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Improving pest management in coffee plantations.

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  • Full or part time
    Prof P. Urwin
  • Application Deadline
    No more applications being accepted
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

This project is funded by a CASE award with Nestlé, co-supervised by Dr James McCarthy. Nestlé provide an additional £2500 p.a. to the student stipend, funding for research, and the project will involve a placement at Nestlé R & D in Tours, France. Specific facilities at Nestlé that will be available to this project include extensive tissue culture production of coffee plantlets, digital PCR technology for accurate quantification of nematodes and in-house next generation sequencing for RNAseq experiments.

Plant parasitic nematodes are soil-borne pests that are an increasing problem for coffee production worldwide as they have adverse effects on coffee plants and bean production. As coffee is a key raw material for Nestlé, they are interested in both better understanding the threat from these pests to the supply chain, and in finding workable solutions to the threat, such as more tolerant coffee plants. Current work has established a PCR-based molecular pipeline that identifies and quantifies economically important Meloidogyne and Pratylenchus nematode species from soil samples. Application of those protocols has shown that diverse and numerous species-complexes exist within coffee plantations in Brazil, Vietnam and Indonesia, associated both with coffee plants and the intercrop species commonly planted by growers.

One aim of this project is therefore to establish the impact of intercropping on the spread of coffee nematode pests. Coffee growers are increasingly intercropping their fields with high-value, marketable crops such as black pepper. We have found that high numbers of parasitic nematodes are often associated with these plants, but there is little information about how this affects spread of the nematode pests and the impact on their management. The student will be involved in setting up a small-scale field trial in Vietnam in which coffee is intercropped with different proportions of black pepper to determine how this affects nematode build-up, competition and spread. Nematode levels and species will be determined pre-planting using the quantitative diagnostics pipeline developed by a current CASE student and at 2-3 times post-planting over the course of the PhD. Established fields with intercrops will also be sampled to gain wider insight into in-field species distribution.

Deployment of resistant or tolerant coffee varieties could help to reduce losses to nematodes and Nestle research teams are developing new varieties that will be available for evaluation within the project. However, the fundamental mechanisms underlying nematode resistance and tolerance in coffee are poorly understood. This project will help to fill that knowledge gap and so inform future breeding efforts.
Firstly the student will carry out glasshouse trials in Leeds to evaluate the resistance or tolerance to major nematode pests for a range of newly developed Nestlé coffee varieties. It is important that commercially useful field resistance/tolerance is robust under attack by a wide range of nematodes and in varying environmental conditions therefore this will be tested as part of the trials. As tolerance is determined by interaction between plant genotype and environment, further evaluations will be carried out under more extreme environmental conditions (e.g. drought-stress, high temperature).

There is currently limited understanding of the physiological, biochemical and molecular basis for tolerance or resistance of coffee varieties to nematodes. Therefore these aspects will be explored using comparisons of the most and least tolerant/resistant varieties characterised. Infected and uninfected plants will be analysed to determine any clear phenotypic rationale to tolerance e.g. larger root system, more vigorous plants, differential transpiration rates. The underlying molecular bases will be explored using RNAseq to identify differential gene expression associated with the observed phenotypes compared with a highly susceptible coffee variety. Targeted expression analysis of the most promising candidate genes in the full range of characterised coffee varieties will validate the link to tolerance/resistance and thus could provide molecular expression markers for future breeding efforts. Biochemical analysis will focus on phenolic compounds such as chlorogenic and caffeic acid that may be associated with nematode resistance in other host plants, together with activities of related enzymes.
This project provides a great opportunity for a student to be involved with commercially relevant plant pathology research at all scales from molecular laboratory experiments, through glasshouse trials to field work in Vietnam.

Funding Notes

The project is fully funded for 4 years jointly by the BBSRC and Nestlé to include
(i) All academic university fees .
(ii) A full BBSRC stipend to support the successful candidate
(iii) An additional payment of £2500 p.a. to the successful candidate from the CASE partner Nestlé.
(iv) Travel and consumables budget

European candidates must have 3 years residency in the UK to be eligible for full support. Non-UK/EU candidates are not eligible.


Jones, J. T., Haegeman, A., Danchin, E. G. J., Gaur, H. S., Helder, J., Jones, M. G. K., Kikuchi, T., Manzanilla-López, R., Palomares-Rius, J. E., Wesemael, W. M. L., Perry, R. N., (2013). Top 10 plant-parasitic nematodes in molecular plant pathology. Molecular Plant Pathology, 14: 946–961.

International Coffee Organisation (2015). http://www.ico.org/new_historical.asp

Souza, R. M. (2008). Plant-parasitic nematodes of coffee. 1st ed. Dordrecht: Springer.

Trinh, P. Q., de la Pena, E., Nguyen, C. N., Nguyen, H. X., Moens, M., (2009). Plant-parasitic nematodes associated with coffee in Vietnam. Russian Journal of Nematology, 17(1): 73-82.

Barros, A. F., OIiveira, R. D. L., Lima, I. M., Coutinho, R. R., Ferreira, A. O., Costa, A., (2014). Root-knot nematodes, a growing problem for Conilon coffee in Espirito Santa state, Brazil. Crop Protection, 55:74-79.

Machado, A. C. Z., (2014). Current nematode threats to Brazilian agriculture. Current Agricultural Science and Technology, 20: 26-35.

Adam, M. A. M., Phillips, M. S., Blok, V. C., (2007). Molecular diagnostic key for identification of single juveniles of seven common and economically important species of root-knot nematode (Meloidogyne spp.). Plant Pathology, 56: 190–197.

Randig, O., Bongiovanni, M., Carneiro, R. M. D. G., Castagnone-Sereno, P., (2002), Genetic diversity of root-knot nematodes from Brazil and development of SCAR markers specific for the coffee-damaging species. Genome, 45(5): 862-870

BieYun, T. (2008). Competition between Pratylenchus coffeae and Meloidogyne incognita. Plant Pathology Bulletin, 17(4): 271-278.

How good is research at University of Leeds in Biological Sciences?

FTE Category A staff submitted: 60.90

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