CRUK Research Projects 43


Funded by CRUK
» University of Reading, UK
(2024 to 2027)
Researcher: Dr. Andrew Daymond/Dr Fiona Lahive/Prof. Paul Hadley
This two year project at the University of Reading builds on previous work on climate change effects on cocoa supported by CRUK and other sponsors. Building on this extensive platform of research, this project seeks to further advance our knowledge of impacts of climate variables on cocoa and potential solutions for mitigation by firstly, understanding how cocoa responds to heatwaves and cold temperature shock events against a background of other stressors; secondly ground-truthing in Ghana the previously conducted greenhouse experiments which identified putative traits associated with tolerance to high-temperature and drought stress; thirdly, to understand how changes in the light environment (as may occur through the adoption of agroforestry practices) might impact the response of cocoa to abiotic stresses.

Funded by CRUK
» University of Reading, UK
(2017 to 2023)
Researchers: Dr. Andrew Daymond/Prof. Paul Hadley, Dr. Fiona Lahive
The overall aim of the project was to provide a broader understanding of the impacts of climate change on growth, yield and quality in cocoa through a combination of experimental studies and modelling, and to develop tools to identify resilience to abiotic stresses resulting from climate change. Although originally funded by CR (UK) Ltd for 5 years, additional complementary funding from other sources allowed the project to run until the end of 2023. The approach involved a combination of short term experiments on young plants grown in controlled environment chambers,together with longer term trials on mature, pod bearing cocoa trees within a greenhouse facility specifically designed for physiological research on cocoa under simulated climate change conditions. Germplasm screening methods for resilience to water deficit and to high temperatures were also developed and used to test responses of a wide range of germplasm held within the International Cocoa Quarantine Centre. Data arising from the project were synthesized within a physiological model simulating the impact of climate change variables on the growth and physiology of cocoa, whilst a collaboration with the School of Meteorology led to a land-surface model calibrated for cocoa under climate change conditions. The research outputs have been published in 10 scientific papers and shared with the research community through workshops and webinars. Key findings include: Identification of traits associated with maintenance of biomass production under drought Genetic variation in thermotolerance when over 100 clones were tested under greenhouse/laboratory conditions, though further studies are needed to establish the potential of the techniques in larger scale screening under field conditions. Mitigating effects of high humidity and CO2 on negative effects of high temperatures on growth and photosynthesis, particularly for some varieties, and changes in biomass accumulation/partitioning and photosynthetic acclimation in response to growth conditions in both juvenile and mature plants. Initial results from metabolomic studies carried out in association with the Leibniz Institute for Food Systems Biology (Technical University of Munich) indicate temperature effects during seed development and pod maturation. A physiological model was developed to simulate the impact of different climate change scenarios on yield determinants and their subsequent effect on productivity/yield. Collaborative work with colleagues in the University of Reading’s Department of Meteorology involved modelling net primary productivity of cocoa (i.e. biomass production) in present and future climates in West Africa and demonstrated that elevated [CO2] ameliorated negative impacts of increases in temperature and variation in precipitation.
10 Published Papers

Funded by CRUK and in collaboration with partners in University of Reading (UK), Cocoa Research Centre-UWI (Trinidad), Imperial College (UK), CIRAD, UWE (UK)
» University of Reading, UK
(2019 to 2022)
Researcher: Dr. I Ullah/Prof. Jim Dunwell
A short study based at the University of Reading to use a yeast assay to assess the functional behaviour of a range of cacao genes which are involved in uptake and movement of metal ions, including cadmium, within the plant. The research, carried out in collaboration with Imperial College-London, indicates that although cacao plants are likely to use similar physiological mechanisms for the uptake of zinc, which is essential for healthy growth, and cadmium, it seems that there are distinct mechanisms for their movement within the plant. Thus it may be possible to breed varieties suitable for use in areas with naturally high levels of cadmium in the soil which grow well but do not accumulate cadmium in their beans. The project also provided training for a staff member from Cocoa Research Centre, UWI, Trinidad in the yeast assay technique. The second part of the project was focussed on the use of molecular techniques to investigate badna viruses and endogenous viral elements in the cacao genome and resulted in improved diagnostic tools for use in virus detection during quarantine procedures.
10 Published Papers

Funded by CRUK and University of the West of England (UWE)
» University of the West of England, Bristol, UK
(2019 to 2022)
Researcher: M. Richardson (Supervisor: Dr. A Wetten/Prof. D Arnold/Dr D Turner
A PhD project based at the University of the West of England (UWE) to gain a better understanding of the pathology of CSSV and its transit in its mealybug vector using a combination of molecular and microscopy techniques. In collaboration with scientists at CIRAD and University of Reading, research also focussed on the identification of non-pathogenic endogenous viral elements which were found to be frequently present within cocoa genomes. A simple stem-peel sampling technique was developed which can be used with the appropriate molecular primers (selected to avoid false positive results due to endogenous viral elements) to test budwood for CSSV infection in quarantine applications. In situ localisation results, using CSSV-antibodies and confocal microscopy, demonstrate that the cocoa phloem is a rich reservoir of CSSV in infected cocoa plants but that the widespread presence of virions within the spongy mesophyll cells constitute another potential source of viral inoculum for probing mealybug vectors.
2 Published Papers

Funded by CRUK and Cranfield University
» Cranfield University, UK
(2018 to 2021)
Researcher: T. Fungenzi (supervisor: Prof. Ruben Sakrabani
Soil organic matter (SOM) plays an essential role in soil health and functionality. SOM levels can be improved through the regular addition of composts and manures but levels can quickly deteriorate in soils where crops are cultivated especially under tropical conditions. This research set out to investigate the impact of application of soil amendments, including locally-available compost and inorganic fertilisers, on cocoa production from cocoa farms at various sites in Indonesia. A model was developed from the results obtained which simulates the rapid depletion of SOM after planting and its gradual recovering once the planting is 10-20 years old as the contribution from leaf litter from the maturing canopy makes an increasing contribution. The model can also predict the compost application rate needed to completely offset the initial loss of SOM. This research highlights that in locations like Sulawesi, the early years after planting can represent a critical period during which organic additions could support cocoa productivity and provide other environmental benefits
3 Published Papers

Funded by CRUK and University of Aberdeen and Esco
» University of Aberdeen, UK
(2017 to 2020)
Researchers: A-S Bouchon (supervisors: Prof. S. Woodward, Prof. D. Burslem and Dr. E. Boa)
This project set out to gain a better understanding of Verticillium wilt and how it can managed in the cocoa growing area in DR Congo (DRC) and Uganda. The project was largely supported by the University of Aberdeen and Esco with a contribution from CRUK. Results were published in Bouchon, A-S (2020). “Vascular wilt disease of Theobroma cacao in Uganda and DR Congo caused by Verticillium dahliae: studies on management using a genetic approach.” PhD Thesis, University of Aberdeen.See the Information Sheet for this project for further details
6 Published Papers

Funded by CRUK and COCOBOD, Embassy of the Netherlands, Accra, Mondelez International, Mars, GCGRA
» Cocoa Research Institute of Ghana
(2013 to 2018)
Researcher: Mr. E.Nsiah/G Lockwood (Consultant)
The supply of improved planting materials to farmers is a vital component in ensuring the sustainability of cocoa production. A public/private partnership between Ghana Cocoa Board (COCOBOD), Embassy of the Kingdom of the Netherlands to Ghana, GCGRA and its sister organisation CR(UK) Ltd, Mars and Mondelez International will contribute over €4million to the continuation of a major breeding programme, the Mabang Megakarya Selection Programme (MMSP) over four years. MMSP’s work will lead to Ghana’s seed gardens supplying farmers with new varieties which have been tested for their performance in an area affected by the devastating Megakarya form of Black Pod disease. In the longer term it will also develop improved clonal varieties which will be at the heart of the modernisation of cocoa production.
1 Published Paper

Funded by CRUK
» University of Reading, UK
(2015 to 2016)
Researchers: Dr. Andrew Daymond/Prof. Paul Hadley, Dr. Fiona Lahive
A 16 month post-doctoral project to screen the accessions in the International Cocoa Quarantine Centre (ICQC) at the University of Reading for traits which are likely to affect their yield potential and stress resilience with a view to identifying interesting materials for priority inclusion in breeding work. The project also involved a study period at the International Cocoa Genebank, Trinidad with the Cocoa Research Centre (UWI, Trinidad)to evaluate some of the same clones grown under field conditions.
1 Published Paper

Funded by CRUK and Bioversity International/CGIAR/Mars/CRA Ltd
» Bioversity International
(2012 to 2016)
Researchers: B. Laliberte, M. End, S. Weise
The review, coordinated by Bioversity International, presents an impartial, evidence-based review of cacao propagation methods, to serve as a basis for the assessment and implementation of strategies for providing farmers with quality planting materials, adapted to current and future needs (cultural, institutional, technical, environmental and financial). It describes the various propagation methods available for the production and supply of large numbers of cacao plants to growers. It is hoped that the result of the efforts of the key authors provides a basis to build on for case-specific recommendations. As the supply of new improved planting material to farmers is at the heart of improving cocoa productivity and modernizing the crop, we hope that the information in the review will make its way into national cocoa plans, and help to make cocoa farming more attractive and more sustainable. The full review is available from http://www.bioversityinternational.org/e-library/publications/detail/supplying-new-cocoa-planting-material-to-farmers-a-review-of-propagation-methodologies/
2 Published Papers

Funded by CRUK
» University of Reading, UK
(2010 to 2016)
Researchers: F. Lahive and L. Handley (supervisors:Prof.P.Hadley, Dr. A.Daymond, Dr. J.Dunwell)
A project involving 2 PhD students to investigate the potential effects of climate change on the growth, physiology and quality of different genotypes of cocoa. The research will be largely undertaken in the new controlled environment glass house facilities at the University of Reading which allow the quantification of factors such as temperature, CO2 and water stress. Fiona Lahive published her PhD thesis entitled "An examination of the impacts of climate change variables on growth and photosynthesis in Theobroma cacao L." in 2015. Her research showed that the responses and interactions varied according to the age of the plants (seedling v older budded plants), and that there were some differences in these responses amongst the limited number of genotypes studied. Liam Handley studied the effects of environmental variables on flower and fruit development. He found that water deficit and CO2 levels did affect characteristics such as pod growth rate, bean weight and fat content though the effects differed between the harvest periods.
7 Published Papers

Funded by CRUK
» University of Reading, UK
(2014 to 2015)
Researcher: Dr. A.Wetten
A six month study to improve our understanding of the basic processes underlying CSSV infection of cacao thereby supporting programmes for the control of the disease. The main objective of this project is to characterise the feeding behaviour of CSSV vector and non-vector mealybugs, and thus the factors that influence virus transmission using the Electrical Penetration Graph (EPG) technique but other potential vectors will also be studied.
2 Published Papers

Funded by CRUK
» University of Reading, UK
» Cocoa Research Institute of Ghana
(2011 to 2015)
Researcher: F. Owusu-Ansah (Supervisors: Dr. F.Baksh & Dr. E. Allan)
This PhD project involved the application of modern statistical techniques to the design and analysis of cocoa breeding programmes and field experiments. Frank Owusu Ansah published his thesis entitled "Methodology For Joint Modelling Of Spatial Variation And Competition Effects In The Analysis Of Varietal Selection Trials" in 2015. The model was developed by extending an existing model by relaxing the assumptions about the competition component to allow for more realistic options and to cope with multiple tree plot layout while simultaneously modelling fertility effects. Autoregressive and cubic spline terms were used to model the competition and fertility effects respectively. An evaluation of the new model indicated its relative superiority in giving efficient and reliable conclusions for both plot and tree level analyses. The comparative advantage of this model over existing methods is demonstrated using data from Cocoa Research Institute of Ghana
5 Published Papers

Funded by CRUK
» University of Reading, UK
(2010 to 2015)
Researchers: P. Hadley, J. Dunwell, N.Cryer, I.Ullah
A post-doctoral research project to investigate the genetic and soil/root environment factors affecting cadmium uptake by cocoa with a view to developing molecular tools to screen for rootstock varieties which accumulate less cadmium even when grown in volcanic soils which contain naturally higher levels.
2 Published Papers

Funded by CRUK
» University of Reading, UK
» Cocoa Research Institute of Ghana
(2010 to 2012)
Researchers: Wetten, A.
A post-doctoral research project to gain a better understanding of the distribution, movement and strain profile of the pathogens responsible for CSSV. A 454 sequencing approach will be used to rapidly and cost-effectively characterise CSSV strains in samples collected from sites throughout West Africa. Information will also be gathered on the extent of non-CSSV viruses and the role of indigenous plant species in the epidemiology of CSSV will be investigated with a view to improving the guidance given to farmers on managing the flora on and near to their farms to reduce the risks of CSSV spread
3 Published Papers

Funded by CRUK and CRIG
» Cocoa Research Institute of Ghana
(2008 to 2012)
Researcher: Dr Rob Lockwood
A joint project with CRIG to analyse and interpret historic and more recent data from CRIG's breeding programme with a view to selecting types for further evaluation in seed garden and MMSP trials.

Funded by CRUK
(2007 to 2011)
Researcher: J. Sarfo (Supervisor:Dr. R. Bateman)
One of two linked post-graduate research projects to evaluate the potential of pheromones and biocontrol agents for integrated pest management and developing improved spray technologies for use with biocontrol agents. Joe Sarfo (CRIG, Ghana) experimented with different formulations of pheromones, trap design, height and density to optimise the methodology. Traps designed with low cost, locally available materials were found to be effective, though the best results were obtained using traps with a sticky outer surface in addition the standard sticky inner surface. Field experiments showed that although catches of male Sahlbergella singularis, the dominant mirid species in this region of Ghana, were significantly reduced in mass-trapped fields, pheromone trapping did not control mirid numbers or damage on cocoa, likely due to a combination of factors including the erratic airflow (sometimes absent) in canopies, patchy distribution of mirids within cocoa plantings, and their flight behaviour. However, the technology offers potential as a tool for monitoring mirid populations with a view to better targetting pest control by other means.
9 Published Papers

Funded by CRUK
(2007 to 2011)
Researcher: N. Jessop (Supervisor: Dr.Roy Bateman)
One of two linked post-graduate research projects to evaluate the potential of pheromones and biocontrol agents for integrated pest management and developing improved spray technologies for use with biocontrol agents.
7 Published Papers

Funded by CRUK
» University of Reading, UK
» University of Aberystwyth, UK
(2010 to 2010)
Researchers: Dr.A.Wetten, Dr.J. Allainguillaume
A post-doctoral research project to develop a sensitive and strain-independent molecular screen for CSSV and to assess its efficacy as part of the quarantine procedure. Geographical variability of CSSV isolates, and putative reservoirs of virus in non-cocoa species will also be investigated to improve our understanding of virus spread.
1 Published Paper

Funded by CRUK
» University of Edinburgh, UK
(2010 to 2010)
Researcher: E. Resende
This MSc study aimed to produce a vulnerability assessment of the cocoa productivity in Cote d'Ivoire using the latest findings of the IPCC reports, building potential scenarios of impacts based also on related literature review and addressing possible ways to adapt to climate change through findings from focus groups and interviews with farmers and policy makers in Cote d.Ivoire.
2 Published Papers

Funded by CRUK and PTPP London Sumatra
» Natural Resources Institute, Kent, UK
» London Sumatra, Medan, Sumatra 20111, Indonesia (See also Bah Lias Research Station)
(2008 to 2010)
Researchers: Prof.D. Hall, Dr. S. Nelson
A research project, jointly supported with PTPP London Sumatra, to isolate the sex pheromone for the Helopeltis mirid which causes significant losses in SE Asia, for use in an integrated pest management system.
1 Published Paper

Funded by CRUK
» Natural Resources Institute, Kent, UK
» Cocoa Research Institute of Ghana
(2008 to 2010)
Researchers: Prof. D. Hall, Dr. S. Lowor, Dr. A Cudjoe
A research project to isolate the sex pheromone of the stem borer, an increasingly important pest in Ghana, for potential use in an integrated pest management system.
1 Published Paper

Funded by CRUK
» University of Reading, UK
(2006 to 2010)
Researcher: G. Ameyaw (Supervisors: Dr. A. Wetten & Dr. J. Allainguillaume)
A post-graduate research project to study the movement of CSSV virus asit moves through the host plant. The research demonstrated that although sections of DNA from CSSV appears to be transmitted from the mother plant to seeds, it is inactivated and does not result in CSSV infection in the seedling.
5 Published Papers

Funded by CRUK and LNV Sustainable Cocoa Subsidy Scheme (Dutch Buffer Stock)
» University of Aberystwyth, UK
(2006 to 2010)
Researcher: S. Pierre (Supervisors: Dr. G. Griffith & Dr. I. Scott)
A post-graduate research project co-funded by the Government of the Netherlands and CRUK to study changes in host metabolism between resistant and susceptible varieties at the biochemical level. The research included the development of new method to quantify the amount of fungus in planta using a realtime quantitative PCR technique and studied the occurence and changes in proteins associated with different strains of fungus during the infection process.
5 Published Papers

Funded by CRUK and LNV Sustainable Cocoa Subsidy Scheme (Dutch Buffer Stock)
(2005 to 2010)
Researchers: Prof. Paul Hadley, Prof. Mike Wilkinson, Dr. Nicholas Cryer, Dr. Penny Tricker, Dr. Carlos Rodriguez-Lopez, Dr. Vladimir Bruhkin
A post-doctoral research project co-funded by the Government of the Netherlands to investigate the control of plant development and its response to environmental conditions and stresses caused by biotic and abiotic factors at the molecular level. This research contributed to our understanding of how regions and genes across the genome are differentially silenced or activated in response to environmental changes and developmental progression. Attention was focused on identifying environmentally sensitive regions of the genome that affect bean quality and yield potential. The results generated are being integrated with existing global genomics and transcriptomics research efforts to identify the particular genes involved and to define conditions for optimal gene expression. In the longer term, this work will assist in the breeding of clones that are well adapted to local conditions and will greatly improve the power of existing genetics research efforts.
11 Published Papers

Funded by CRUK
» University of Reading, UK
(2009 to 2009)
Researchers: Prof. P.Hadley, Dr. N.Cryer
A short project to collate genetic fingerprinting data from various sources and, in collaboration with scientists at USDA, CIRAD and Mars, to carry out an analysis to prioritise the accessions to conserve in the CacaoNet Global Strategic collection.
2 Published Papers

Funded by CRUK
» Imperial College, UK
» Cocoa Research Institute of Ghana
(2009 to 2009)
Researcher: R. Smith (supervisor Dr. R. Bateman
An MSc student placement to test novel nozzle designs against standard spraying equipment in Ghana.
2 Published Papers

Funded by CRUK
» University of Reading, UK
(2009 to 2009)
Researchers: Agung Susilo (UK Supervisors: Dr. P. Hatcher, Prof. P. Hadley)
A short project to enable an Indonesian student to carry out histological studies on the cocoa pod wall as part of his PhD studies at the Gadjah Mada University, Indonesia. The thickness of the lignified layer and its cell structure appear to be correlated with resistance to CPB, suggesting that this physical barrier is important in preventing emergence of the CPB larvae from the pod.

Funded by CRUK
» CATIE, Costa Rica
(2001 to 2009)
Researchers: U. Krauss, J.Crozier, G.M. ten Hoopen
Short placements for UK students to learn and develop fungal biocontrol techniques at a centre of expertise in CATIE, Costa Rica.
14 Published Papers

Funded by CRUK
» University of the West Indies
(2007 to 2008)
Researcher: F. Higgins (Supervisors: D. Butler/J Flood
A research placement for an undergraduate studentship for a student from University of Bath at the Cocoa Research Unit, Trinidad. The project involved determing the factors affecting conversion of wet weight to dry weight in cocoa, as well as training in vegetative propagation, small scale fermentationa and flavour evaluation techniques.

Funded by CRUK
» University of Nottingham, UK
(2004 to 2004)
Researcher: Dr P.C. Garnsworthy
A feasability study to determine potential use of NIR to replace cut test to assess cocoa quality.

Funded by CRUK
(2004 to 2004)
Researcher: J. Frith
This research was undertaken to monitor temperature and humidity conditions in containers of cocoa as they are shipped from producing countries to Europe.

Funded by CRUK
» University of Reading, UK
(2001 to 2004)
Researcher: C.Rodriguez Lopez (Supervisor: Dr. A. Wetten)
A PhD research project which set out to examine variation at the genetic level in somatic embryos produced using a tissue culture technique. This project constituted the first large-scale molecular characterisation of changes that occur during primary and secondary somatic embryogenesis in cocoa. The novel techniques developed during the project allow a rapid assessment of variation at both genetic and epi-genetic levels. The effects of time in culture, embryo origin, and genotype on somaclonal variation were assessed and this enabled recommendations to be made on the most appropriate procedures to reduce the risk of mutation/variation in somatic embryo production.
8 Published Papers

Funded by CRUK
» University of Reading, UK
(2001 to 2004)
Researchers: P. Hadley, A.Daymond
A post-doctoral research project to investigate the responses of different varieties of cocoa to changes in temperature, light levels and water stress under greenhouse and field conditions with a view to matching varieties to local growing conditions.
5 Published Papers

Funded by CRUK
» University of Reading, UK
(2000 to 2004)
Researcher: Y. Charters (Supervisors: Dr. M. Wilkinson
A post-graduate research project to develop a new genetic fingerprinting technique based on ISSR-PCR which could be used to distinguish large numbers of closely related accessions and link genetic markers with traits of interest to breeders.
5 Published Papers

Funded by CRUK
» University of Aberystwyth, UK
(2001 to 2003)
Researchers: Dr. G.Griffiths, Dr. I.Scott, Dr. T. Carver
A post-doctoral research project using electron microscopy to study the infection process. The study demonstrated that infection usually occurs through hair cells rather than stomata as had previously been thought.
4 Published Papers

Funded by CRUK
» University of Reading, UK
(2000 to 2003)
Researchers: Dr. M. Wilkinson, Dr. Nicholas Cryer, Dr. Yvonne Charters
The main objective of this project was to fingerprint all material held in the Reading Intermediate Quarantine Collection and to generate a SNP-based marker system that is fully transferable, related to target genes, and could be applied with minimal equipment. The programme of work was adjusted to take account of a USDA initiated programme to use the microsatellites generated at CIRAD to fingerprint Germplasm collections in the Americas. Allelic standards were created for each locus to replace the generic standards previously used to ensure transferability of results between laboratories. A total of 89 SNPs were identified across divergent material and these generated 39 CAPS markers across 30 loci. Some of these markers were used to screen large numbers of genotypes.
8 Published Papers

Funded by CRUK
» University of Aberystwyth, UK
(1998 to 2002)
Researchers: R. Birch (Supervisors: Dr. G.Griffiths, Dr. I.Scott)
A post-graduate research project to study the changes at the gene expression level for key enzymes as the infected cocoa shoot dies and the Witches' Broom fungus prepares to produce its spores.
5 Published Papers

Funded by CRUK
» University of Aberystwyth, UK
(1998 to 2002)
Researchers: J Nicholson (Supervisors: Dr. G.Griffiths, Dr. I.Scott)
A research project to use AFLP genetic fingerprinting to study the relationships between different strains of Witches' Broom fungus and its close relationship to Frosty Pod fungus (Moniliophthora roreri).
4 Published Papers

Funded by CRUK
(2000 to 2000)
Researcher: Dr. A.Moxon

Funded by CRUK
(2000 to 2000)

Funded by CRUK
» University of Reading, UK
(1997 to 1997)
Researcher: Dr. M.J. Wilkinson
A short project to evaluate the potential of the Inter-Simple Sequence Repeat (ISSR)-PCR technique to assess levels of homozygosity/heterozygosity in cocoa germplasm.

Funded by CRUK
» University of Reading, UK
(1996 to 1997)
Researchers: Y. Charters (Supervisors: Dr. A. Culham, Dr. M.J. Wilkinson, Dr. P. Hadley
A short project to evaluate the potential of the Inter-Simple Sequence Repeat (ISSR)-PCR technique for the genetic characterisation of cocoa germplasm.
2 Published Papers

Funded by CRUK
» University of Reading, UK
(1995 to 1995)
Researchers: M.J.Wilkinson, N.Cryer
Pyrosequencing is a new technique that allows for real time, simultaneous sequencing of DNA of up to 96 samples. The system has been widely used in medical genetics for screening for single base sequence mutations associated with genetically inherited disease but there has only been a couple of papers that use the technique on plants. The recently aquired pyrosequencer at The University of Reading will be used in a feasibility study to assess the value of the technique for large-scale screening of trees for valuable alleles of resistance genes

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