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Drivers of chemical diversity, niche-partitioning and insect resistance in cultivated and wild species of Coffee

Primary Supervisor: Dr Simon T Segar, HAU

Secondary supervisor: Professor Simon Edwards, Dr Heather Campbell and Dr Joe Roberts

PhD project title: Drivers of chemical diversity, niche-partitioning and insect resistance in cultivated and wild species of Coffee

University of Registration: Harper Adams University

Project outline:

While two species from the genus Coffea (Rubiaceae) are used to produce the vast majority of the World’s coffee beans an additional 122 species are found growing in the wild. Globally the retail value of coffee was US$ 83 billion in 2017. A number of issues threaten this important commodity, not least pests and pathogens such as the coffee berry borer (Hypothenemus hampei) (CBB) and coffee rust (Hemileia vastatrix), CBB being responsible for damage at $US 500 million/year. Changing climates are set to compound these problems across existing commercial genotypes (Jaramillo et al., 2011). Indeed, quantifying the abiotic and biotic niches and variable resistance of domesticated and closely related wild species is an urgent task, as we seek to enhance the resilience of the industry. In addition to being a highly valued stimulant, the purine alkaloid caffeine has a role to play in defence against biotic threats. The tissue of many species also contains a wealth of polyphenolic compounds and other deterrents. The genus is ripe for comparative study across biomes and taxa. We know that wild coffee populations generally have fewer pests and incidences of disease. Why is this? Pests and diseases can also worsen as environmental conditions change. We expect variation in chemical composition to play a central role in explaining these observations.

Hybridisation has also been central to the commercial success of coffee, with Coffea arabica being a natural allotetraploid cross between C. canephora and the wild C. eugenoides. Breeding programmes will benefit greatly from detailed phenotypic and resistance data from multiple populations of wild coffee, while these data would also be central to any investigation into the evolutionary drivers of chemical diversity in the genus. This project therefore requires cross pollination between the traditional disciplines of both ‘applied’ and ‘curiosity driven’ research.

We will relate resistance to CBB and prevalence of other insect pests to i) chemical composition and/or ii) environmental factors (Vega et al., 2019). This project will explore drivers of chemical diversity across habitats (e.g. non-domesticated vs. domesticated, forest vs. savanna) in one domesticated, one semi-domesticated and two wild coffee species in Kenya. There is wide potential student led research, but the underlying expectation is the generation of a comparative data set sensitive to variation across habitats. These data should be used to help define the axes along which pests and/or pathogens exploit their resources. For example, how does within species chemical composition differ among habitats and how does inter-species niche occupancy relate to chemical diversity? Do we see changes following the transition from forest to agro-ecosystems through domestication? This would help us to understand the potential for niche-partitioning and pre-adaptation of wild populations/species to cultivated environments, identify resistance traits and allow us to quantify the role of habitat specialization in shaping chemical diversity. These outcomes would potentially contribute directly to establishing the next generation of cultivated coffee genotypes.

Field work and resistance trials will be conducted in collaboration with icipe (Kenya) and Kew Gardens (UK) will focus on up to three regions in Kenya to cover the ranges of our focal species C. arabica, C. pseudozanguebariae and C. eugenioides. The new UHPLC-Orbitrap-MS analysis protocol developed by the Natural Chemistry Research Group (University of Turku, Finland) allows the qualitative and quantitative analysis of polyphenols and alkaloids. Molecular laboratory work may seek to explore population structure and diversity of Coffea, using shallow screening (e.g. microsatellites) in the first instance followed by bait capture for a subsample. Insects collections will be curated for morphological and DNA barcode-based identification.

BBSRC Strategic Research Priority: Sustainable Agriculture and Food: Plant and Crop Science

    Techniques that will be undertaken during the project:

    Lab techniques include:

    • DNA/RNA extraction, potentially phylogenomics and/or population genetics.
    • Use of HPLC-MS and GC-MS.

    Field work

    • Organisation and implementation of field collection expeditions across a range of natural habitats.
    • Design and implementation of host preference and resistance trials and rearing of insect herbivores.

    Analytical techniques

    • Statistical analysis of large metabolomic data sets
    • Integration of species distribution models, chemical data sets and insect performance.

    Contact: Dr Simon Segar, HAU