Research

  • Dissecting the role of light signalling in plant immunity
  • Characterising Phytophthora rubi: Root rot disease of Raspberry and sustainable methods of crop protection
  • Investigating the role of effectors and their host targets in manipulating plant disease resistance
  • Exploring crosstalk between development and plant disease resistance

 

Dissecting the role of light signalling in plant immunity

Light is essential for regulating every aspect of plant growth and development. Recent studies have revealed that light quality and duration can influence plant immune response onset as well as the virulence of some pathogens.  Phytophthora infestans, the casual agent of Potato Late Blight, secretes effector proteins characterised by an RXLR motif which are translocated into host cells during infection to manipulate the host to benefit the pathogen. A number of RXLR effectors target host proteins with roles in light-mediated responsesto both blue and red light. Thus, pathogen effectors are tools to reveal the strategies by which pathogens can remodel light and immunity responsiveness in their hosts.

Potato NRL protein for chloroplast movement (NCH1) is targeted by a P. infestans RXLR Pi02860 effector.

The effector protein, Pi02860 from P. infestans, targets a potato NON-PHOTOTROPIC HYPOCOTYL 3 (NPH3) and ROOT PHOTOTROPISM 2 (RPT2)-like (NRL) family member, which is an orthologue of Arabidopsis NCH1. NRLs are widespread in land plants and often act as substrate adaptors for the Cullin-RING E3 ubiquitin ligase (CUL3) complex involved in protein ubiquitination. RPT2 and NCH1 are NRL family members known to transduce signals from the blue light receptors, phototropins to regulate chloroplast movement.

Potato Phytochrome B is targeted by a P. infestans RXLR effector, Pi06099.

The essential effector protein, Pi06099 from P. infestans interacts with Potato Phytochrome B to suppress immunity. Phytochrome B is synthesised in its inactive form and is activated by red light. Phytochrome B is involved in regulating germination, inhibition of elongation, shade avoidance, chloroplast development, leaf expansion, flowering, JA and SA signalling, disrupts COP1/SPA complex and differentially modulates PIF and HY5 transcription factor activities. We are currently investigating the role of Pi06099 on red light-regulated immunity that could be exploited to boost crop immunity.

In collaboration with Paul Birch, Gabriela Toledo-Ortiz, Ingo Hein and Gaynor McKenzie we are currently investigating the role of light quality, intensity and duration on plant development and plant health. We will be investigating the diversity of these responses in Solanum accessions from our Commonwealth Potato Collection.

Phytophthora rubi: insight into root rot of raspberry

At least 90 species of Phytophthora have been isolated from a wide range of horticultural crop plants worldwide and improvements in molecular diagnostics are continually identifying more. Although several species of Phytophthora can infect raspberry (P. syringae, P. drechsleri, P. cactorum, P. cambivora and P. megasperma), P. rubi is the most common causal agent of the devastating root rot and cane death disease in raspberry.  P. rubi belongs to clade 7 of the Phytophthora (“plant destroyer”) phylogeny along with other root rot causing Phytophthoras of warmer climates such as P. cinnamomi and P. sojae.

Raspberry root rot disease, first identified in Europe in the 1980s, is now a widespread contaminant of established raspberry plantations and the disease, once established is extremely difficult to control. The major impact of root rot disease is causing a rapid decline in raspberry plantations grown in soil by more than 70%. Farmers worldwide are being driven to switch to annual replenishment of pot-based systems or adapting to growing alternative fruit crops. Europe is the largest producer of raspberries worldwide and the industry (worth est. €2.2 billion) is being devastated by root rot disease. See Raspberry genetics for more information.

Understanding how organisms distinguish friend from foe is one of the key and fascinating questions in biology. I am currently building a team to investigate the population genomics of P. rubi, determine its pathogenicity arsenal and better understand the enigmatic relationship between root infecting oomycetes and the host rhizosphere.

Visit the following pages for additional information: Julie Graham, Craig Simpson, Linda Milne, Susan Macallum, Ingo Hein and Steve Whisson.

Can soft fruit species engage with beneficial microorganisms and restrict oomycete pathogens? (2022-2026)

Arbuscular mycorrhizal fungi (AMF) grow in association with the roots of over 70% of plant species. These fungi form a network of hyphae which supplies nutrients and water to the plants, while the plants supply hydrocarbons to the fungi. However, impacts go far beyond this exchange and AMF can impact almost every aspect of plant growth and health.  This project aims to investigate the AMF species and isolates which associate with raspberry plants and determine their impact on plant growth and the development of phytophthora root rot.

Studying the mechanism of auxin regulated resistance in Raspberry Root Rot caused by Phytophthora rubi  (2019-2023)

This study aimed at understanding the mechanism of host resistance in raspberry during PRR development. RNA-sequencing was utilised to study host and pathogen responses at a molecular level. The transcriptional response of raspberry roots to P. rubi infection was examined in a resistant (Latham) and a susceptible (Glen Moy) cultivar. Several pathogenesis-related (PR) genes, along with a selected number of auxin-related genes, were significantly upregulated in infected Latham, prompting an inquiry into the influence of auxin on the pathogen and root-pathogen system. To assess auxin’s impact on pathogen growth, P. rubi isolates were screened with different chemicals related to auxin or auxin transport inhibitors. Analysing transcriptional responses of the pathogen to these treatments led to the identification of important genes that may have a putative role in fungicide resistance. Furthermore, the host transcriptional response to infection and treatment with an auxin transport inhibitor, was studied. This led to the identification of PR genes and auxin-related genes related to host resistance. Several genes upregulated in infected Latham were also upregulated in auxin transport inhibitors + infected roots. Moreover, a gene encoding a germin-like auxin-binding protein, ABP19 was highly expressed under both experimental conditions which was found to be closely located to a root rot resistant marker in Latham. Raspberry ABP19 genes were characterised and their role in host resistance was investigated.

Advances made in the understanding of the biology and genetics of Phytophthora rubi and Phytophthora fragariaePhD Project (2017-2021)

This project aimed to increase the understanding of P. rubi and P. fragariae. Phenotypic studies showed their potential to adapt to current control chemicals and to changing climatic conditions. Parallel genetic studies, using target enrichment sequencing on pathogen sequences associated with virulence (PenSeq), found evidence for variation in the effector families between and within species and suggests that P. rubi has significant potential for adaptation and evolution to adjust to environmental stresses in the field. Finally a propagate raspberries was developed, using hydroponics systems, to grow soft fruits disease-free in fully controlled environments for infection assays. This allowed us to follow the life cycle of P. rub,i in a number of Raspberry cultivars with ranging susceptibilities and root architecture,  using recently generated GFP and TdT expressing fluorescent strains.

This work provides scientific knowledge to help strengthen the horticultural industry by supporting the existing raspberry breeding programmes at JHL (Nikki Jennnings) and development of novel pathogen control approaches with the soft fruit genetics group.

These projects are linked to on going activities funded by RESAS in JHI-B1-1: Protecting Scotland’s crops – Disease Resistance and Pathogen Biology.

  • WP2-Objective 1: Pathogen Biology (potato and soft fruit): examining the lifecycle, infection process using fluorescent microbes and mechanism of resistance
  • WP2-Objective 2: Effector research (potato and soft fruit): identifying effector diversity in softfruit infecting phytophthoras and examining function for P. infestans effectors.
  • WP2-Objective 3: Understanding and enhancing the plant immune system: determining the crosstalk between major signalling pathways and how effectors are manipulating these to cause disease
  • WP3-Objective 2: The role of beneficial microbes in protecting soft fruit: Investigating how the interaction between soft fruit and AMFs may influence the infection process of P. rubi/P. fragariae

Work package lead for WP3: Plant Soil interface

Past research

UKRI Crop Pest and Disease 2022 “Seeking new tools to manipulate soil and root microbiology for biocontrol of soft fruit Phytophthora diseases” with Susan McCallum, Andy Taylor, Julie Graham

Innovate UK grant 48163- “RASP” Examining the link between root architecture and auxin on Raspberries resistance to root rot pathogen P. rubi

BSA Rural Community Event “Super Spud” 12th March 2023

BSPP knowledge exchange grant “Super Spuds” exhibit and teaching resources. Funded generation of graphics, teaching resources and primary school visit and activity. 2023

Investigating the virulence function of P. infestans effectors in the manipulation of the host to cause disease (2008-2020)

  • PiAvr2, recognition by R2 family, MCQ1 and maniupulation of host targets in the Brassinosteroid (BR) Pathway
  • Potato ortholog of VASCULAR HIGHWAY1-interacting kinase (StVIK), is a MAP3K required for the Phytophthora infestans Effector Pi17316 to Promote Disease

Genomia Fund (2013-2016) with Industrial Support

  • Activating and guarding the Brassinosteroid pathway as a novel means to protect plants against disease.

Publications

Journals

Books / chapters

  • Feechan, A.; Turnbull, D.; Stevens, L.J.; Engelhardt, S.; Birch, P.R.J.; Hein, I.; Gilroy, E.M. (2015) The hypersensitive response in PAMP- and effector-triggered immune responses., In: Gunawardena, A. & McCabe, P. (eds.). Plant Programmed Cell Death. Springer, New York, Chapter 10, pp235-258.
  • Toth, I.K.; Moleleki, L.N.; Pritchard, L.; Liu, H.; Humphris, S.N.; Hyman, L.; Axelsen, G.W.; Brurberg, M.B.; Ravensdale, M.; Gilroy, E.M.; Birch, P.R.J. (2006) Erwiniae: genomics and the secret life of a plant pathogen., In: Bailey, M.J., Lilley, A.K., Timms-Wilson, T.M. & Spencer-Phillips, P.T.N. (eds.). Microbial Ecology of Aerial Plant Surfaces. CABI Publishing, Wallingford, pp191-201.

Technical / contract reports

  • Hrubikova, K.; Gilroy, E.M.; Faivre-Rampant, O.; Loake, G.; Birch, P.R.J.; Taylor, M.A.; Lacomme, C. (2003) Viral induced gene silencing in crop species., Annual Report of the Scottish Crop Research Institute for 2002/2003, pp98-99.

Conference papers

  • Chen, X.; Bayer, M.; Harrower, B.; Stevens, L.; Chapman, S.; Gilroy, E.; van Weymers, P.; Jupe, F.; Witek, K.; Jones, J.; Birch, P.; Bryan, G.; Hein, I. (2014) Using the potato genome to map and clone durable resistance genes more rapidly., Crop Protection in Northern Britain, Environmental Management and Crop Protection, West Park Conference Centre, Dundee, 25-26 February 2014.
  • Turnbull, D.; Breen, S.A.; Naqvi, S.; Armstrong, M.R.; Engelhardt, S.; Brunner, F.; Birch, P.R.J.; Gilroy, E.M. (2014) Phytophthora infestans effector PiAVR2 targets StBSL1 to activate the Brassinosteriod pathway., XVI International Congress on Molecular Plant-Microbe Interactions 2014, Rhodes, Greece, 6-10 July 2014.
  • Turnbull, D.; Breen, S.A.; Naqvi, S.; Yang, L.; Murphy, F.S.; Armstrong, M.R.; Engelhardt, S.; Welsh, L.; Hein, I.; Zhan, J.; Birch, P.R.J.; Gilroy, E.M. (2014) Pumped up on (brassino) steroids: multiple Phytophthora infestans effectors manipulate the Brassinosteroid pathway in potato., FESPB/EPSO 2014 Congress, The Convention Centre, Dublin, 22-26 June 2014.
  • Whisson, S.C.; Gilroy, E.M.; Avrova, A.O.; Tian, Z.D.; Breen, S.; Armstrong MR.; Squires, J.; Vieeshouwers, V.; McLellan, H.; Seman, Z.; Kandel, K.; Boevink, P.C.; Pritchard, L.; Hein, I.; Cooke, D.E.L.; Birch, P.R.J.; (2011) Phytophthora infestans effectors in late blight disease development and exploitation for disease control., 18th Triennial Conference of the European Association for Potato Research, Oulu, Finland, 24-29 July 2011.
  • Toth, I.K.; Birch, P.R.J.; Pritchard, L.; Liu, H.; Hedley, P.E.; Humphris, S.; Douglas, E.; Gilroy, E.M.; Moleleki, L.N.; Ravensdale, M.; Hardy, D.; Mayer, C.; Husmeier, D.; Lin, K. (2010) From bully to master tactician: a genomics approach reveals unexpected traits in the life of the bacterial plant pathogen Pectobacterium., IFR Seminar Series. Institute of Food Research, 4 March 2010.
  • Toth, I.K.; Birch, P.R.J.; Pritchard, L.; Humphris, S.N.; Douglas, E.; Gilroy, E.M.; Morris, J.; Hedley, P.E. (2010) Using genomics approaches to investigate the life of the bacterial potato pathogen Pectobacterium atrosepticum., COST 872 Nemagenics. Exploiting genomics to understand plant-nematode interactions, 4th Annual Meeting. Lisbon, Portugal, 24-27 May 2010.
  • Jantsch, C.; Chen, Y.; Gilroy, E.M.; Birch, P.R.J.; Brunner, F. (2010) Identification of Phytophthora infestans RXLR-(EER) effectors suppressing PAMP-triggered immunity., Oomycete Molecular Genetics Network Congress, Toulouse, France, 6-8 June 2010.
  • McLellan, H.; Tian, Z.D.; Avrova, A.O.; Gilroy, E.M.; Pritchard, L.; Whisson, S.C.; Birch, P.R.J. (2010) Identification of RXLR effectors essential for virulence in Phytophthora infestans., Oomycete Molecular Genetics Network Congress, Toulouse, France, 6-8 June 2010.
  • Breen, S.; Gilroy, E.M.; Armstrong, M.R.; Morales, J.G.; Hein, I.; Douglas, E.; Boevink, P.; McLellan, H.; Randall, E.; Tian, Z.D.; Avrova, A.O.; Pritchard, L.; Lokossou, A.A.; Govers, F.; van der Vossen, E.A.G.; Vleeshouwers, V.G.A.A.; Brunner, F.; Whisson, S.C.; Birch, P.R.J. (2010) Avr2, an RXLR effector from Phytophthora infestans., Oomycete Molecular Genetics Network Congress, Toulouse, France, 6-8 June 2010.
  • Armstrong, M.R.; Boevink, P.; Bukharova, T.; McLellan, H.; Ramos, M.; Gilroy, E.M.; Pritchard, L.; Whisson, S.C.; Beynon, J.; Birch, P.R.J. (2010) Identifying candidate host ‘targets’ of Phytophthora infestans translocated RXLR proteins., Oomycete Molecular Genetics Network Congress, Toulouse, France, 6-8 June 2010.
  • Engelhardt, S.; Armstrong, M.R.; Boevink, P.; Ramos, M.; Gilroy, E.M.; Birch, P.R.J. (2010) R3a-mediated recognition of AVR3a: Cell biological and biochemical characterisation., Oomycete Molecular Genetics Network Congress, Toulouse, France, 6-8 June 2010.
  • Gilroy, E.M.; Hein, I.; McLellan, H.; Breen, S.; Engelhardt, S.; Tian, Z.D.; Seman, Z.A.; Pritchard, L.; Armstrong, M.R.; Randall, E.; Avrova, A.O.; Cooke, D.E.L.; Lees, A.K.; Vleeshouwers, V.G.A.A.; van West, P.; Whisson, S.C.; Birch, P.R.J. (2010) Using knowledge of RXLR effectors to seek durable resistance., Oomycete Molecular Genetics Network Congress, Toulouse, France, 6-8 June 2010.
  • Gilroy, E.M.; Breen, S.; Hein, I.; Tian, Z.D.; Armstrong, M.R.; Douglas, E.; Lokossou, A.A.; Boevink, P.; McLellan, H.; Randall, E.; Morales, J.G.; Avrova, A.O.; Pritchard, L.; van der Vossen, E.A.G.; Whisson, S.C.; Birch, P.R.J. (2009) Amino acid polymorphisms upstream of the RXLR motif in Phytophthora infestans effector Avr2 condition R gene recognition., The Fungal Cell, British Mycological Society Meeting, Westpark Conference Centre, Dundee, 1-4 September 2009.
  • Gilroy, E.M.; Armstrong, M.R.; Bos, J.; Taylor, R.; Morales, J.; Hein, I.; Douglas, E.; Boevink, P.; Avrova, A.O.; Breen, S.; van West, P.; Pritchard, L.; Whisson, S.C.; Sadanandom, A.; Kamoun, S.; Birch, P.R.J. (2009) Functional analysis of Phytophthora infestans RXLR effectors Avr2 and Avr3a., Fungal Genetics Conference, Asilomar Conference Grounds, Pacific Grove, California, USA, 17-22 March 2009.
  • Wawra, S.; Phillips, A.J.; Minor, K.; Grouffaud, S.; Bain, J.; Gilroy, E.M.; Robertson, E.J.; Anderson, V.L.; Bruce, C.R.; Grenville-Briggs, L.J.; Homer, N.R.; Whisson, S.C.; Birch, P.R.J.; Porter, A.J.; Secombes, C.J.; van West, P. (2009) Unravelling the mechanism of RXLR mediated translocation of oomycete effector proteins., Fungal Genetics Conference. Asilomar Conference Grounds, Pacific Grove, California, USA, 17-22 March 2009.
  • Hein, I.; Gilroy, E.M.; Whisson, S.C.; Pritchard, L.; Bryan, G.J.; Birch, P.R.J. (2009) Exploiting the Phytophthora infestans genome to determine targets for sustainable potato protection., XIV MPMI Conference, Montreal, Canada, 19-23 July 2009.
  • Birch, P.R.J.; Armstrong, M.R.; Gilroy, E.M.; Bos, J.; Taylor, R.M.; Morales, J.G.; Hein, I.; Douglas, E.; Boevink, P.; Breen, S.; Pritchard, L.; Whisson, S.C.; Sadanandom, A.; Kamoun, S. (2009) Localisation and function of Phytophthora infestans RXLR effectors and their host targets., XIV MPMI Conference, Montreal, Canada, 19-23 July 2009.
  • Boevink, P.; Ramos, M.; Armstrong, M.R.; Allen, R.; Gilroy, E.M.; Donovan, S.; Rehmany, A.; Beynon, J.; Birch, P.R.J. (2009) Evolutionarily distinct RXLR effectors from distantly related oomycetes target the plant exocyst., 14th International Congress on Molecular Plant-Microbe Interactions, Quebec, Canada, 19-23 July 2009.
  • Toth, I.K.; Birch, P.R.J.; Pritchard, L.; Moleleki, L.N.; Ravensdale, M.; Robert, C.; Liu, H.; Humphris, S.N.; Hedley, P.E.; Gilroy, E.M. (2008) What will a genome sequence do for fire blight research? Pectobacterium atrosepticum and potato – a case study., 11th International Workshop on Fire Blight, Portland, Oregon, 12-17 August 2007.
  • McLellan, H.; Gilroy, E.M.; Hein, I.; Boevink, P.; Birch, P.R.J.; Loake, G. (2007) The roles of cathespin B-like proteases in plant disease resistance., XIII International Congress on Molecular Plant-Microbe Interactions, Sorrento, Italy, 22-26 July 2007.
  • Whisson, S.C.; Boevink, P.; Moleleki, L.N.; Avrova, A.O.; Morales, J.G.; Gilroy, E.M.; Armstrong, M.R.; Toth, I.K.; Pritchard, L.; Birch, P.R.J. (2007) A translocation signal for delivery of oomycete effector proteins into host plant cells., XIII International Congress on Molecular Plant-Microbe Interactions, Sorrento, Italy, 22-26 July 2007.
  • Armstrong, M.R.; Gilroy, E.M.; Birch, P.R.J. (2006) Gene signalling in the Phytophthora infestans-potato interaction., Oomycete Molecular Genetics Network, Wageningen, 4-7 May 2006.
  • Gilroy, E.M.; Venter, E.; McLellan, H.; Hein, I.; Hrubikova, K.; Holeva, M.C.; Boevink, P.; Loake, G.J.; Lacomme, C.; Birch, P.R.J. (2006) Inducible disease resistance involves an apoplastic cysteine protease Cathepsin B., Proceedings of IOBC/wprs Joint Working Group Meeting: Breeding for Inducible Resistance against Pests and Diseases, Heraklion, Crete, 27-29 April 2006.
  • Toth, I.K.; Hyman, L.J.; Moleleki, L.N.; Ravensdale, M.; Robert, C.; Liu, H.; Humphris, S.N.; Hedley, P.E.; Gilroy, E.M.; Pritchard, L.; Birch, P.R.J. (2006) What has genomics ever done for us? A study of Erwinia and blackleg disease., Proceedings of Crop Protection in Northern Britain, Dundee, 28 February – 1 March 2006, 239-242.
  • Venter, E.; Gilroy, E.M.; Avrova, A.O.; Kamoun, S.; Whisson, S.C.; Birch, P.R.J. (2004) Functional screening of Phytophthora infestans protease inhibitors in potato., Molecular Biology of Fungal Pathogens XV, University of Wales, 13 (Talk).
  • Rokka, V.; Avrova, A.O.; Hein, I.; Gilroy, E.M.; Cardle, L.; Birch, P.R.J. (2002) Unravelling signalling processes in the potato R gene resistance response to Phytophthora infestans., GILB GILB’02 conference – Late Blight: Managing the Global Threat, Hamburg, Germany, 11-13 July 2002, 152.

Conference posters / abstracts

  • Hein, I.; Gilroy, E.; Hornyik, C.; Bryan, G.; Milne, I.; Toth, I.K.; Ducreux, L.; Torrance, L.; Milne, L.; Cock, P.; Pritchard, L.; Sharma, K.; MacFarlane, S.; Zhang, R.; Hedley, P.; Jones, J.; Birch, P.; Taylor, M.; Dale, F.; McNaughton, I.; Wright, J.; Prashar, A.; Blok, V.; Carnegie, P.; Chapman, S. (2013) Utilising the potato genome., Potatoes in Practice 2013, Balruddery Farm, Invergowrie, Dundee, 8 August 2013.
  • Birch, P.R.J.; Boevink, P.C.; Gilroy, E.M.; Hein, I.; Pritchard, L.; Whisson, S.C. (2012) Effectors from the potato late blight pathogen: their roles in suppressing or triggering the plant immune system., EPS Autumn-school, Wageningen, 6 March 2012.
  • Birch, P.R.J.; Boevink, P.C.; Gilroy, E.M.; Hein, I.; Pritchard, L.; Randall, E.; Whisson, S.C. (2011) Effectors from the potato late blight pathogen: their roles in suppressing or triggering the plant immune system., British Mycological Society Meeting, Exeter, September 2011.
  • Boevink, P.; Bukharova, T.; McLellan, H.; Armstrong, M.R.; Gilroy, E.M.; Birch, P.R.J. (2010) Imaging plant-pathogen interactions: Phytophthora infestans RXLR effector localisation in planta., 9th International Mycological Congress,The Biology of Fungi, Edinburgh, 1-6 August 2010 (Poster).
  • Hein, I.; Whisson, S.C.; Armstrong, M.; Gilroy, E.M.; Avrova, A.O.; Tian, Z.; Chapman, S.N.; Birch, P.R.J.; Bryan, G.J. (2010) Identifying key Phytophthora infestans effectors as targets for more durable late blight resistance., 7th Solanaceae Conference 2010, Dundee, 5-9 September 2010, 155 (Poster).
  • Gilroy, E.M.; Breen, S.; Morales, J.G.; Lokossou, A.A.; Ramos, B.; Armstrong, M.R.; Hein, I.; Boevink, P.; Pritchard, L.; van der Vossen, E.A.G.; Vleeshouwers, V.G.A.A.; Whisson, S.C.; Birch, P.R.J. (2009) Cloning and functional analysis of Phytophthora infestans RXLR effector, Avr2., 22nd New Phytologist Symposium on Effectors in Plant-Microbe Interactions, INRA Versailles Research Centre, Paris, France, 13-16 September 2009 (Poster).
  • Blok, V.C.; Phillips, M.S.; Booth, A.; Smith, A.; Holt, A.; Gilroy, E.M.; Jones, J.T. (2007) Chorismate mutases of Globodera pallida: genetic and functional characterisation., XIII International Congress on Molecular Plant-Microbe Interactions, Sorrento, Italy, 22-26 July 2007 (Abstract).
  • Lacomme, C.; Faivre-Rampant, O.; Gilroy, E.M.; Valentine, T.A.; Shaw, J.; Hrubikova, K.; Blok, V.C.; Hein, I.; Haupt, S.; Loake, G.; Birch, P.R.J.; Taylor, M.A.; Oparka, K.J. (2004) Virus-induced gene silencing vector development for functional studies in Solanaceae., 1st Solanaceae Genome Workshop. Wageningen, The Netherlands, 19-21 September 2004 (Abstract).