2022). The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication. Plant J. doi: 10.1111/tpj.15908.

Schreiber, M., Mascher, M., Wright, J., Padmarasu, S., Himmelbach, A., Heavens, D., et al. (2020). A Genome Assembly of the Barley ‘Transformation Reference’ Cultivar Golden Promise. G3 (Bethesda) 10(6), 1823-1827. doi: 10.1534/g3.119.401010.

Jayakodi, M., Padmarasu, S., Haberer, G., Bonthala, V.S., Gundlach, H., Monat, C., et al. (2020). The barley pan-genome reveals the hidden legacy of mutation breeding. Nature 588(7837), 284-289. doi: 10.1038/s41586-020-2947-8.

Barakate, A., Orr, J., Schreiber, M., Colas, I., Lewandowska, D., McCallum, N., et al. (2020). Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I. Front Plant Sci 11, 619404. doi: 10.3389/fpls.2020.619404.

Schreiber, M., Barakate, A., Uzrek, N., Macaulay, M., Sourdille, A., Morris, J., et al. (2019). A highly mutagenised barley (cv. Golden Promise) TILLING population coupled with strategies for screening-by-sequencing. Plant Methods 15(1), 99. doi: 10.1186/s13007-019-0486-9.

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

Sebastian Raubach

Bioinformatics Research Software Engineer, Information & Computational Sciences Department, James Hutton Institute, Dundee

sebastian.raubach@hutton.ac.uk

Research Interests

I am responsible for the conceptualisation, management and development of cutting-edge mobile applications, databases and web applications for funders (BBSRC, EU, CGIAR, Crop Trust, Norwegian Government) as well as commercial breeding companies through James Hutton Limited (JHL). My role is to drive the development of software solutions for plant genetic resources collections, phenotypic data collection and visualization tools.

Some Recent Publications

For a complete list of publications see:Sebastian Raubach (0000-0001-5659-247X) (orcid.org)

Dr Chiara Campoli

Barley geneticist, Cell and Molecular Sciences, the James Hutton Institute/International Barley Hub (IBH)

chiara.campoli@hutton.ac.uk

Research Interests

Chiara is a geneticist and has worked in barley genetic research for over 12 years. Her research focussed on the composition and distribution of the cuticle, a primary line of defence for plants against environmental stresses. Her work, exploiting a variety of genetic resources (natural and induced mutations, available germplasm, mapping populations) identified key genes controlling cuticle synthesis and accumulation and having a broader impact on other fundamental traits (e.g., stomata development and seed quality). Chiara is interested in understanding how variation at these genes impacts barley’s adaptation to different environments and, ultimately, how this knowledge can be utilised for sustainable crop production.

Research Projects:

2023-2026: BBSRC Response Mode. Understanding epidermal development in cereals (Facing Forwards, BB/Y001990/1) (Co-I)

2017-2022: BBSRC Response Mode. Mechanisms underlying variation in barley hull adhesion (Skinning, BB/R010315/1). Total value £613.746, (RCo-I, PI Sarah McKim University of Dundee)

Publications:

Müller Y, Patwari P, Stöcker T, Zeisler‐Diehl V, Steiner U, Campoli C, Grewe L, Kuczkowska M, Dierig MM, Jose S, Hetherington AM, Acosta IF, Schoof H, Schreiber L, Dörmann P (2023) Isolation and characterization of the gene HvFAR1 encoding acyl‐CoA reductase from the cer‐za.227 mutant of barley (Hordeum vulgare) and analysis of the cuticular barrier functions. New Phytologist 239, 5

Liu L, Jose SB, Campoli C, Bayer MM, Sánchez-Diaz MA, McAllister T, Zhou Y, Eskan M, Milne L, Schreiber M, Batstone T, Bull ID, Ramsay L, von Wettstein-Knowles P, Waugh RW, Hetherington AM, and McKim SM(2022) Conserved signalling components coordinate epidermal patterning and cuticle deposition in barley. Nat Comms 13, 6050

McAllister T, Campoli C, Eskan, M, Liu L, McKim SM (2022) A Gene Encoding a SHINE/WAX INDUCER1 Transcription Factor Controls Cuticular Wax in Barley. Agronomy 12(5):1088

For a complete list of publications see https://orcid.org/0000-0001-7809-2927

Dr. Gwendolyn K. Kirschner

Marie Curie Postdoctoral Fellow

gwendolyn.kirschner@hutton.ac.uk

@GwenKirschner | @gwenkirschner.bsky.social

Research Interests: 

Within my 2-year Marie Curie fellowship, I analyse how the gravitropic set-point angle in barley roots is regulated transcriptionally, the signalling mechanism of known players in gravitropism, and the role of the root angle in regard to nutrient and water availability.

Current Research Projects

Marie Curie Postdoctoral Fellowship, “Uncovering the mechanisms of the root gravitropic set-point angle and its application in agriculture”, Horizon Europe Guarantee, EP/Y014820/1 [Nov 23 – Oct 25; £187.096]

Publications

Kirschner, G.K., Hochholdinger, F., Salvi, S., Huang, G., Bhosale, R.A., and Bennett, M.J. (2024). Genetic regulation of the root angle in cereals. Trends in Plant Science. https://doi.org/10.1016/j.tplants.2024.01.008

Guo, L., Klaus, A., Baer, M., Kirschner, G. K., Salvi, S., & Hochholdinger, F. (2023). ENHANCED GRAVITROPISM 2 coordinates molecular adaptations to gravistimulation in the elongation zone of barley roots. New Phytologist, 237(6), 2196–2209. https://doi.org/10.1111/nph.18717

Kirschner, G. K., Rosignoli, S., Guo, L., Vardanega, I., Imani, J., Altmüller, J., Milner, S. G., Balzano, R., Nagel, K. A., Pflugfelder, D., Forestan, C., Bovina, R., Koller, R., Stöcker, T. G., Mascher, M., Simmonds, J., Uauy, C., Schoof, H., Tuberosa, R., … Hochholdinger, F. (2021).  ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIF–containing protein that controls root growth angle in barley and wheat. Proceedings of the National Academy of Sciences, 118(35), e2101526118. https://doi.org/10.1073/pnas.2101526118

For a complete list of publications see: Google scholar

Prof Adrian C Newton

Honorary Associate

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

Malcolm Macaulay

Barley Molecular Geneticist

Cell and Molecular Sciences
James Hutton Institute
Dundee, UK

01382568845

malcolm.macaulay@hutton.ac.uk

Research Interests

My research focuses on the development of genetic tools and genomic resources for barley, with a particular emphasis on their application to breeding. This work supports my broader interest in association genetics for agronomically important traits, which has included the establishment of high-throughput SNP genotyping capabilities. Moving forward, my research will focus on dissecting the genetic control of economically important traits and developing pre-breeding material to support future breeding efforts. Additionally, I have a keen interest in developing technologies and their application to my work such as dPCR and ONT technology. I am also involved in running variuous plant science STEM outreach projects.

Current Research Projects

BBSRC Follow on Fund INCREACR (2023-2025)(£240K)
EU Horizon program BEST-CROP Grant Agreement No 101082091 (2023-2028)(€400K)
BBSRC Response Mode ‘R-Evolve’ BB/V016938/1 2021-2025 (£657,162)
The Global Crop Diversity Trust/Norwegian Government ‘BOLD’ Biodiversity for Opportunities, Livelihoods and Development 2022-2032
2022-2027 EU Horizon Europe “Root2Res: Root phenotyping and genetic improvement for rotational crops resilient to environmental change”

Publications

For a complete list of publications see: https://orcid.org/0000-0002-9008-0053

Dr Yunqing Yu

UKRI Future Leaders Fellow, Cell and Molecular Sciences, the James Hutton Institute/International Barley Hub

yunqing.yu@hutton.ac.uk

Research Interest: 

My research program studies comparative development of plant morphological traits at the cellular level and their underlying genetic bases. I aim to understand how plant structures differentiate and develop and what controls their morphological and functional variation. I use Poaceae (the grass family) as my study system. Poaceae, including all cereal crops such as wheat, rice, maize and barley, is one of the largest plant families rich in morphological diversity, and is essential for human diet and animal feed. Specifically, my research combines cellular and molecular biology, genetics, gene editing, and phylogenetics to study the comparative development and evolution of grain disarticulation. Recently, my research interests extend to establishing transformation systems for wild barley species, aiming to provide molecular tools for exploiting wild relatives of barley and wheat.

Current Research Project:

2024-2028: UKRI Future Leaders Fellowship – Development and evolution of abscission zones in the Triticeae. Role: PI. (£1,877,793)

Publications: 

Yu Y, Kellogg EA. (2024) Multifaceted mechanisms controlling grain separation in the Poaceae. Current Opinion in Plant Biology 81:102564.

Yu Y,Hu H, Voytas D, Doust A, Kellogg EA. (2023) The YABBY gene SHATTERING1 controls activation rather than patterning of the abscission zone in Setaria viridis. New Phytologist 240:846–862.

Yu Y, Beyene G, Villmer J, Duncan KE, Hu H, Johnson T, Doust AN, Taylor NJ and Kellogg EA. (2023) Grain shattering by cell death and fracture in Eragrostis tef. Plant Physiology 192(1): 222. 

Yu Y,Hu H, Doust A, *Kellogg EA. (2020). Divergent gene expression networks underlie morphological diversity of abscission zones in grasses. New Phytologist 225(4):1799–1815.  

Yu Y,Leyva P, Taverse R, Kellogg EA. (2020). Abscission zone anatomy of grasses changes rapidly in evolutionary time. American Journal of Botany 107(4): 549–561.

For a complete list of publications, see: ‪Yunqing Yu – ‪Google Scholar

Dr 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