Julie Graham

The fruit industry relies on a small number of varieties and a decreasing number of chemicals, presenting serious challenges for future sustainable growth. No suitable high-quality varieties with resistant to pests and diseases are available. This is coupled with climate change where unpredictability in phenotypic expression is resulting at both small and large spatial scales. The ultimate aim of much of the research, therefore, is to understand the development of phenotype and to facilitate knowledge-based breeding of sustainable high quality resistant soft fruit varieties through the development of tools and training of modern breeders. The identification of links between genotype and phenotype, and the subsequent identification of molecular markers for deployment in a breeding context is essential so that efficiency of selection and ultimately time to cultivar release can be improved and accelerated beyond current timescales. The research has been possibly through the development of genetic linkage maps in raspberry and blueberry and other fruit crops and mapping QTL to assist in the understanding of complex traits of commercial and environmental importance. In raspberry genome sequences and GbS maps have allowed us to link traits to underlying genes. A range of other genomics tools are being utilised to study changes in gene expression in response to various conditions. The traits of most interest include pest and disease resistance, season and fruit quality traits including flavour, colour and softening.

InnovateUK-funded research

Imaging sensor solutions in the soft fruit industry for high-throughput phenotyping and monitoring of abiotic and biotic stresses for premium variety production and maximised yields TSB 101819

New crop varieties that can tolerate abiotic/biotic stresses are essential for maintaining crop productivity in current and future growing environments. Breeding stress-tolerant crop varieties, however, is limited by the precision and throughput of plant phenotyping. This project will develop and apply a novel method for precise and high-throughput field phenotyping of soft fruit crops using infrared thermography and hyperspectral imaging combined with precision agriculture to optimise crop inputs. Changes in shoot and leaf physiology can provide an indirect indicator of abiotic and biotic root stresses, which can be monitored with imaging techniques. Soft fruit crops such as raspberry can experience multiple stresses in field conditions, including poor soil conditions, variable water availability, and attack by root rot pathogens and root-feeding vine weevil larvae. Phenotyping data will be linked to genetic markers to facilitate breeding of productive, stress-resistant soft fruit varieties. This novel high-throughput phenotyping platform will accelerate the development and release of productive high-quality soft fruit varieties that perform well in sustainable reduced input cropping.

Using genomics technologies to determine the mechanism of resistance to phytophthora root rot in raspberry for future breeding applications to raspberry and other crops Agri-Tech Catalyst 1408

In the Northern Hemisphere with damper conditions, Phytophthora root rot is causing a rapid decline in raspberry plantations grown in soil and also greatly decreasing the life span of production of raspberries grown in substrate with negative environmental consequences. Plant-based resistance is the only way forward and limited material exists that consistently withstands infection with little/no symptom production. The development of gene-based techniques offers an opportunity to identify genes that have a significant role in this plant-pathogen interaction to determine the mechanisms of resistance and develop novel strategies of protection including breeding. How both resistant and susceptible varieties respond at the level of gene expression and how the pathogen responds to the differing phenotypes will identify gene markers and allow strategies for control to be developed.

Application of genomics in raspberry variety development  TSB 118134

Significant advances have been made in the development of genomics and metabolomics technologies in raspberry. Industry has recently identified a gap in the process of transferring these technologies into breeding platforms which can be utilised to improve speed and precision in variety development possibly reducing 5 years or more in development. Currently there is an unmet demand for UK-grown soft fruit and great scope for increasing the number of consumers who purchase soft fruit in season with currently only 36% uptake. The fruit industry relies on a small number of varieties and a decreasing number of chemicals, presenting serious challenges for the future. No suitable high-quality varieties with resistant to pests and diseases are available. A technology platform for breeding multiple traits utilised in high throughput format would lead to significant advances in time to variety development, precision in selection, cost and the pipeline could be transferred to other berry crops.

Breeding for physical resistance traits - protecting soft fruit crops from pests and pathogens TSB 153

This project aims to understand and utilise plant physical mechanisms for resistance to pest and diseases in soft fruit bush crops, to overcome changes in EU Directive 91/414/EEC and WFD and satisfy future consumer demand for residue-free, high-quality fruit grown in the UK. Fresh fruit accounts for a market of £4 billion in the UK, and berries account for 17% of this. UK raspberries have a value of £121 million, strawberries £196 million, blackcurrants £12 million and blueberry, currently a minor player in cropping area has a value of £95 million. Demand for UK-grown fruit is increasing dramatically; however, few high-quality soft fruit varieties are available with adequate pest and disease resistance due to the emphasis placed on fruit quality by major commercial fruit breeding companies. For production to be sustainable, a greater understanding of plant-derived resistances to pests and diseases is required that can be deployed in IPDM programmes to reduce reliance on chemicals but still produce high-quality fruit. Physical resistance traits are particularly promising for crop protection because they tend to be more durable against pest and disease adaptation, and unlike chemically-based resistance traits, are less likely to adversely affect fruit quality. This work aims to look at root architecture and morphology, leaf trichomes, cane/stem architecture and plant habit to determine how variation in these physical traits contributes to resistance against major soft fruit pest and diseases. Using raspberry as a model, key genes in chromosomal regions controlling variation in these traits can be selected across different fruits and used to greatly reduce the timescale for variety development.

Developing genetic resources in blueberries Agri-Tech catalyst 360151

Lack of blueberry cultivars with high fruit and nutritional quality combined with early and late ripening is a key issue negatively impacting UK blueberry growers. UK growers are currently planting mixtures of existing varieties, mainly from the USA, but the long-term performance, fruit quality, yield and consumer acceptance of these varieties in the UK varies considerably. This proposed project aims to develop genetic resources in blueberries to identify appropriate breeding and new mapping populations, with pre-selection for traits of economic importance for the UK in order to produce new cultivars that are specifically suited for UK production. A parallel examination to explore genotyping by sequencing as a rapid method to identify SNP dosages in a mapping population of autotetraploid blueberry, will be conduced in order to construct a high-density SNP linkage map and to relate the map information to phenotypic data to improve the speed and precision of a targeted breeding programme.

Improving yield stability in UK blueberry production Agrt-Tech Catalyst 229147

Lack of yield stability is a key issue negatively impacting UK soft fruit growers, preventing accurate profit prediction and maximisation, causing volatility of UK supply.  The problem is now well recognised within industry, though the causes of significant season to season yield variation are unknown. This proposal aims to identify the physiological, biochemical & genetic processes underlying yield limitations, thereby identifying causes of the yield volatility phenotype. An examination of the impact of growing environment and management on yield will be undertaken to allow development of predictive yield maps & models that provide frameworks for yield optimisation in the short to medium term. This underpinning knowledge will be transferred to growers and also used to develop molecular markers for yield stability allowing long-term solutions to the problem, thereby future proofing the UK soft fruit industry, particularly blueberry crops with application to other fruit crops. 

Raspberry Auxin Soil/Substrate Protectant (RASP) IUK48163

Phytophthora infestans is the pathogen that caused the Great Irish Potato Famine and today over 170 described species of Phytophthora cause crop disease on a global scale, costing commercial crop industries billions of dollars. The UK fruit industry and raspberry particularly has been decimated by Phytophthora root rot (PRR) with an 80% reduction in field production leading to a smaller pot based short term industry supported by extensive fruit imports. Methods to control infection and spread are limited by current legislation that limit the use of prophylactic fungicides and increase the importance of novel control methods based on host resistance, growing media and watering. Phytophthora rubi and P. fragariae are PRRs which spread through plant propagation, growth media and water flow in plantations. Manipulating the physical, chemical and biological properties of the growth medium has the potential to play a key role in inhibiting PRR. Commercial plant growth substrates can be designed specifically to meet a crops individual needs with regards to nutrient requirement, water management and grower preferences. Manipulating the growing media's physical, chemical and biological properties can lead to a stronger healthier root and plant system, while also limiting and actively suppressing the growth and spread of harmful root pathogens, such as PRR. Specific additives have previously been incorporated into growing media to control and prevent other root pathogens and pests such as Vine Weevil, Fusarium spp. and Pythium spp. A recent JHI study identified multiple responses triggered in a PRR resistant raspberry plant upon challenge with P. rubi, including a mechanism, which has the potential to improve a plants resistance to PRR. The growth medium can be improved by the manipulation of these plant-derived chemical signals that are normally induced upon pathogen challenge in resistant cultivars, to boost the immune capabilities of susceptible cultivars. Using molecular methods such as gene expression, genetic markers and fluorescent pathogen cultures we can track disease development in the root-zone environment in different growing media substrate formulations. The innovative range of growth substrate additives developed in this project will stimulate raspberry root growth signal to improve the root system under a controlled irrigation regime and secondly actively inhibit the growth and spread of root pathogens. Establishment of optimal raspberry growing conditions integrated with early pathogen detection and control of PRR spread will transform raspberry agronomy, maximising yield and securing the UK soft fruit industry with application to other crops worldwide.

Plant Sensing to determine environmental impacts on developmental processes leading to crop yield. IUK 9712

Throughout their life cycle, plants are subjected to many adverse environmental conditions including low light levels and periods of drought or extreme temperatures which can dramatically affect plant survival and limit productivity. In order to cope with such stresses, plants adjust metabolically and physiologically. Unanticipated variation in crop development is already in evidence in a range of crop varieties resulting in yield instability with significant negative impacts on the rural economy, environment and wellbeing. Cherry and blueberry are prime examples where, depending on season, a condition known as Cherry June Drop can occur where unripe fruit fall from the tree to excessive levels, drastically reducing yield. Similarly in blueberry widely varying yield is achieved depending on season with factors such as bud initiation being important. Currently no methods exist to understand when and how a plant's development has been disrupted or to characterise the key environmental signals responsible. The lack of knowledge in these two areas severely limits the capacity for active crop management to optimise yield or to breed for future environmental resilience. This work will use a field based plant and environmental monitoring approach to develop environmental models of blueberry bud initiation and cherry June Drop. We will attempt to identify signals that arise from the plants short-term responses to environmental conditions ('sensing'), to identify the point(s) at which the plant's development leads to the unwanted phenotype (excessive June Drop or excessive vegetative bud development). Blueberry and Cherry are key crops with great potential for UK production but which currently supply only 7% and 5% respectively of the market with UK fruit. Current expansion particularly in cherry is presently impeded by this unpredictable developmental phenotype, 'June Drop', which can lead to fruit losses of 80%. In blueberry, yield varies as much as 50% across seasons. Project outputs will allow, for the first time, the ability to carry out in-field environmental monitoring and crop phenotyping to understand environmental factors controlling crop production and develop bespoke crop management systems that will mitigate the effect of environmental variation and ensure future crop yield stabilisation and for cherry to encourage new plantations to reduce imports. The outputs would also have application to a wide range of other crops where other phenotypic disorders can be detected and methods developed for mitigation and also for plant breeding where varieties can be selected based on imaging signals of plant responses to environmental conditions.

Feasibility of developing a novel breeding methodology to improve berry flavour Agri-Tech 447185

This feasibility study aims to improve raspberry flavour by utilising omics data alongside historic genotype, phenotype, met & QTL data with novel flavour profiling research to develop new breeding models and decision support tools. Season and environment have a significant impact on flavour often resulting in poor consumer liking, characterised by excess acidity in relation to sweetness. Flavour a complex traits with a large GxE effect already poses a challenge to breeders and will be more problematic with extreme weather events and climate changes. Conventional breeding and selection techniques are slow, hindered by seasonal and environmental variation with QTL mapping also varying with the environment. Recently developed omics tools (GbS maps, genome scaffolds, gene expression & metaboloics data, correlation networks) will allow us to investigate and validate links between berry flavour and its controlling factors (metabolites, genes, environment) to develop a breeding model.