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Stuart MacFarlane

Staff picture: Stuart MacFarlane
Cell and Molecular Sciences
Cell and Molecular Sciences
Research Scientist
+44 (0)344 928 5428 (*)

The James Hutton Institute
Dundee DD2 5DA
Scotland UK


Current research interests

  • Plant viruses are widespread in the natural environment and exhibit enormous variation in their structure and composition. Agricultural crops are under constant attack from viruses making an understanding of virus biology a necessity for devising new, more effective approaches to prevent virus disease in plants.
  • Current work includes a range of studies of viruses of raspberry, an important crop in Scotland in terms of both economics and nutritional health. Viruses are a major cause of disease in raspberry and other woody perennial crops and over time their disease impact increases as the plants become infected with mixtures of different viruses. We have characterised a number of viruses that are known to exist in the UK raspberry crop but are not well understood, (Black raspberry necrosis virus (BRNV), Raspberry leaf mottle virus (RLMV) and Raspberry vein chlorosis virus (RVCV)), to develop molecular diagnostics to be used in The James Hutton Institute High Health Certification Scheme. We also have generated an infectious clone system to aid research into Raspberry bushy dwarf virus (RBDV), a virus of great importance to the raspberry industry because of its involvement in crumbly fruit disease.
    Recently we discovered a new, negative-strand RNA virus that is transmitted by eriophyid mites and is responsible for the emerging problem of leaf blotch disorder in many raspberry plantations. This new virus, Raspberry leaf blotch virus (RLBV), belongs to a newly identified group of plant viruses that cause disease in a wide variety of important crops. The molecular structure of these plant viruses shows that they are related to an important group of human and animal-infecting viruses, the bunyaviruses, and further study of RLBV may reveal parallels between the infection processes of these different viruses.
  • New work has been started to study the resistance reactions of different potato cultivars to aphid-transmitted viruses, such as PVY, and to the nematode-transmitted virus, TRV, which causes spraing in potato tubers.

Past research

  • In recent years I have researched the mechanism of action of the P19 protein of Tomato bushy stunt virus (TBSV). This is a pathogenicity protein that has a role in suppression of RNA silencing, symptom production in plants, and long- and short-distance movement of the virus within the plant. We have discovered an interaction between P19 and members of the ALY family of plant proteins.
  • Other aspects of my research have included fundamental studies, primarily on Tobacco rattle virus (TRV), an important pathogen of potatoes in Scotland, Europe and North America, and Pea early-browning virus (PEBV), to understand the mechanism of transmission of these viruses by nematodes, a process that is central to the diseases they cause in the field.
  • More recently it has been realised that plant viruses can be developed into tools that have great potential for functional genomic analysis of plants. I have engineered TRV, and the related viruses PEBV and Pepper ringspot virus (PepRSV), to be useful as vectors for gene expression and gene silencing in a variety of plant species.


  • Dolan, A.; MacFarlane, S.; Jennings, S.N. (2018) Pathogens in raspberry and other Rubus spp., In: Graham, J. & Brennan, R. (eds.). Raspberry: Breeding, Challenges and Advances. Springer International Publishing, Cham, Chapter 4, pp41-61.
  • MacFarlane, S.A.; Zasada, I.A.; Lemaire, O.; Demangeat, G. (2016) Nematode-borne plant viruses., In: Brown, J.K. (ed.). Vector-Mediated Transmission of Plant Pathogens. American Phytopathological Society Press, St. Paul, MN., 365-378.
  • MacFarlane, S.; McGavin, W.; Tzanetakis, I. (2015) Virus-testing by PCR and RT-PCR amplification in berry fruit., In: Lacomme, C. (ed.). Plant Pathology: Techniques and Protocols. (Methods in Molecular Biology, 1302) Springer, New York, 227-248.
  • MacFarlane, S.A. (2009) Rubus viruses: Blackberry chlorotic ringspot virus (BCRV)., American Phytopathological Society, Minesota, USA, Volume 2.
  • MacFarlane, S.A.; Neilson, R. (2009) Testing of transmission of Tobraviruses by nematodes., In: Coico, R., Kowalik, T., Quarles, J.M., Stevenson, B. & Taylor, R.K. (eds.). Current Protocols in Microbiology. John Wiley & Sons, Inc., Chichester, UK, Chapter Suppl 12, 16B.5.1-16B.5.16.
  • MacFarlane, S.A. (2008) Tobravirus., In: Mahy, W.J. & Van Regenmortel, M.H.V. (eds.). Encyclopedia of Virology. 3rd edition. Elsevier, Oxford, Chapter 5, 72-76.
  • Uhrig, J.F.; MacFarlane, S.A. (2008) Protein-protein interactions in plant virus movement and pathogenicity., In: Nautiyal, C.S. & Dion, P. (eds.). Molecular Mechanisms of Plant and Microbe Coexistence. Springer, Dordrecht, Chapter 15, 319-338.
  • MacFarlane, S.A.; Uhrig, J.F. (2008) Yeast two-hybrid assay to identify host-virus interactions., In: Foster, G.D., Johansen, I.E., Hong, Y. & Nagy, P.D. (eds.). Plant Virology Protocols: From viral sequence to protein function. 2nd edition. Humana Press, Totowa, New Jersey, Chapter 44, pp649-672.
  • Palukaitis, P.; MacFarlane, S.A. (2006) Viral counter-defense molecules., In: Loebenstein, G. & Carr, J.P. (eds.). Natural Resistance Mechanisms of Plants to Viruses. Springer, Berlin, pp165-185.
  • MacFarlane, S.A.; Neilson, R.; Brown, D.J.F. (2002) Nematodes., In: Plumb, R.T. (ed.). Advances in Botanical Research - Plant Virus Vector Interactions. Academic Press, 36, 169-198.
  • MacFarlane, S.A.; Neilson, R.; Brown, D.J.F. (2002) Plant Virus Vector Interactions., In: Plumb, R.T. (eds.). Advances in Botanical Research No 36 - Interctions Between Plant Viruses and Their Vectors. Academic Press, London and New York, pp169-198.
  • MacFarlane, S.A. (1997) Natural recombination among plant virus genomes: evidence from tobraviruses., In: Mayo, M.A. (ed.). Aspects of ssRNA Virus Genome Organization. Academic Press, pp25-31.

  • Dolan, A.; MacFarlane, S.A.; Pitkin, Y.; McGavin, W.J. (2011) Validation of an improved diagnostic test to accelerate the certification of blackcurrant (Ribes nigrum L.) plants for breeding and propagation., Annual Report of the Scottish Crop Research Institute for 2010, pp28-29.
  • MacFarlane, S.A.; McGavin, W.J.; Dolan, A. (2008) Discovering new viruses in raspberry crops., Annual Report of the Scottish Crop Research Institute for 2007, pp28-29.
  • Kim, S.; Ryabov, E.V.; Gillespie, T.; MacFarlane, S.A.; Haupt, S.; Brown, J.W.S.; Taliansky, M.E. (2007) Nuclear voyage of a plant virus protein., Annual Report of the Scottish Crop Research Institute for 2006, pp22-23.
  • Reavy, B.; MacFarlane, S.A. (2001) Cross-kingdom activity of plant virus-encoded silencing suppressors., Annual Report of the Scottish Crop Research Institute for 2000/2001, pp120-123.
  • MacFarlane, S.A.; Brown, DJ.F.; Vassilakos, N.; Mooney, A.; Schmitt, C.; Mueller, A.; Prior, D.A.M.; Oparka, K.J. (1998) Molecular biology of the tobravirus genome., Annual Report of the Scottish Crop Research Institute for 1997/98, pp129-131.

  • Karley, A.J.; Graham, J.; Mitchell, C.; Williams, C.; Mitchell, D.; Jennings, N.; Dolan, A.; McFarlane, S.; Prashar, A.; Begg, G.; Birch, A.N.E. (2018) IPM tools for pest and disease management in raspberry plantations., Crop Protection in Northern Britain 2018: The Dundee Conference, Environmental Management and Crop Production, Apex City Quay Hotel, Dundee, 27-28 February 2018. Conference Proceedings, pp55-58.
  • Taliansky, M.E.; Shaw, J.; Kim, S.; Ryabov, E.; Kalinina, N.O.; MacFarlane, S.A.; Brown, J.W.S. (2011) Involvement of the cell nucleus in plant virus systemic infections., Society for General Microbiology Spring Conference, Harrogate, 11-14 April 2011. Session: Seeing the cell through the Eyes of the Virus.
  • McMenemy, L.S.; MacFarlane, S.A.; Hartley, S.E.; Johnson, S.N. (2009) Co-operation between plant enemies - do raspberry viruses attract more aphid vectors., 8th International Symposium on Aphids, Catania, Italy, 8-12 June 2009.
  • McMenemy, L.S.; MacFarlane, S.A.; Hartley, S.E.; Johnson, S.E. (2009) Plant mediated interactions with the large raspberry aphid., Ento'09 National Meeting of the Royal Entomological Society, University of Sheffield, 15-17 July 2009.
  • McMenemy, L.S.; Johnson, S.N.; Hartley, S.E.; MacFarlane, S.A. (2008) Cooperation between plant enemies - do raspberry viruses attract more aphid vectors?., British Ecological Society Annual Meeting 2008, Imperial College, London, 3-5 September 2008.
  • Kim, S.; MacFarlane, S.A.; Kalinina, N.; Rakitina, D.V.; Ryabov, E.; Gillespie, T.; Haupt, S.; Brown, J.W.S.; Taliansky, M.E. (2007) Interaction between a plant virus-encoded protein and the major nucleolar protein fibrillarin, is required for virus systemic infection., AAB Advances in Virology, University of Greenwich, 11-12 September 2007.
  • Taliansky, M.E.; Kim, S.; Ryabov, E.V.; Kalinina, N.; Rakitina, D.V.; Gillespie, T.; MacFarlane, S.A.; Brown, J.W.S. (2006) Involvement of the nucleolus in plant virus systemic infection., EMBO Workshop 'The Nucleolus: New Perspectives'. York, 27-30 March 2006.
  • Kim, S.; Ryabov, E.V.; MacFarlane, S.A.; Kalinina, N.O.; Rakitina, D.V.; Gillespie, T.; Brown, J.W.S.; Taliansky, M.E. (2006) Involvement of the nulceolus in Umbravirus long-distance movement., Plasmodesmata 2006, Pitlochry, 30 July - 3 August 2006.
  • MacFarlane, S.A.; Robinson, D.J. (2004) Transmission of plant viruses by nematodes., In: Gillespie, S., Smith, G.L. & Osbourn, A. (eds.). SGM Symposium 63, Microbe-Vector Interactions in Vector-Borne Diseases. Cambridge University Press, pp263-285.
  • Palukaitis, P.; Canto, T.; MacFarlane, S.A. (2004) Further characterization of the TMV4.8 kDa protein., Abstracts of the 23rd Annual Meeting of the American Society for Virology, Montreal, Quebec, Canada, 10-14 July 2004.
  • Birch, P.R.J.; Blok, V.C.; Phillips, M.; Jones, J.T.; Stewart, H.E.; Duncan, J.M.; Bryan, G.J.; Waugh, R.; Lyon, G.D.; MacFarlane, S.A.; Avrova, A.O.; Whisson, S.C.; Toth, I.K. (2003) Current and future research at SCRI on the molecular genetics of the interactions between potato and its major pathogens., Acta Horticulturae, 619, 95-119.
  • Palukaitis, P.; Canto, T.; MacFarlane, S.A. (2003) Pathogenicity and localization of the tobacco mosaic virus 4,8 kDa protein., Proceedings of the Korean Society of Plant Pathology, Annual Regular Meeting and Special Scientific Presentations, Dunnae, Korea, 9-11 October 2003.
  • Karanastasi, E.; Roberts, I.M.; MacFarlane, S.A.; Brown, D.J.F. (1999) The location of specifically retained tobacco rattle virus particles in the oesophageal tract of the vector., Proceedings of the Zoological Institute, Russian Academy of Sciences,St Petersburg, Russia, 280, 107-108.
  • Karanastasi, E.; Roberts, I.M.; MacFarlane, S.A.; Brown, D.J.F. (1998) Staining with safranin: a new approach to handling nematodes., Proceedings of the 21st Congresso Brasileiro de Nematologia, Maringa, Brazil, 55-56.

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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.