Improving pest management in coffee plantations.

Nematode parasitism has adverse effects on coffee plants and bean production. Current work (Nestlé-sponsored KTN CASE student) has established a PCR-based molecular pipeline that identifies 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, associated both with coffee plants and intercrop species. Deployment of resistant/tolerant coffee varieties could reduce losses but the fundamental mechanisms underlying resistance and tolerance are undescribed. This project will help to fill that knowledge gap and so inform future breeding efforts.
Objective 1. Establish the impact of intercropping on the spread of coffee nematode pathogens.
A small-scale field trial in Vietnam will determine the consequence of intercropping coffee and black pepper. The field will be planted with coffee and 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 the 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.
Objective 2. Determine the level and robustness of nematode resistance/tolerance for a range of coffee varieties
Glasshouse trials will establish the resistance or tolerance of 4-6 newly developed Nestlé coffee varieties to four major nematode pathogens. Inclusion of the "best" tolerant rootstock used for grafting will allow benchmarking. Parameters to be assessed include nematode invasion, gall number and reproductive factor. Tolerance will be evaluated by assessing plant growth under control and nematode-infected conditions. Measurements of chlorophyll fluorescence will report nematode-related plant stress and image analysis will quantify the extent of root necrosis.
Commercially useful field resistance/tolerance should be robust under attack by a wide range of nematodes and in varying environmental conditions. The 1-2 most tolerant/resistant varieties will therefore be challenged with additional nematode species. 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).
Objective 3. Characterise the physiological, biochemical and molecular basis for tolerance to nematodes.
Physiology of the most and least tolerant coffee varieties (Objective 2), both infected and uninfected, 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 for resistance/tolerance will be explored using RNAseq to identify differential gene expression associated with the observed phenotypes. Infected and uninfected roots of a highly susceptible coffee variety and two that display resistance or tolerance to nematodes will be compared. Targeted qPCR 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 breeding.
Biochemical analysis will focus on phenolic compounds such as chlorogenic and caffeic acid, that may be associated with nematode resistance in other host plants. Activities of related enzymes e.g. peroxidase, polyphenoloxidase will also be assessed.