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David Marshall

Staff picture: David Marshall
Information and Computational Sciences
Information and Computational Sciences
Honorary Associate
+44 (0)1382 568744 (*)

The James Hutton Institute
Dundee DD2 5DA
Scotland UK

  • 2019 - current    Honorary Associate, James Hutton Institute
  • 2011 - 2015    ICS Science Group Leader, James Hutton Institute
  • 2008 - 2009    Associate Programme Leader, Genetics Programme, SCRI 
  • 2005 - 2008    Director Postgraduate Studies, SCRI
  • 2005 - 2009    Bioinformatics Theme Leader, Genetics Programme, SCRI
  • 2000 - 2005    Leader Computational Biology Programme, SCRI
  • 1999 - 2000    Deputy Head Genomics Unit Scottish Crop Research Institute
  • 1997 - 1999    Head of Bioinformatics and IT Unit SCRI.
  • 1995 - 1997    Programme Manager BBSRC Plant and Animal Genome Analysis Initiative
  • 1984 - 1997    Lecturer  Department of Genetics, University of Birmingham
  • 1982 - 1984    NERC Post Doc, Department of Genetics, University of Birmingham
  • 1979 - 1982    Demonstrator, Department of Agricultural Botany, UCW, Aberystwyth

Current research interests

From a background of population genetics and the evolution of plant mating systems my research interests have increasingly focussed on the development of genetic marker technologies and DNA sequence diversity in both crop and wild plants and their deployment in applications from the analysis of the genetic structure of natural and breeding populations of crop plants to genome analysis and comparative genomics. The major focus of my interests has been on genetic marker applications with barley, potatoes, wheat  and soft fruit (blackcurrant and raspberry) in collaboration with Professor Robbie Waugh and other Geneticists at Dundee, in particular, the    design and application of SNP-based genotyping arrays. The original focus was initially from public domain EST sequence resources but with the advent of Next Generation Sequencing technologies this has shifted first to the extensive RNA-seq data that have been developed with colleagues in the ICS and CMS Groups at Dundee and with Dr Andrew Flavell from the University of Dundee. The advent of RNA-seq data is also leading to a step change in the analysis of alternative splicing in plants and we are currently working with Professor John Brown’s group to analyse RNA seq data sets from a range of tissues to identify the extent and significance of transcript diversity in barley.  New sequencing technologies have also enabled Whole Genome shotgun sequencing of our target genomes as well as novel approaches to diversity analysis through Genotyping by Sequencing (GbyS) or Exome Capture and re-sequencing.   The resulting availability of more extensive genome sequence resources is currently underpinning major new developments in the characterisation of key gene families in our target crops.  

Past research

 In the last five years the major achievements of our team has been in a) the development of software tools to support the analysis of genotype and sequence data. Particularly good examples of this are  Flapjack(Milne et al,  2010b)  which has been widely adopted as the graphical genotyping standard by  the international plant breeding and genetics communities and Tablet (Milne et al, 2010b)  which is widely used by researchers  for the visualization of NGS assemblies and mappings. b) The establishment of  genomics resources that have been widely abopted by researchers in our target crops. A key example is the recent development of  barley  9K iSelect genotyping array (Comdran et al., 2012). Finally the translation of  these resources and tools in to  major new advances in our target organisms e.g. (Ramsay et al, 2011)   


  • Milne, I.; Bayer, M.; Stephen, G.; Cardle, L.; Marshall, D. (2016) Tablet: visualizing next-generation sequence assemblies and mappings., In: Edwards, D. (ed.). Plant Bioinformatics: Methods and Protocols, Methods in Molecular Biology. Springer Science+Business Media, New York, 14, pp253-268.
  • Marshall, D.F.; Hillman, J.R. (2000) New concepts and approaches to biodiversity., In: Biodiversity. New Leads for the Pharmaceutical and Agrochemical Industries (eds. S.K. Wrigley, M.A. Hayes, R. Thomas, E.J.T. Chrystal and N. Nicholson). Royal Society of Chemistry, Cambridge, pp17-21.

  • Hollingsworth, P.M.; O’Brien, D.; Ennos, R.A.; Yahr, R.; Neaves, L.; Ahrends, A; Ballingall, K.T.; Brooker, R.W.; Burke, T.; Cavers, S.; Dawson, I.K.; Elston, D.A.; Kerr, J.; Marshall, D.F.; Pakeman, R.J.; Trivedi, C.; Wall, E.; Wright, F.; Ogden R. (2020) Scotland's biodiversity progress to 2020 Aichi targets. Conserving genetic diversity - Development of a national approach for addressing Aichi biodiversity target 13 that includes wild species., Scottish Natural Heritage, Inverness, 33pp.
  • Thomas, W.T.B.; Comadran, J.; Ramsay, L.; Shaw, P.; Marshall, D.F.; Newton, A.C.; O'Sullivan, D.; Cockram, J.; Mackay, I.; Bayles, R.; White, J.; Kearsey, M.J.; Luo, Z.; Wang, M.; Tapsell, C.; Harrap, D.; Werner, P.; Klose, S.; Bury, P.; Wroth, J.; Argilllier, O.; Habgood, R.; Glew, M.; Bochard, A-M.; Gymer, P.; Vequaud, D.; Christerson, T.; Allvin, B,; Davies, N.; Broadbent, R.; Brosnan, J.; Bringhurst, T.; Booer, C.; Waugh, R. (2014) Association genetics of UK elite barley (AGOUEB)., Final Project Report to HGCA, No 528, 125pp.
  • Ramsay, L.; Thomas, W.T.B.; Comadran, J.; Marshall, D.F.; Shaw, P.; Waugh, R. (2011) Genetic diversity in modern barley varieties., Annual Report of the Scottish Crop Research Institute for 2010, pp23-24.
  • Milne, I.; Shaw, P.; Milne, L.; Bayer, M.; Stephen, G.; Marshall, D.F. (2010) Visualising genetic diversity., Annual Report of the Scottish Crop Research Institute for 2009, pp21-22.
  • Ramsay, L.; Rostoks, N.; Marshall, D.F.; Mudie, S.; Close, T.J.; Waugh, R. (2006) Breeding facilitates whole genome LD-mapping., Annual Report of the Scottish Crop Research Institute for 2006, pp16-17.
  • Macaulay, M.; Russell, J.R.; Ramsay, L.; Marshall, D.F.; Powell, W.; Waugh, R.; Thomas, W.T.B. (2004) Lessons from barley recommended lists., Annual Report of the Scottish Crop Research Institute for 2003/2004, pp144-145.
  • Caldwell, D.; McCallum, N.; Mudie, S.; Hedley, P.E.; Ramsay, L.; Liu, H.; Marshall, D.F.; Waugh, R. (2002) A physical/chemical mutation grid for barley functional genomics., Annual Report of the Scottish Crop Research Institute for 2001/2002, pp157-158.
  • Ramsay, L.; Hedley, P.E.; Liu, H.; McCallum, N.; Mudie, S.; Cardle, L.; Harrower, B.E.; Machray, G.C.; Marshall, D.F.; Waugh, R. (2002) Barley transcriptome resources., Annual Report of the Scottish Crop Research Institute for 2001/2002, pp151-152.
  • Cardle, L.; Macaulay, M.; Marshall, D.F.; Milbourne, D.; Ramsay, L.; Waugh, R. (2000) SSR frequency and occurrence in plant genomes., Annual Report of the Scottish Crop Research Institute for 1999/2000, pp108-110.
  • De Jong, W.; Davidson, J.; Bryan, G.J.; Birch, P.R.J.; Waugh, R.; Marshall, D.F. (2000) Gene discovery in potato., Annual Report of the Scottish Crop Research Institute for 1999/2000, pp105-107.
  • Squire, G.R.; Augustin, N.; Bown, J.; Crawford, J.C.; Dunlop, G.; Graham, J.; Hillman, J.R.; Marshall, B.; Marshall, D.F.; Ramsay, G.; Robinson, D.J.; Russell, J.R.; Thompson, C.; Wright, G.M. (1999) Gene flow in the environment: genetic pollution?, Annual Report of the Scottish Crop Research Institute for 1998/99, pp45-54.

Scientific Posters / Conferences

File Arabidopsis Databases at the Scottish Crop Research Institute (SCRI) 889.25 KB
File Barley SNP Databases and GVT 2.05 MB
File The Plant Genomics Database Infrastructure at the Scottish Crop Research Institute 424.92 KB
File An update on the GERMINATE project the database and tools 791.72 KB
File The Genotype Visualisation Tool (GVT) 1.07 MB
File Germinate: A Database for Plant Genetic Resources 1.86 MB
File Determination of non-steady-state fluxes and kinetic information using stable isotope labelling and metabolite pool size data: theory and application 212.02 KB
File The Visualization and Analysis of Barley SNPs 817.23 KB
File Barley Mutant and SNP Databases at SCRI 993.59 KB
File The Plant Genomics Database Infrastructure at the Scottish Crop Research Institute 213.29 KB
File Single nucleotide polymorphism discovery and mapping in barley 4.01 MB
File Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress 4.63 MB
File Germinate 2 A Platform for Storage and Analysis of Experimental Plant Data 4.72 MB
File Association Genetics of UK Elite Barley 877.79 KB
File Germinate CPC
The Commonwealth Potato Collection database at SCRI
5.3 MB
File Hordeum Relator a visualization tool for relating unigene datasets 217.57 KB
File Hordeum Relator: a visualization tool for relating unigene datasets 210.52 KB
File Bioinformatics Resources at the Scottish Crop Research Institute 1.58 MB
File Germinate 2: Storage Visualization and Analysis of High Volume Genotypic Phenotypic and Pedigree Data 992.31 KB
File Integration of Experimental Plant Data to Develop Novel Visualizations for Genetic Analysis of Quantitative Traits 1.41 MB
File Tablet Flapjack CurlyWhirly and Strudel : SCRI Visualization Tools To Support SNP Discovery 4.74 MB
File Association Genetics of UK Elite Barley (AGOUEB) 429.19 KB
File Flapjack 4.15 MB
File Steptoe x Morex - the weakest link? 1.11 MB

Printed from /staff/david-marshall on 08/02/23 09:10:45 PM

The James Hutton Research Institute is the result of the merger in April 2011 of MLURI and SCRI. This merger formed a new powerhouse for research into food, land use, and climate change.