• West Mains Road, Kings Buildings, Peter Wilson Building

    EH9 3JG Edinburgh

    United Kingdom

1980 …2020

Research activity per year

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Personal profile

Research interests

I have a research career spanning 36 years focused on plant genomics and understanding patterns of genetic diversity in wild and cultivated plants. A major focus of my work is developing and utilising software tools to analyze SNP variation in crop plants and their wild relatives in genetic resources and breeding applications. As a valuable byproduct of this work, the research team which I led gained an international reputation for the development of visualization approaches to understanding complex patterns of genetic diversity. The software tools we developed are in routine use with an extensive range of university and research institutes, as well as many plant breeding and biotechnology companies, around the world.


Recent projects I have participated in include working with the Crop Trust to provide public access to the data generated by their Crop Wild relatives project funded by the Norwegian Government; working with CIMMYT to develop the software infrastructure to support the MasAgro Seeds of Discovery Project and a portal for access to data generated through the International Wheat Yield Partnership; working on BBSRC funded Newton projects with NIAB, the Earlham Institute CIAT and CIMMYT to develop and deploy tools to support the analysis of molecular diversity data from their genetic resource collections; working with Cornell University, CIMMYT, ICRISAT and IRRI as part of the BMGF funded GOBII project to develop the computational infrastructure to support modern molecular breeding programs; and Biometris at WUR and VSNi to develop analysis workflows to underpin breeding programs.  I have worked with both the CGIAR Genebank and Excellence in Breeding Platforms to help define their priorities and current workplans.  I have advisory roles for the Malaysian Rubber Board, the Malaysian, Palm Oil Board, the BMGF AfricaYam Project and the ITPGRFA’s Global Information System.

Previous employer

Senior Research Scientist, James Hutton Institute, 50% part post

Head of Information & Computational Sciences, James Hutton Institute

Associate Programme Leader, Genetics Programme, SCRI

Director, Postgraduate Studies, SCRI

Bioinformatics Theme Leader, Genetics Programme, SCRI

Leader, Computational Biology Programme, SCRI

Deputy Head, Genomics Unit, SCRI

Head of Bioinformatics and IT Unit, SCRI

Programme Manager, BBSRC Plant and Animal Genome Analysis Initiative

Lecturer, Department of Genetics, University of Birmingham

NERC Postdoc, Department of Genetics, University of Birmingham

Demonstrator, Department of Agricultural Botany, UCW, Aberystwyth


I have developed and teach both Postgraduate Modules and Advanced Courses focussed on Bioinformatics Applications in Plant Breeding as well as short training courses  for  a number of software tools supporting genetics and genomics applications in plant breeding and plant genetic resources.

Education/Academic qualification

PhD, University of St Andrews

Award Date: 21 Jul 1982

Bachelor, University of St Andrews

Award Date: 2 Jul 1976


  • QK Botany
  • Plant Gentics
  • Plant Genomics
  • Plant Bioinformatics


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  • Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints

    Sansaloni, C., Santos, B., Percival-Alwyn, L., Singh, S., Petroli, C., Dreher, K., Payne, T., Marshall, D., Kilian, B., Milne, I., Raubach, S., Shaw, P. D., Stephen, G., Carling, J., Saint Pierre, C., Burgueno, J., Crosa, J., Li, H., Guzman, C., Kehel, Z., & 7 othersAmri, A., Kilian, A., Wenzl, P., Uauy, C., Banziger, M., Caccamo, M. & Pixley, K., 11 Sep 2020, (First published) In: Nature Communications. 11, 4572.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    59 Citations (Scopus)
    18 Downloads (Pure)
  • From bits to bites: Advancement of the Germinate platform to support prebreeding informatics for crop wild relatives

    Raubach, S., Kilian, B., Dreher, K., Amri, A., Bassi, F. M., Boukar, O., Cook, D., Cruickshank, A., Fatokun, C., El Haddad, N., Humphries, A., Jordan, D., Kehel, Z., Kumar, S., Labarosa, S. J., Nguyen, L. H., Mace, E., McCouch, S., McNally, K., Marshall, D. F., & 15 othersMikwa, E. O., Milne, I., Odeny, D. A., Plazas, M., Prohens, J., Rieseberg, L. H., Schafleitner, R., Sharma, S., Stephen, G., Tin, H. Q., Togola, A., Warschefsky, E., Werner, P., All our CWR Pre-Breeding Partners and Collaborators & Shaw, P. D., 20 Aug 2020, (First published) In: Crop Science. 61, 3, p. 1538-1566 29 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    18 Citations (Scopus)
    32 Downloads (Pure)
  • Genomics of Rubber Biosynthesis in Hevea brasiliensis

    Chow, K-S., Bahari, A., Taylor, M. A. & Marshall, D., 31 May 2020, The Rubber Tree Genome.. Chow, KS. & Matsui, M. (eds.). Springer, p. 93-115 22 p. (Compendium of Plant Genomes).

    Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

  • BrAPI - an application programming interface for plant breeding applications

    Selby, P., Abbeloos, R., Backlund, J. E., Basterrechea Salido, M., Bauchet, G., Benites-Alfaro, O., Birkett, C., Calaminos, V. C., Carceller, P., Cornut, G., Vasques Costa, B., Edwards, J. D., Finkers, R., Gao, S. Y., Ghaffar, M., Glaser, P., Guignon, V., Hok, P., Kilian, A., König, P., & 30 othersLagare, J. E. B., Lange, M., Laporte, M-A., Larmande, P., LeBauer, D., Lyon, D., Marshall, D., Matthews, D., Milne, I., Mistry, N., Morales, N., Mueller, L., Neveu, P., Papoutsoglou, E., Pearce, B., Perez-Masias, I., Pommier, C., Ramirez-Gonzalez, R. H., Rathore, A., Raquel, A. M., Raubach, S., Rife, T., Robbins, K., Rouard, M., Sarma, C., Scholz, U., Sempéré, G., Shaw, P., Simon, R. & Soldevilla, N., 15 Oct 2019, In: Bioinformatics (Oxford, England). 35, 20, p. 4147-4155 9 p., btz190.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    46 Citations (Scopus)
    25 Downloads (Pure)
  • RNAi-suppression of barley caffeic acid O-methyltransferase modifies lignin despite redundancy in the gene family

    Daly, P., McClellan, C., Maluk, M., Oakey, H., Lapierre, C., Waugh, R., Stephens, J., Marshall, D., Barakate, A., Tsuji, Y., Goeminne, G., Vanholme, R., Boerjan, W., Ralph, J. & Halpin, C., Mar 2019, In: Plant Biotechnology Journal. 17, 3, p. 594-607 14 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    19 Citations (Scopus)
    22 Downloads (Pure)