Research Interests
Research Interests
- Population biology of plant pathogens in wild and agricultural ecosystems
- Ecology and epidemiology of plant pathogens
- Biological control of plant pathogens
- Plant disease forecasting and modelling
- Developing systems to identify plant disease resistance
- Plant pathogen and research project information
Biography
John is a plant pathologist and research leader in the Warwick Crop Centre specialising mainly in pathogens of vegetable crops. The Crop Centre has a remit of translating research into solutions for the industry and hence he is involved in a range of different projects from basic/strategic to applied, funded by government, research councils and industry. Areas of interest and expertise include plant pathogen biology, epidemiology, ecology and diversity with particular focus on soilborne diseases such as Sclerotinia and Fusarium and disease management approaches such as biological control and disease forecasting. John has 20 years of pathology experience and strong links with the industry and other researchers through collaborative projects.
- Armitage, Andrew D., Cockerton, Helen M., Sreenivasaprasad, Surapareddy, Woodhall, James, Lane, Charles R., Harrison, Richard J., Clarkson, John P., 2020. Genomics evolutionary history and diagnostics of the Alternaria alternata Species group including apple and Asian pear pathotypes. Frontiers in Microbiology, 10
- Gálvez, L., Clarkson, John P., Palmero, D., 2020. IGS region polymorphisms are responsible for failure of commonly used species-specific primers in Fusarium proliferatum isolates from diseased garlic. Plant Pathology, 69 (4), pp. 713-722
- Armitage, Andrew D., Taylor, Andrew, Hulin, Michelle T., Jackson, Alison C., Harrison, Richard J., Clarkson, John P., Rokas, Antonis, 2019. Draft genome sequence of an onion basal rot isolate of fusarium proliferatum. Microbiology Resource Announcements, 8 (1)
- Taylor, Andrew, Jackson, Alison C., Clarkson, John P., 2019. First report of Fusarium oxysporum f. sp. lactucae Race 4 causing lettuce wilt in England and Ireland. Plant Disease, 103 (5)
- Taylor, Andrew, Barnes, Adam, Jackson, Alison C., Clarkson, John P., 2019. First report of Fusarium oxysporum and Fusarium redolens causing wilting and yellowing of wild rocket (Diplotaxis tenuifolia) in the UK. Plant Disease, 103 (6)
- Taylor, Andrew, Teakle, Graham R., Walley, Peter G., Finch-Savage, William E., Jackson, Alison C., Jones, Julie, Hand, Paul, Thomas, Brian, Havey, Michael J., Pink, David A. C., Clarkson, John P., 2019. Assembly and characterisation of a unique onion diversity set identifies resistance to Fusarium basal rot and improved seedling vigour. Theoretical and Applied Genetics, 132 (12), pp. 3245-3264
- Taylor, Andrew, Armitage, Andrew D., Handy, Claire, Jackson, Alison C., Hulin, Michelle T., Harrison, Richard J., Clarkson, John P., 2019. Basal rot of narcissus : understanding pathogenicity in fusarium oxysporum f. sp. narcissi. Frontiers in Microbiology, 10
- Taylor, Andrew, Rana, Kusum, Handy, Claire, Clarkson, John P., 2018. Resistance to Sclerotinia sclerotiorum in wild Brassica species and the importance of Sclerotinia subarctica as a Brassica pathogen. Plant Pathology, 67 (2), pp. 433-444
- Navaud, Olivier, Barbacci, Adelin, Taylor, Andrew, Clarkson, John P., Raffaele, Sylvain, 2018. Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens. Molecular Ecology, 27 (5), pp. 1309-1323
- Rutolo, Massimo, Clarkson, John P., Covington, James A., 2018. The use of an electronic nose to detect early signs of soft-rot infection in potatoes. Biosystems Engineering, 167, pp. 137-143
- Armitage, Andrew D., Taylor, Andrew, Sobczyk, Maria K., Baxter, Laura, Greenfield, Bethany P. J., Bates, Helen J., Wilson, Fiona, Jackson, Alison C., Ott, Sascha, Harrison, Richard J., Clarkson, John P., 2018. Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae. Scientific Reports, 8 (1)
- Taylor, Andrew, Coventry, Emma, Handy, Claire, West, Jon S., Young, Caroline S., Clarkson, John P., 2018. Inoculum potential of Sclerotinia sclerotiorum sclerotia depends on isolate and host plant. Plant Pathology, 67 (6), pp. 1286-1295
- Rutolo, Massimo F., Clarkson, John P., Harper, Glyn, Covington, James A., 2018. The use of gas phase detection and monitoring of potato soft rot infection in store. Postharvest Biology and Technology, 145, pp. 15-19
- Brodal, G., Warmington, Rachel, Grieu, C., Ficke, A., Clarkson, John P., 2017. First report of Sclerotinia subarctica nom. prov. (Sclerotinia sp. 1) causing stem rot on turnip rape (Brassica rapa subsp. oleifera) in Norway. Plant Disease, 101 (2), pp. 386-386
- Clarkson, John P., Warmington, Rachel J., Walley, Peter G., Denton-Giles, Matthew, Barbetti, Martin J., Brodal, Guro, Nordskog, Berit, 2017. Population structure of Sclerotinia subarctica and Sclerotinia sclerotiorum in England, Scotland and Norway. Frontiers in Microbiology, 8
- Rutolo, Massimo, Iliescu, Daciana, Clarkson, John P., Covington, James A., 2016. Early identification of potato storage disease using an array of metal-oxide based gas sensors. Postharvest Biology and Technology, 116, pp. 50-58
- Warmington, Rachel, Clarkson, John P., 2016. Volatiles from biofumigant plants have a direct effect on carpogenic germination of sclerotia and mycelial growth of Sclerotinia sclerotiorum. Plant and Soil, 401 (1), pp. 213-229
- Taylor, Andrew, Vágány, Viktória, Jackson, Alison C., Harrison, Richard J., Rainoni, Alessandro, Clarkson, John P., 2016. Identification of pathogenicity-related genes in Fusarium oxysporum f. sp. cepae. Molecular Plant Pathology, 17 (7), pp. 1032-1047
- Raza, Shan-e-Ahmed, Prince, Gillian, Clarkson, John P., Rajpoot, Nasir M., 2015. Automatic detection of diseased tomato plants using thermal and stereo visible light images. PLoS One, 10 (4)
- Armitage, A. D., Barbara, Dez J., Harrison, R. J., Lane, C. R., Sreenivasaprasad, S., Woodhall, J. W., Clarkson, John P., 2015. Discrete lineages within Alternaria alternata species group : identification using new highly variable loci and support from morphological characters. Fungal Biology, 119 (11), pp. 994-1006
- Raza, Shan-e-Ahmed, Sanchez Silva, Victor, Prince, Gillian, Clarkson, John P., Rajpoot, Nasir M., 2015. Registration of thermal and visible light images of diseased plants using silhouette extraction in the wavelet domain. Pattern Recognition, 48 (7), pp. 2119-2128
- Taylor, Andrew, Coventry, E., Jones, J. E., Clarkson, John P., 2015. Resistance to a highly aggressive isolate of Sclerotinia sclerotiorumin a Brassica napusdiversity set. Plant Pathology, 64 (4), pp. 932-940
- Clarkson, John P., Fawcett, Laura, Anthony, Steven G., Young, Caroline, 2014. A model for Sclerotinia sclerotiorum infection and disease development in lettuce, based on the effects of temperature, relative humidity and ascospore density. PLoS One, 9 (4)
- Raza, Shan-e-Ahmed, Smith, Hazel K., Clarkson, Graham J. J., Taylor, Gail, Thompson, Andrew J., Clarkson, John P., Rajpoot, Nasir M. (Nasir Mahmood), 2014. Automatic detection of regions in spinach canopies responding to soil moisture deficit using combined visible and thermal imagery. PLoS One, 9 (6)
- Rutolo, Massimo, Covington, James A., Clarkson, John P., Iliescu, Daciana, 2014. Detection of potato storage disease via gas analysis : a pilot study using field asymmetric ion mobility spectrometry. Sensors, 14 (9), pp. 15939-15952
- Taylor, Andrew, Vagany, V., Barbara, Dez J., Thomas, Brian, Pink, David, Jones, J. E., Clarkson, John P., 2013. Identification of differential resistance to six Fusarium oxysporum f. sp. cepae isolates in commercial onion cultivars through the development of a rapid seedling assay. Plant Pathology, 62 (1), pp. 103-111
- Clarkson, John P., Coventry, E., Kitchen, James, Carter, H. E., Whipps, J. M., 2012. Population structure of Sclerotinia sclerotiorum in crop and wild hosts in the UK. Plant Pathology, 62 (2), pp. 309-324
- Clarkson, John P., Phelps, Kath, Whipps, John A., Young, Caroline, Smith, Julie A., Watling, Marlyn, 2007. Forecasting sclerotinia disease on lettuce: a predictive model for carpogenic germination of Sclerotinia sclerotiorum sclerotia. Phytopathology, Vol.97 (No.5), pp. 621-631
- Clarkson, John P., Scruby, A., Mead, A. (Andrew), Wright, Carole, Smith, B., Whipps, J. M., 2006. Integrated control of Allium white rot with Trichoderma viride, tebuconazole and composted onion waste. Plant Pathology, Vol.55 (No.3), pp. 375-386
- Gilles, Tijs, Phelps, Kath, Clarkson, John P., Kennedy, Roy, 2004. Development of MILIONCAST, an improved model for predicting downy mildew sporulation on Onions. Plant Disease, 88 (7), pp. 695-702
- Clarkson, John P., Mead, A. (Andrew), Payne, Tina, Whipps, J. M., 2004. Effect of environmental factors and Sclerotium cepivorum isolate on sclerotial degradation and biological control of white rot by Trichoderma. Plant Pathology, 53 (3), pp. 353-362
- Jones, E. E., Clarkson, John P., Mead, A. (Andrew), Whipps, J. M., 2004. Effect of inoculum type and timing of application of Coniothyrium minitans on Sclerotinia sclerotiorum : influence on apothecial production. Plant Pathology, 53 (5), pp. 621-628
- Young, C. S., Clarkson, John P., Smith, J. A., Watling, M., Phelps, Kath, Whipps, J. M., 2004. Environmental conditions influencing Sclerotinia sclerotiorum infection and disease development in lettuce. Plant Pathology, 53 (4), pp. 387-397
- Clarkson, John P., Phelps, Kath, Whipps, J. M., Young, Caroline S., Smith, Julie A., Watling, Martyn, 2004. Forecasting sclerotinia disease on lettuce : toward developing a prediction model for carpogenic germination of sclerotia. Phytopathology, 94 (3), pp. 268-279
- Clarkson, John P., Staveley, John, Phelps, Kath, Young, Caroline, Whipps, J. M., 2003. Ascospore release and survival in Sclerotinia sclerotiorum. Mycological Research, Vol.10 (No.2), pp. 213-222
- Finch-Savage, William E., Clay, H. A., Budge, S. P., Dent, K. C., Clarkson, John P., Whipps, J. M., 2003. Biological control of Sclerotinia and other fungi during moist storage of Quercus robur seeds. European Journal of Plant Pathology, 109 (6), pp. 615-624
- Clarkson, John P., Whipps, J. M., 2002. Control of sclerotial pathogens in horticulture. Pesticide Outlook, 13 (3), pp. 97-101
- Clarkson, John P., Payne, Tina, Mead, A. (Andrew), Whipps, J. M., 2002. Selection of fungal biological control agents of Sclerotium cepivorum for control of white rot by sclerotial degradation in a UK soil. Plant Pathology, 51 (6), pp. 735-745
- Smith, B. M., Crowther, T. C., Clarkson, John P., Trueman, L., 2000. Partial resistance to rust (Puccinia allii) in cultivated leek (Allium ampeloprasum ssp.porrum) : estimation and improvement. Annals of Applied Biology, 137 (1), pp. 43-51
- Clarkson, John P., Kennedy, Roy, Phelps, Kath, 2000. The effect of temperature and water potential on the production of conidia by sclerotia of Botrytis squamosa. Plant Pathology, 49 (1), pp. 119-128
- Di Bonito, Marcello, Clarkson, John P., Wienhold, Michelle L., Pecchia, Leandro, 2013. Integrating analytic hierarchy process (AHP) and geographical information systems (GIS) for prioritising and planning conservation choices in Wales. ISAHP2013, Kuala Lumpur, Malaysia, 23-26 Jun 2013
- Ghaffari, Reza, Zhang, Fu, Iliescu, Daciana, Hines, Evor, Leeson, Mark S., Napier, R., Clarkson, John P., 2010. Early detection of diseases in tomato crops : an electronic nose and intelligent systems approach. 2010 International Joint Conference on Neural Networks IJCNN 2010, Barcelona, 18-23 July 2010, Published in IEEE International Conference on Neural Networks. Proceedings, pp. 1-6
- Clarkson, John P., Clewes, E., Whipps, J. M., 2008. Diversity of Sclerotinia sclerotiorum from agricultural crops and meadow buttercup in the UK. ICPP 2008 9th International Congress of Plant Pathology, Torino, Italy, 24-29 Aug 2008, Published in Journal of Plant Pathology
- Clarkson, John P., Young , C.S.. New dawn for Sclerotinia control. HDC News, Horticultural Development Company, pp. 24-25
- Taylor, Andrew, Sims, Isabel, Jackson, Alison C., Clarkson, John P., 2017. First report of Fusarium oxysporum causing a vascular wilt of statice (Limonium sinuatum) in the UK. Plant Disease, American Phytopathological Society
- Clarkson, John P., Michel, Vincent, Neilson, Roy, 2015. Biofumigation for the control of soil-borne diseases. Soil borne disease focus group
- Michel, Vincent, Urba, Karolis, Clarkson, John P., 2015. Green manures and cover crops to reduce the pressure of soil-borne diseases in annual crops. Soil borne disease focus group
- Clarkson, John P., Debode, Jane, Furlan, Lorenzo, Neilson, Roy, Wallenhammar, Ann-Charlotte, Zahrl, Johann, 2015. Monitoring of soil-borne pathogens (fungi, protists and nematodes) and soil tests. Soil borne disease focus group
- Clarkson, John P., Carter, H. E., Coventry, E., 2010. First report of Sclerotinia subarctica nom. prov. (Sclerotinia species 1) in the UK on Ranunculus acris. Plant Pathology, Wiley-Blackwell Publishing Ltd, pp. 1173-1173
- Chandler, Dave, Bending, G. D., Clarkson, John P., Davidson, G. (Gill), Hall, S., Mills, P. R., Pink, David, Skirvin, David J., Neve, Paul, Kennedy, Richard, Greaves, Justin, Grant, Wyn, Collier, R. H., 2008. The consequences of the ?cut off' criteria for pesticides : alternative methods of cultivation. European Parliament
| Title | Funder | Award start | Award end |
|---|---|---|---|
| Exploiting pathogenomics and resistance for control of Fusarium wilt of lettuce PhD MIBTP iCASE | AHDB (Formerly HDC) | 01 Oct 2019 | 30 Sep 2023 |
| Development of molecular methods to determine the risk of Fusarium disease, select effective rotation crops and monitor F. oxysporum pathogens and associated microbial communities UPDATED 63905 (milestone added as per funders request) | AHDB (Formerly HDC) | 01 Apr 2020 | 31 Mar 2023 |
| VeGIN Tender re-costed budget - link with 57218 that contains the original Tender application | Department for Environment, Food and Rural Affairs | 01 Feb 2018 | 31 Jan 2023 |
| h20 SMARTPROTECT: SMART agriculture for innovative vegetable crop PROTECTion: harnessing advanced methodologies and technologies | European Commission | 01 Jan 2020 | 31 Dec 2022 |
| RootCause - Understanding the causal agent of tip rot and management of cavity spot to reduce carrot loss and waste within the supply chain | Research Council of Norway | 01 Feb 2019 | 31 Jan 2022 |
| iCASE with G's under Waitrose DTP | G's Growers Ltd | 31 Dec 2017 | 30 Dec 2021 |
| iCASE studentship - Understanding and mitigating against the causes of yield decline in pea | Processors and Growers Research Organisation (PGRO) | 25 Sep 2017 | 24 Sep 2021 |
| Sceptre plus | AHDB (Formerly HDC) | 03 Apr 2017 | 02 Apr 2021 |
| Field Macrocosm Development - Under AHDB Sceptre Plus project (Ideate 54235) | AHDB (Formerly HDC) | 01 May 2020 | 31 Mar 2021 |
| Onions: Integrated control of Allium White rot | AHDB (Formerly HDC) | 01 Mar 2018 | 28 Feb 2021 |
| HDC Fellowship for Andy Taylor - Maintaining and developing capability in vegetable crop pathology | AHDB (Formerly HDC) | 01 Nov 2013 | 28 Feb 2021 |
| Application and management of biopesticides for efficacy and reliability (AMBER) | AHDB (Formerly HDC) | 01 Jan 2016 | 31 Dec 2020 |
| Mature Plant Test Development - Under AHDB Sceptre Plus project (Ideate 54235) | AHDB (Formerly HDC) | 01 Apr 2020 | 30 Sep 2020 |
| Lettuce: biology and management of Fusarium wilt caused by Fusarium oxysporum f.sp. lactuscase race 4 | AHDB (Formerly HDC) | 01 Oct 2018 | 31 Mar 2020 |
| Developing disease prediction of onion basal rot using a quantitative molecular test | AHDB (Formerly HDC) | 14 Oct 2019 | 29 Feb 2020 |
| Pre-breeding for fungal disease resistance in lettuce (costing linked to 61699) | University of York | 01 Mar 2019 | 30 Sep 2019 |
| Narcissus: Investigation into the effects of a range of potential biocides in hot water treatments | AHDB (Formerly HDC) | 01 Jan 2016 | 30 Jun 2019 |
| Biology and control of Fusarium diseases across multiple crops. Phase 1: Development of molecular tools to identify and quantify multiple Fusarium species | AHDB (Formerly HDC) | 01 Apr 2017 | 31 Dec 2018 |
| Carrots: Further development of artificial inoculation techniques for cavity spot caused by Pythium violae | AHDB (Formerly HDC) | 01 Aug 2017 | 30 Sep 2018 |
| A Systems Approach to Disease Resistance Against Necrotrophic Fungal Pathogens (HAPI stage 2) | BBSRC | 01 Jun 2015 | 30 Sep 2018 |
| Vegetable Genetic Improvement Network (VeGIN) extension 2017 | Department for Environment, Food and Rural Affairs | 01 Apr 2017 | 31 Mar 2018 |
| Vegetable Genetic Improvement Network (VeGIN) Tender - Sep 2014 | Department for Environment, Food and Rural Affairs | 28 Nov 2014 | 31 Dec 2017 |
| Understanding the ecology and epidemiology of Pythium violae to enable disease management | AHDB (Formerly HDC) | 01 Oct 2014 | 30 Sep 2017 |
| Carrots: Development of artificial inoculation techniques for cavity spot caused by Pythium violae. | AHDB (Formerly HDC) | 01 Apr 2016 | 31 Jul 2017 |
| Exploiting next generation sequencing technologies to understand pathogenicity and resistance in Fusarium oxysporum | BBSRC | 01 Sep 2013 | 31 Mar 2017 |
| BBSRC GCRF IAA - Sustainable oil palm cropping | BBSRC | 21 Oct 2016 | 31 Mar 2017 |
| To establish protocols to collect, identify and store pathogens which cause vegetable and herb crop diseases and us them to improve plant resistance breedign programmes. | Elsoms Seeds Limited | 09 Sep 2014 | 16 Feb 2017 |
| Establishing an African-UK innovation hub for common bean health and protection. BBSRC GCRF IAA | BBSRC | 01 Sep 2016 | 31 Dec 2016 |
| White rot Integrated control Treatments Evaluated (WHITE) - Phase 1 - Recosting of 50164 | AHDB (Formerly HDC) | 01 Apr 2016 | 30 Sep 2016 |
| Genotyping Alien Introgression Lines of Brassica juncea..; British Council: Newton Bhabha PhD Placement Programme award - Kusum Rana | British Council | 01 Apr 2015 | 29 Feb 2016 |
| Exploiting Next Genreation Sequencing Technologies to understand Pathology and Resistance in Fusarium.Collaboration agreement for BBSRC HAPI application 33387; linked to InfoEd 34637; RLFJL3009 | Horticultural Development Council | 01 Jan 2013 | 01 Jan 2016 |
| Sclerotina in lettuce - biology and control in Norway | Bioforsk Plant Health and Plant Protection Division | 01 Jan 2013 | 31 Dec 2015 |
| WCPRS Studentship: Detection of potato storage diseases using Field Asymmetric Ion Mobility Spectrometry (FAIMS) The Potato Council under AHDB | AHDB (Formerly HDC) | 01 Oct 2012 | 30 Sep 2015 |
| Control of carrot cavity spot through the use of Pre-crop green manures/biofumigation | AHDB (Formerly HDC) | 01 Sep 2014 | 31 Mar 2015 |
| HDC Studentship 2011 - Pathogen diversity, epidemiology and control of Sclerotina disease in vegetable crops | AHDB (Formerly HDC) | 01 Oct 2011 | 31 Dec 2014 |
| Extension to VeGIN: Vegetable Genetic Improvement Network for leafy and field vegetables CH0101 | Department for Environment, Food and Rural Affairs | 01 Mar 2014 | 30 Sep 2014 |
| Digital imaging for phenotyping roots crops | Technology Strategy Board | 01 Sep 2013 | 31 Aug 2014 |
| Development of Novel Biological Seed Treatment Technologies | Technology Strategy Board | 01 Sep 2010 | 28 Feb 2014 |
| Extension to PH0436 - Plant Health Fellowship VII - molecular phogenetic methodologies in EC listed alternarias - no cost extension to new end date of 31 December 2013 - RLFDB0501 | Department for Environment, Food and Rural Affairs | 01 Dec 2012 | 31 Dec 2013 |
| Project continuation proposal: Defra IF0188 - Plant pathogen populations in wild and agricultural hosts and interactions with plant genotype | Department for Environment, Food and Rural Affairs | 01 Aug 2012 | 30 Nov 2013 |
| Sub-contract of HortLink project (at EMR) Optimising field-scale control of Fusarium basal rot and white rot of onion using composts, Trichoderma and biofumigant (HL1108) | East Malling Research | 10 May 2012 | 31 Aug 2013 |
| Protected edible crops: biological control of plant diseases using insect pathogenic fungi with dual activity against plant pathogens: 2 year version | AHDB (Formerly HDC) | 01 Aug 2011 | 31 Jul 2013 |
| LINK: reducing the impact of sclerotinia disease on arable rotations, land use and vegetable | Department for Environment, Food and Rural Affairs | 01 Oct 2009 | 31 Mar 2013 |
| IF0188 - Plant Pathogen Populations in Wild and Agricultural Hosts and interactions with Plant Genotype | Department for Environment, Food and Rural Affairs | 01 Aug 2009 | 31 Jul 2012 |
| Onions: Relationship between disease incidence in stored bulb onions and first year sets | AHDB (Formerly HDC) | 01 Apr 2011 | 31 Mar 2012 |
| In vitro screening of fungicides with potential to control basal rot of narcissus caused by Fusarium oxysporum f.sp. narcissiBOF 74 | AHDB (Formerly HDC) | 01 Sep 2011 | 31 Mar 2012 |
| IF0158 Vegetable Genetic Improvement Network (VeGIN): Per-breeding research to support sustainable farming of carrot and onion | Department for Environment, Food and Rural Affairs | 01 Apr 2009 | 31 Mar 2012 |
| FV352: Disease management in organic brassica seed and transplants | AHDB (Formerly HDC) | 01 Jun 2009 | 31 May 2011 |
| DEFRA Core: IF0193 Developing resources to identify sources of resistance to sclerotinia disease and variability in pathogen aggressiveness | Department for Environment, Food and Rural Affairs | 03 Jan 2009 | 31 Jul 2009 |
| Factors affecting the inoculum potential of soilborne plant pathogens | Department for Environment, Food and Rural Affairs | 01 Apr 2005 | 31 Mar 2009 |
| Hortlink: Integrated Allium while rot control using composts and trichoderma viride | Department for Environment, Food and Rural Affairs | 01 Jan 2006 | 31 Dec 2008 |
| Outdoor Lettuce: Forecasting and Control of Sclerontinia | Horticultural Development Council | 01 Oct 2006 | 30 Sep 2008 |
| FV220a Hortlink Project Improved crop health and establishment using beneficial micro-organisms | Horticultural Development Council | 01 Sep 2003 | 28 Feb 2007 |
