emr: research, development & innovation annual

Transcription

1 emr: research, development & innovation annual report 2014

2 Governing Board Chairman: Mr Frank Attwood Professor Ian Crute CBE Professor John Mumford Science & Industry Advisory Board Chairman: Professor Ian Crute CBE Dr Paul Burrows Professor Nick Battey Professor William Davies CBE Dr Helen Ferrier Mrs Marion Regan Professor Leon Terry Technical Advisory Committee Chairman: Dr Oliver Doubleday Mr Neil Franklin Mr Richard GreatRex Mr Tony Harding Mr Richard Harnden Dr Theresa Huxley Mr Robert James Dr Jon Knight Dr Edwin Moorhouse Mr James Simpson Mr Alan Wilson Resigned Jan 2015 Auditors: Crowe Clark Whitehall LLP, 10 Palace Avenue, Maidstone, Kent, ME15 6NF Solicitors: Brachers LLP, Somerfield House, 59 London Road, Maidstone, Kent, ME16 8JH Banking: Barclays Bank, 40/46 High Street Maidstone, Kent, ME14 1SS Patent Agents: Marks & Clerk LLP, 90 Long Acre, London, WC2E 9RA East Malling Research New Road, East Malling, Kent, ME19 6BJ, UK A private company limited by guarantee. Registered in England. Registration No Charity Registration No Registered office as above Telephone: +44(0) Fax: +44(0) Electronic mail: enquiries@emr.ac.uk Website: Editors: Angela Chapple and Jane Gregory Graphics Design & Photography: Penny Greeves East Malling Research 2015

3 annual report 2014: contents Page Introduction 1 Professor Peter Gregory Genetics and Crop Improvement 7 Dr Xiangming Xu Pest and Pathogen Ecology for Sustainable Crop Management 15 Professor Jerry Cross Resource Efficiency for Crop Production 27 Dr Mark Else Update on Rootstock Research at EMR - a Case Study 32 Dr Mark Else Studentships 38 Feli Fernández & Nicola Harrison Glasshouse and Field Services 40 Graham Caspell Wealth and Job Creation through Innovation 42 Ross Newham Communications 45 Dr Ursula Twomey & Ross Newham Staff Publications 48 Accounts 52 Staff List 53 EMR Research Projects 57 EMR Postgraduate Research Projects 64

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5 introduction: Professor Peter Gregory 1 After the excitement of EMR s Centenary celebrations in 2013, this year was more down-to-earth, with the focus returning to ensuring the long-term future of our activities. The last event of our Centenary year was the Amos Memorial Lecture at the end of February, at which I spoke on The Scope of Scientific Research in Fruit Growing the same title that Professor Dunstan, Principal of Wye College, had spoken to in October 2012 to stimulate the creation of a fruit research institute in Kent. The lecture provided an opportunity to reflect on the practical benefits that had flowed to horticulture-related industries from the scientific and research activities at East Malling, and to look forward to the challenges that our society faces in the coming decades. Chief among those new challenges are the opportunities and threats posed by a warming and more variable climate (2014 having had the wettest winter and being the warmest year since records began), the introduction of new pests and diseases, a greater focus on the nutritional aspect of food security in which fruits play a major role, and the development of new fruits and fruit products to meet the needs of an urban and ageing population. The historic and current impacts of research at East Malling are profound. During the year, we commissioned Brookdale Consulting to assess the social and economic impacts of our research. This showed that the historic value of our work on apple rootstocks and controlled storage is estimated at 8.9 billion to the global economy, and that the ongoing impact of our work is estimated to be worth 216 million over the last ten years. For every 1 spent at EMR, at least 7.5 is returned to the UK economy. Looking forward, their analysis demonstrates that EMR has a strong contribution to make to major challenges facing the UK, and beyond, including resilience of supply chains, demand for British products, climate change, water and energy efficiency, emerging pests and diseases, healthy eating and food security. Furthermore, consultations with industry partners showed that our role is valued, and that they anticipate EMR making a strong future contribution to sustainable intensification. v Steve Visscher, Deputy Chief Executive of BBSRC, and Peter at the launch of the Brookdale Consulting report (above) and the report (below)

6 2 introduction Petunias in the glasshouse being used for media trialling one of the suite of new EMS businesses Roger Carline, Managing Director of East Malling Services v Our relationships with industry partners have deepened and broadened during the year, mainly as a result of our continuing success with Innovate UK (formerly the Technology Strategy Board) and the growth of our commercial subsidiary, East Malling Services Ltd. Our investment in staff and facilities has been rewarded through our successes in winning industrial partnership awards with a wide range of companies in both an agricultural engineering call and via the Catalyst Fund of the AgriTech Strategy. Besides our more usual partnerships with producer and marketing organisations, we are now working with instrument manufacturers, imaging specialists, weather service companies and specialist food and juice processors to research and develop a wide range of products for horticulture-related industries. EMR currently has eight projects under the AgriTech banner, and conversations about new projects continue. Meanwhile, business in East Malling Services Ltd, under the leadership of Roger Carline, is growing as well. Our commercial services of growing media evaluation, crop protection trialling, and DNA fingerprinting have been marketed more effectively resulting in greater profitability, and we are looking to launch a new service in 2015 encompassing novel crop and variety trialling. The strawberry breeding club was successfully renewed, apple and pear rootstock breeding was re-funded by its two sponsors, and apple breeding has been restarted following an agreement with a commercial sponsor. One consequence of this increased activity is that our income from external sources is increasing in it was up by 18% on the previous year. We also had significant success in winning competitive funding from the Horticulture Development Company (HDC) to manage three pest and disease research programmes for soft and top fruits for the next five years. This was the first example of a new style of funding from the HDC, which involved working with others to form consortia that could deliver the range of research requirements that the HDC research committees wished to commission. These programmes provide a much firmer base for future planning.

7 3 Peter Gregory with Tony Harding of Worldwide Fruit after the signing of the variety breeding contract (left) and talking to George Eustice MP, the Parliamentary Under Secretary of State for farming, food and marine environment at Fruit Focus 2014 < As in recent years, our research staff have continued to increase in number. Much of the increase in 2014 occurred in the area of genetics, with Drs Charlotte Nellist, Helen Cockerton, Bo Li and Robert Vickerstaff joining Richard Harrison s team to work on a range of externally-funded projects. Dr Louisa Robinson-Boyer and Charles Whitworth also joined our genetics programme, while Jennifer Kingsnorth added to the expertise in the pest and pathogen programme, mostly to undertake projects funded by Innovate UK. Finally, we were pleased eventually to recruit a tree physiologist, Dr Julien Lecourt, who is initiating research on the culture of vines in southern England and on new growing systems for apples. All of these new appointments are adding significant depth to the skills base available at EMR. We also continued with our successful policy of partial retirements, which aid scientific continuity, with Jean Fitzgerald moving to part-time working in mid-year. Our research activity is now thriving and producing new knowledge across our three programmes and five cross-cutting themes. In our Genetics and Crop Improvement programme, substantial progress has been made in the characterisation of determinants that facilitate the jumping of hosts by pathogens. Sequencing and analysis of 19 pathovars of Pseudomonas syringae (the cause of cherry and plum canker) has led to greater understanding of how pathogens evolve and specialise on different hosts and the strategies that they adopt to suppress resistance. The investment in new DNA sequencing technologies and improved bioinformatics capabilities at EMR has underpinned this rapid progress such work would have been inconceivable only a few years ago. We were very pleased that one of our PhD students, Michelle Hulin, was awarded a prize by the Marsh Christian Trust for her contribution to this work. v Michelle Hulin receiving the Marsh Christian Trust prize In Pest and Pathogen Ecology and Crop Management, 2014 saw significant advances in our research with industry into the behaviour of Spotted Wing Drosophila (SWD) in the UK.

8 4 introduction Bethan Shaw explaining how to identify Spotted Wing Drosophila to growers Drosophila suzukii male image taken from a poster at an information day hosted by the HDC and EMR v produced by Bethan to help with identification v The national SWD adult monitoring programme showed large fluctuations in the timing and abundance of the pest from year to year; the pest appeared earlier and numbers were higher following the mild winter of 2013/14 compared with 2012/13. Monitoring of different habitats showed that numbers were higher in woodland and tree crops than elsewhere, and in cherry orchards it was found that attacks on the fruit can occur before the first adults are caught in traps. This latter observation is crucial to developing effective strategies for management of the pest and suggests that current traps cannot be relied on to determine whether insecticide sprays are required. This research is ongoing, but is already contributing to the effective practical management of the pest in commercial crops. New research in one of our cross-cutting research themes (the science underpinning rootstock performance) has led to the development of a two-locus model and molecular markers that can predict the level of dwarfing an apple rootstock will confer to the scion based on its genotype. Two Quantitative Trait Loci (QTL) that co-localise with previously determined major dwarfing loci (as well as QTL for early bearing, flower density and fruit yield), have been identified. Transcriptome sequencing to identify key genomic regions and genes associated with rootstock-conferred control of vigour, combined with fine-mapping of these QTL regions, will enable us to develop reliable markers for marker-assisted breeding and to improve our understanding of the genetic interactions between dwarfing rootstocks and their scions. In my last two reports I mentioned that the Biotechnology and Biological Sciences Research Council (BBSRC) had invited us to apply for some strategic funding. Despite an enormous amount of work by staff at the University of Reading and EMR, this funding did not materialise. The consequence has been that the Boards of EMR and the East Malling Trust are now looking elsewhere for a potential partnership that could ensure the

9 5 Taking a leaf sample for DNA analysis v long-term sustainability of EMR both intellectually and financially. Talks with potential partners are at an exploratory stage, but will be a major focus of effort in early Meanwhile, we are continuing to explore means of securing capital investment to renew our ageing glasshouse, insect rearing and controlled growth room facilities, and update our instrumentation and storage rooms for research on produce quality. We had hoped that an Innovation Centre for Fresh and Prepared Produce might provide the vehicle for this via the AgriTech Strategy, but this now appears unlikely. However, as 2015 dawns, other funding opportunities are emerging that we shall be pursuing vigorously. A personal highlight of the year was my attendance at the Congress of the International Society of Horticultural Science at Brisbane. I received many comments from international well-wishers delighted to see EMR present and participating in the programme of oral papers. In the week prior to the Congress, I was pleased to visit Plant & Food Research in New Zealand to see something of their work. I gave talks at four locations about our renewed research activity, and this has been followed by several exchanges of correspondence to develop joint research projects between them and us. Finally, this will be my last annual report as I have decided that after four years at the helm, and ten years as a chief executive of a research institute, it is time to focus on other academic interests. So, I hope that you will enjoy reading about our activities in 2014 and be as enthusiastic as I am about what has been achieved by our skilled and dedicated staff.

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11 genetics and crop improvement: Professor Xiangming Xu 7 The Genetics and Crop Improvement Programme (GCI) focuses on understanding the genetic basis of agriculturally important traits to underpin the genetic improvement of Rosaceous fruit crops. It undertakes breeding programmes, with support from industrial partners, producing commercially viable cultivars of strawberry, raspberry, cherry and scions and rootstocks for apple and pear. Research skills within the group encompass genetics, molecular biology, image analysis and bioinformatics. One important research output is molecular markers for important plant traits to facilitate breeding with improved precision and efficiency, thus accelerating the breeding process. Basic research is currently focused on understanding the genetic basis of the mode of pathogenicity of plant and insect pathogens, host responses to colonisation by arbuscular mycorrhizal fungi (AMF), and water use efficiency in herbaceous and woody perennials. Researchers also work to elucidate the genetic variants controlling resilience to a variety of abiotic and biotic stresses and how these affect yield potential and fruit quality. In addition to studies on fruit crops, the GCI programme is also undertaking research on host-pathogen interactions on UK native trees, and expanding research and development for novel crops. Several large projects began in 2014 in the area of host-pathogen interactions led by Richard Harrison. A collaborative project began in April between Warwick Crop Centre, Hazera Seeds and EMR, funded by the BBSRC and Horticultural Development Company (HDC), to identify pathogenicity chromosomes in the vascular wilt Fusarium oxysporum f.sp. cepae and host resistance in onion; this has already led to the identification of novel proteins implicated in pathogenicity. Another four-year research programme also began in April, funded by Innovate UK, Driscoll s Genetics and Berry Gardens Growers, to study

12 8 genetics and crop improvement Arbuscule in root tissue and in vitro culture (right) Mycorrhizal spore (AMF) strawberry resistance to the vascular wilt Verticillium dahliae and the interaction between this pathogen and nematodes. This project is using hyperspectral imaging to identify infection in root tissue. The research capacity of the programme was boosted by three new projects funded by Innovate UK in Two of the projects were led by Richard Harrison and the third by Xiangming Xu. The first two projects aim to understand the response of strawberry plants to AMF colonisation in substrate and its genetic control related to root architecture. These two projects firmly establish EMR as a centre for researching the use of AMF in commercial horticulture. A key deliverable from these projects is molecular markers for increased resource efficiency of strawberry plants grown in substrate to which AMF is applied (since AMF is usually absent in substrate). Substrate production of strawberry has increased significantly in recent times, primarily because of the threat of soil-borne diseases. Another Agri-Tech catalyst project, funded by BBSRC and Innovate UK, also commenced in late 2014, examining aspects of improving mycoprotein production efficiency. The UK leads the world in the production of mycoprotein and this project, harnessing EMR s capabilities in fungal genetics and bioinformatics, is made possible by collaboration with Marlow Foods. The aim is to understand how different sugars (all derived from plants) can be used to produce high-quality protein on a commercial scale. In parallel with the success in securing research funding, GCI has been equally successful in securing funding for the long-term future of several commercial breeding programmes. Felicidad Fernández secured five-year funding from the International Nursery group (INN) and HDC to continue breeding rootstocks of apple and pear. This new phase of the project will focus on the early evaluation of selections for pest and disease resistance,

13 9 Rootstock trials in the glasshouse Table-top strawberries grown in a substrate including tolerance to replant disease and Phytophthora. Validation of suitable markers for marker-assisted breeding will also be expanded in the coming years. Currently, there are a few advanced selections in this breeding programme being considered for commercialisation. The strawberry breeding team, led by David Simpson, has successfully obtained funding from CPM Ltd to extend the current breeding programme for glasshouse production for another five years in a project that will be led by Abi Johnson. Finally, Richard Harrison has secured funding from Worldwide Fruit and ENZA to start a new apple scion breeding programme. This long-term programme aims to produce dessert apples with exceptional storage and fruit quality, coupled with disease resistance to Neonectria distissima, the causal agent of apple canker. The commercial strawberry breeding programme once again had a successful year with the annual sales of EMR varieties reaching 28.6 million, representing a 5.6% increase compared to the previous year. Uptake of the East Malling Strawberry Breeding Club s (EMSBC) latest variety, Malling Centenary, was very encouraging, with excellent feedback from growers, triallists and retailers within the UK and Europe. From the EMSBC programme, ten promising selections (six June-bearer and four everbearer) were identified to proceed to offsite growers trials for commercial assessment, with another four advanced selections (two June-bearer and two everbearer) progressing to commercial-scale trials. The utilisation of molecular markers in the breeding programme using a directed, marker-assisted breeding approach to disease resistance is to be implemented from spring The second strawberry breeding programme develops cultivars for table-top production in glasshouses exclusively for CPM Ltd. We have selected three lines for assessment of their commercial potential in large scale grower trials in 2015.

14 10 genetics and crop improvement Range of colours in existing raspberry selections The CPM glasshouse where table-top strawberry variety trials take place Both raspberry and cherry breeding programmes (led by Felicidad Fernández) progressed well in The UK and overseas industry reacted positively to raspberry advanced selections from EMR, and firm commitments are being put into place to continue breeding under a commercially-funded agreement with East Malling Services Ltd (EMS) starting in April We expect to see commercial releases from this programme, which builds on our existing relationship with Lubera, in the next two years, starting with two outstanding primocane selections for the professional market and an exciting purple hybrid for gardeners. The number of cherry seedlings produced (including some interspecific hybrids) increased significantly in 2014 in the cherry breeding programme (funded by Univeg in collaboration with AIGN). Four cherry advanced selections have been established in multisite trials in the UK and Europe as part of the East Malling Cherry Group evaluation process, with larger plantings planned for Researchers in the programme participated and presented invited talks at many international conferences. Richard Harrison presented an invited talk on understanding genetics of key strawberry traits for effective breeding at an International Horticulture Conference in Nanjing Agricultural University, China. He also visited Anhui Academy of Agricultural Sciences and Beijing Academy of Agricultural Sciences and discussed future collaborations. Xiangming Xu was invited to visit the strawberry production base in Sichuan Province in China and discussed the possibility of establishing a joint strawberry production base in that area to demonstrate application of modern technologies. He also presented an invited talk on combining models to improve prediction accuracy at the Institute of Plant Protection, Chinese Academy of Agricultural Sciences, and on application of meta-genomics to plant disease epidemiology in Nanjing Agricultural University. Adam Whitehouse presented several invited talks in Europe on strawberry breeding and the latest cultivar from EMR Malling Centenary.

15 11 Dr Helen Cockerton preparing strawberry root samples which have been innoculated with Verticillium Cherry-plum hybrids dahliae for fluorescence microscopy (left) and an example image of the fungal infection (right) Several researchers joined the GCI programme in 2014: Dr Robert Vickerstaff (bioinformatician), Dr Bo Li (post-doctoral researcher in imaging analysis), Dr Helen Cockerton (post-doctoral researcher in breeding), Dr Louisa Robinson-Boyer (post-doctoral researcher in microbiology), Dr Helen Bates (molecular biologist), Dr Charlotte Nellist (post-doctoral researcher in plant-microbe interaction), Calum Bridson (entomologist) and Emma Cascant-Lopez (PhD student working on molecular clock in Verticillium dahliae in collaboration with Reading University). Dr Laura Lewis left EMR in Understanding the genetic control of flesh colour in sweet cherry After decades of decline, sweet cherry production is once more on the increase in the UK and northern Europe, in great part due to the adoption of dwarfing rootstocks and protected cropping. Breeding programmes aim to produce improved varieties for these intensive growing systems that combine outstanding fruit quality with good productivity. Season extension, storage potential, tolerance to pests and diseases, and shelf life are also key breeding objectives, most of which can only be characterised in mature trees, making cherry breeding a lengthy and expensive endeavour. Research groups worldwide are working to develop DNA markers to streamline breeding populations and reduce evaluation cost. Cherry cultivars display a great variety of colours when ripe, with flesh and skin pigments being controlled independently. At its most basic, flesh colour can be classified as black (ranging from light red to almost black) or white (cream or yellow flesh, occasionally with a trace of red around the stone). While the skin of black cherries appears to range from reddish purple to black, white-fleshed cherries can display anything from a clear

16 12 Colour segregation in C417 family (below) and C417 linkage map (right) skin through varying degrees of blushing to solid red. Segregations for most families indicate that white flesh is recessive to black, although aberrant segregations have been reported in crosses with Emperor Francis, Belle Agathe, Bohemian Black and Early Rivers. Black cherries are preferred for most markets, including Europe, but most black-fleshed cultivars are heterozygous, so that many families segregate for black versus white when they crop four or more years after germination; thus many breeding programmes would benefit from early determination of this trait in juvenile seedlings. A large-scale study led by Felicidad Fernández was undertaken to map traits of agronomic importance in the EMR cherry collections. The most common approach to locating areas of the genome involved in the control of specific trait(s) is to raise a family that segregates for the trait(s) of interest and to develop a linkage map with molecular markers to identify the marker alleles that are jointly inherited with the phenotypes of interest. Traditionally, PCR-based markers such as microsatellites have been the tools of choice to create such maps, but high-throughput genotyping using single nucleotide polymorphisms (SNPs) is becoming increasingly common. EMR s cherry mapping progeny (C417) is derived from an intra-specific cross between Colney and C210-7 (an EMR breeding line from the cross Lapins Sweet September ). It comprises more than 300 seedlings and segregates for a number of traits including cropping season and flesh colour. With support from BBSRC, and in collaboration with colleagues in the RECP programme and FEM-IASMA (Italy), we have created a saturated linkage map for part of this population using SSR markers and the Illumina Infinium 6K SNP array developed by the US project RosBREED for whole-genome genotyping of sweet and sour cherry. Only 15% of the markers in the array were informative in our cross; even so, more than 750 markers spanning around 600cM could be assigned to the linkage groups corresponding to the eight chromosomes of sweet cherry.

17 13 Cherry samples awaiting colour classification Cherry selections in the polytunnel This map is being used to further our understanding of the genetic control underlying flesh colour. Previous studies of at EMR, using low density maps, located the control of this trait as a single major gene in linkage group 3 (G3). Similar findings have been reported by another group that carried out analysis of colour as a quantitative (continuous) trait in a population derived from Emperor Francis (previously associated with unusual segregations). We firstly characterised the trait as a single gene scoring the adult seedlings for ripe flesh colour as white or black ; additionally both skin and flesh colour were measured quantitatively using a hand-held colourimeter on 25 mature fruits per seedling by taking two readings on the cheeks of the cherry fruit for skin colour and two readings of the mesocarp for flesh colour. We were able to map the single major gene (Bf) responsible for pigmented flesh ( black phenotype) in an area of G3 that corresponded with previous EMR findings, based on SSRs markers alone in two unrelated families, but located some distance away from the main QTL identified in the Emperor Francis family. Using the peach genome sequence as a reference, we have identified a candidate gene for Bf and gene expression experiments are planned to validate the findings. We believe that the area we have identified is responsible for the control of flesh colour in a large proportion of the cultivated germplasm, while the previously described QTL would account for a secondary locus explaining unusual segregations in certain genetic backgrounds. To verify this hypothesis, we are developing transferable PCR markers for screening of germplasm and breeding populations. We hope these markers will be useful for marker-assisted breeding in the near future.

18 Bees in a commercial hive. The queen is marked with a green spot (circled) so that she can be located easily

19 pest and pathogen ecology for sustainable crop management: Professor Jerry Cross 15 The focus of this science programme is the development of sustainable solutions to important pests and pathogens, especially of perennial crops. Dealing with new alien invasive species, climate change and changing horticultural practices continue to present many new challenges. Three five-year Horticulture LINK research projects were completed or had their final year of experimental work in One entitled Developing biocontrol methods and their integration in sustainable pest and disease management in plum and cherry production was completed on 31 March. The overall aim of the project was to develop alternative, sustainable, non-pesticidal methods for managing brown rot, aphids, plum fruit moth and light brown apple moth, the most important pests and diseases in UK plum and cherry crops, by incorporating biocontrol approaches into the management strategies. Several new bicontrol approaches were developed, including two new microbial BCAs for control of brown rot, and the use of alternative sugar sources to disrupt ant defence of aphid pests so that they are controlled by generalist predators, thus obviating the need for aphicide sprays. Sex pheromone mating disruption of plum fruit and light brown apple moths, and granulovirus biocontrol for summer fruit tortrix moth were also researched. Other approaches were shown to be less promising, including passive vectoring of entomopathogenic fungi by ants to control aphids, use of volatiles from plum fruits to attract plum fruit moth females and autumn applications of entomopathogenic nematodes to infect and kill overwintering plum fruit moth larvae. In the final two years of the project Integrated Pest and Disease Management (IPDM) strategies for plums and cherries combining the biological methods developed with best crop husbandry practices were evaluated in large-scale trials in commercial practice. The IPDM programmes developed were

20 16 Western Flower Thrip and damaged strawberries (right) demonstrated to be, in general, as effective as the growers standard programmes. In addition, the IPDM programme reduced the number of detectable pesticide residues in harvested fruit in both cherry and plum. The average annual cost for crop protection products was not very different between the two programmes, though there were large differences among sites and years. The final year of the Horticulture LINK project Biological, semiochemical and selective chemical management methods for insecticide resistant western flower thrips (WFT) on protected strawberry with science partners ADAS Boxworth, Warwick Crop Centre, University of Keele and Natural Resources Institute was completed in Practical methods for assessing WFT populations in strawberry flowers with attendant damage thresholds, strategies for introduction of Neoseiulus cucumeris predatory mites and Orius predatory bugs and semiochemical based mass trapping methods were developed and evaluated in the field. WFT, which has developed resistance to insecticides, is proving to be a very damaging pest of strawberry and difficult to manage. The methods developed in the project have been shown to be crucial to the effective management of WFT. The final year of the Horticulture LINK project Developing biocontrol methods and their integration in sustainable pest and disease management in blackcurrant production was also completed in For disease management, biological control agents (BCAs) for botrytis were evaluated, and the physiological basis for variation between varieties in botrytis susceptibility and the relationships between cultivar, weather conditions and post-harvest disease were investigated. Pollination studies showed that insect pollinators of blackcurrant mainly consisted of solitary bees and bumble bees, and contributed up to 35% of fruit set. Insect pollinated fruits were also

21 17 Solitary bee Sawfly caterpillars significantly larger than wind pollinated fruits. In cage trials, managed bumblebees mitigated the effects of poor pollination by wild bees. The majority of the solitary bees consisted of Andrenid species ground nesting bees. Some wild bee species were found to be in and around the crop before and after flowering and so forage and nesting provision would be likely to enhance wild pollinator numbers in the crop in following years. There was some evidence that bees transmit botrytis spores, but the contribution to fruit set outweighed these effects. For pests, experiments to assess crop damage showed that blackcurrant leaf midge attacks in established plantations have no significant effect on yield, though they cause severe growth stunting in young and re-growing cut-down bushes. The use of sex pheromone traps to time sprays was also determined and trap thresholds developed. The blackcurrant sawfly sex pheromone has been identified and used to develop a sensitive pest specific trap for monitoring this sporadic pest in crops. Several significant staff changes occurred in the programme during Dr Jean Fitzgerald retired from East Malling Research in May, after a long career as a fruit entomologist. She is an acknowledged expert on biocontrol in fruit crops, with special expertise in phytoseiid predatory mites. Jean s retirement is only partial as she will continue to work for East Malling Services Ltd (EMS) for the foreseeable future. Jennifer Kingsnorth and Bethan Shaw were recruited as technicians to support plant pathology and entomology work, respectively. Dr Charles Whitfield was recruited in October as a new research leader entomologist and spray application specialist to work on a three-year Innovate UK project to develop methods of quantifying spray deposits on crops. Charles studied for his PhD on Floral derived compounds as attractants for agricultural pests in the family Noctuidae part-time while working as a laboratory technician and has practical laboratory skills in insect culture, GC-EAG, Jean Fitzgerald talking to Dutch growers about the effect of root architecture on vine weevils Charles Whitfield

22 18 pest and pathogen ecology for sustainable crop management Soft fruit growers identifying larvae of Spotted Wing Drosophila (SWD) at an HDC/EMR Agronomists Day Ed Dobbs talking at the Illumina Day on developing methods for managing SWD behavioural bioassays, tissue culture and molecular work. At the end of the year Dr Edward Dobbs was recruited as a molecular entomologist in the PPESCM team to work on a new three-year EU FACCE JPI climate change project GENOMITE: New generation sustainable tools to control emerging mite pests under climate change. Three new students started their PhD studies: Nathan Medd on The identification of viral pathogens suitable for the control of Drosophila suzukii in the UK funded by AHDB and based jointly at the Institute of Evolutionary Biology, Centre for Immunity, Infection, and Evolution, University of Edinburgh; Callum Martin on the ecological and economic impacts of parasites in bumble bees, a four- year BBSRC CASE funded in collaboration with Royal Holloway University of London; and Dylan Hodgkiss Multitrophic ecosystem services of hoverflies resulting from Integrated Pest Management jointly funded by Royal Holloway University of London and EMR, registered at Royal Holloway University and based at EMR. In 2014 the programme team invested great efforts in securing new research grants from Innovate UK, EU and AHDB, substantially increasing research income. New large projects include: (i) developing methods for managing Spotted Wing Drosophila (SWD) (AHDB); (ii) a hand-held device for measuring and optimising spray deposits (Innovate UK); (iii) feasibility of developing autonomous SmartTraps for remote monitoring SWD (Innovate UK); (iv) GENOMITE: New generation sustainable tools to control emerging mite pests under climate change (EU climate change project); and (v) non-invasive detection of latent infection in fruit using electronic noses (Innovate UK).

23 19 Hoverfly photo taken from a poster by Dylan Hodgkiss entitled Multitrophic Ecosystems, Tetranychus Urticae (Two spotted spider mite) Services of Hoverflies in Strawberry Exploiting arthropods and antagonists in fruit crops Tree and bush fruits are grown as long-term perennial crops of varying duration (tree fruits typically for years). The plant canopy is semi-permanent and fruit crops thus provide relatively stable ecological habitats which can support rich and diverse faunas of arthropods and microorganisms including harmful, beneficial and benign species. The soil beneath perennial crops is generally undisturbed by cultivation. Additionally, fruit crops are usually surrounded by, and often contain, hedgerows and/or natural windbreaks, the composition of which varies greatly from single species to diverse. The exception is strawberry, which is increasingly grown for 1 2 years and where the soil is regularly cultivated and sterilised between crops. However, strawberry is vegetatively propagated, and planting material often has pre-existing communities of arthropods and microorganisms, the latter especially on roots, which can be exploited to increase plant health in fruiting crops. PPESCM is engaged in several research projects which aim to develop ways of exploiting and enhancing existing beneficial organisms for controlling or managing harmful species in fruiting crops, including the nature of disease suppressive soils. Exploiting hoverflies Hoverflies (Syrphids) are important biological control agents in many fruit and vegetable crops, with larvae that are voracious predators which can effectively reduce populations of aphid pests. Dylan Hodgkiss (a PhD student co-supervised by Dr Michelle Fountain) will identify the ecological and economic impact of hoverflies on pest control and pollination in strawberry crops. He will determine environmental features that drive hoverfly populations, so that growers can foster

24 20 pest and pathogen ecology for sustainable crop management Leaf damage caused by rosy apple aphid Earwig eating an aphid Hoverflies part of the project is to determine which wild flowers attract hoverflies this key pest control agent. HDC project TF 218, led by Dr Chantelle Jay, will determine whether hoverflies can be increased or manipulated in apple orchards using synthesised plant or aphid volatiles as attractants. Attractive chemicals will also be combined with visual cues. This aims to reduce populations of aphids such as the rosy apple aphid, Dysaphis plantaginea, which can lead to curled leaves and misshapen fruits with resultant crop loss. These projects are compatible with IPM and organic systems and support the Sustainable Use Directive which aims to protect horticultural crops against pests by using resilient integrated management systems, with less reliance on pesticide products, alongside protecting human health and the environment. Exploiting and enhancing earwigs in apple and pear orchards Earwigs (Forficula auricularia) are now recognised as important natural predators of many important pests of apples and pears, including aphids (especially woolly aphid), psyllids (including pear sucker), scale insects and codling moth. They are voracious nocturnal predators with a high prey consumption rate. They are omnivorous and can cause economic damage to some crops, particularly those with a thin or soft skin (e.g. peaches, strawberries). They were once considered to be an important pest of apples and pears and growers attempted to control them with pesticide sprays, but damage to apple and pear fruits is now generally considered to be only secondary, at points where the skin has already been damaged. Feeding on leaves and blossoms is common but of minor importance. EMR is engaged in a three-year Innovate UK research project led by WorldWide Fruit Ltd and Fruition PO, together with the Chemical Ecology Group, Natural

25 21 Resources Institute, Russell IPM and Agrovista as partners to study earwig populations in UK apple and pear orchards and their impact on pests. In the project so far, we have shown that populations vary greatly between orchards and in many orchards they are absent. A survey of 40 orchards (26 apple, 14 pear) in South East England for two successive years ( ) using bottle refuges showed enormous orchard-to-orchard variation in earwig abundance. Over half the apple orchards had no or virtually no earwigs, with numbers varying up to 80/refuge in the others. Numbers were considerably greater in pear orchards, though some pear orchards had none or few. Orchards with high woolly aphid, pear sucker or codling moth populations all had low earwig populations and conversely orchards with high earwig populations had low levels of these pests. Earwig numbers stayed consistent in individual orchards for the two successive years, despite the unusually wet winter of , which it was feared might kill earwigs overwintering in soil. Patterns of use of insecticides known to be harmful to F. auricularia (especially chlorpyrifos) and orchard age accounted for a significant part, but by no means all, of the variability. Significant progress has been made in developing new technologies to enhance earwig populations, and these will be made available commercially in 2016 after commercial testing in Pollination Insects are required for pollination in more than 75% of the world s crops and are essential for maintaining UK fruit productivity. Declines in numbers of wild pollinating insects have been reported for several years, but the causes are probably many and varied (e.g. changes in climate and weather patterns, pesticide use and land use resulting in loss of habitat). Coupled with more intensive fruit A plastic bottle and corrugated cardboard make an effective refuge for earwigs in the orchard

26 22 pest and pathogen ecology for sustainable crop management Solitary bee pollinating apple growing systems, this could have implications for the sustainability of fruit growing in the future. To build resilience in key insect crop pollinators, there is a need to identify the main contributing pollinator species of UK fruit crops. Research funded by the Worshipful Company of Fruiterers, GSK, HDC, Sainsbury s and HortLINK has identified the most frequent insect fruit blossom visitors. In apple, insect visits were dominated by honeybees (Apis mellifera), bumblebees and solitary bees. The number of bees visiting pear and blackcurrant were about half the number of those visiting apple blossoms. Honeybees and solitary bees were the dominant visitors to pear blossoms, but far fewer honeybees visited blackcurrant flowers. The solitary mining bees Andrena dorsata, A. haemorrhoa, A. flavipes and the bumble bees Bombus terrestris/lucorum and B. lapidarius) were common in all three crops. In experiments which excluded insects from blossoms insect pollinators contributed up to 35% of blackcurrant and 10% of pear fruit set. Future research will examine the effects of insect pollinators on fruit nutrition and other quality traits important for human health and long-term fruit storage. We will identify the most efficacious insect pollinators, i.e. how much pollen honeybees, solitary bees, bumblebees or hoverflies deposit on the stigma of the flower. Results will lead to a better understanding of how fruit growing systems can be optimised sustainably, to mitigate the effects of pollination shortfalls and to manage insect pollination in fruit crops.

27 23 Metagenomic analysis of soil samples using the illumina MiSeq The findings of the soil profiles for bacteria (top) and fungi (below) Nature of disease suppressive soils Yield decline in strawberry due to weak plant growth was recently observed in non-chemo-fumigated soils. The decline was not associated with the soil fungal pathogen Verticillium dahliae, the main target of fumigation. In a project led by Professor Xiangming Xu, amplicon-based metagenomics were used to profile soil microbiota in samples from sites with and without yield-decline. More than 2,000 fungal or bacterial operational taxonomy units (OTUs) were found in these samples. The relative abundance of individual OTUs was statistically compared for differential abundance between samples from sites with or without yield decline. Results suggested that yield decline resulted probably from one or more of the following factors: (i) low abundance of Bacillus and Pseudomonas populations, which are well known for their ability to suppress pathogen development and/or promoting plant growth; (ii) lack of nematophagous fungus (Paecilomyces species); (iii) high levels of two non-specific fungal root rot pathogens (Ilyonectria spp., releated to Cylindrocarpon); and (iv) wet soil conditions. This illustrates the complex nature of interactions among biotic and abioctic factors affecting plant growth and the importance of abundant beneficial microbes in soil for crop production. Further, the study also demonstrated the usefulness of an amplicon-based metagenomics approach to profile soil microbiota, to detect differential abundance in microbes, and to identify candidate organisms for further hypothesis testing and confirmatory studies.

28 24 pest and pathogen ecology for sustainable crop management Youngest leaves Oldest leaves Petiole Crown In an HDC funded project to determine the endophytic profile of strawberry, Robert Saville is using an amplicon-based metagenomics approach to identify the species present in different strawberry tissues (left), cultivars and growing situations to form a baseline for future study and exploitation Endophytes and Epiphytes Endophytes are micro-organisms (usually fungi or bacteria) which live within the cells of plants without causing apparent disease. Endophytic associations with plants are ubiquitous across the plant kingdom, and yet this area of plant-microorganism interaction is little understood and potentially under-exploited. Conversely, epiphytic microorganisms (i.e. microorganisms which live on the plant surface) have long been recognised as potential antagonists and several have been exploited commercially for the control of their pathogenic contemporaries. It has been reported that endophytic associations between microorganism and plant tends to be mutualistic, with the former benefiting from the protected, long-lived and nutrient-rich environment of the host and the latter benefiting from one or more of the following: an increase in systemic resistance to pathogens and pests, improved tolerance to abiotic stresses, enhanced uptake of water and minerals and increased growth. Other shades of endophytism have been reported where associations are commensal (such as latent saprophytic micro-organisms, which have a competitive advantage over other saprophytes when the host tissue dies) and potentially parasitic (such as endophytic micro-organisms which switch to a pathogenic phase when the host experiences a stress which weakens the defence system). We are applying the amplicon-based metagenomics approach mentioned above to gain a greater insight into the epiphytic and endophytic communities associated with Rosaceous crops. These findings will contribute to a greater understanding of the epidemiology of pathogenic microorganisms and offer the potential to exploit native antagonistic microorganisms in the future.

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31 resource efficiency for crop production: Dr Mark Else 27 UK horticulture continues to invest heavily in science and technology and significant increases in marketable yield have been achieved in recent years, due to more intensive plantings of new, high-yielding varieties with improved organoleptic qualities. However, further increases are possible if agronomy can be optimised to improve resource partitioning and consistency of cropping and to minimise pre- and post-harvest losses. A better understanding of how to predict and manage the influence of environmental variables on the timing and intensity of cropping will also help to improve accuracy of crop yield forecasts, thereby ensuring higher product pricing and improved grower margins. Research in the Resource Efficiency for Crop Protection (RECP) science programme aims to develop and deliver new approaches, tools and technologies to help the industry achieve consistently higher yields of first class, phytonutritious produce with an assured shelf-life, while ensuring that resources such as water, fertiliser, energy and light are used more effectively and efficiently. Scientific, technological and meteorological solutions are being developed in ongoing and new research projects funded by Innovate UK, the Agri-Tech Catalyst, the HDC, retailers including Marks & Spencer Ltd and Waitrose Ltd, and in commissioned R&D from Berry Gardens Growers Ltd and Worldwide Fruit Ltd. One facet of this work is to develop precision irrigation and fertigation systems that match demand with supply to help improve resource use efficiency and consistency of produce quality. In addition to delivering the anticipated 20% savings in water and fertiliser inputs, experiments at EMR and on-farm have again shown that marketable yields can be increased by 20% and consistency of berry quality can be improved. At the same time, innovative imaging systems are being developed to ease the integration of these low-input approaches into commercial practice, so that consistency of cropping, plant performance and crop responses to abiotic and biotic stresses can be monitored and measured in real time to inform and improve on-farm decision making. Mike Davies checking irrigation set points on a commercial site

32 28 resource efficiency for crop production Soil moisture probes are being used to target water and fertilisers to the rooting zone of tree fruit crops In intensive orchards under commercial fertigation regimes, Dr Eleftheria Stavridou has shown that during the growing season, nitrate concentrations in the soil solution at 60 cm depth were similar or higher to the concentrations in the fertigation solution, suggesting that a substantial proportion of added N is lost via leaching. Results indicate that the extent of nitrate leaching differs between apple varieties, and further research will help to identify the underlying mechanisms. The effects of different management practices on soil quality and the consequences for soil health are being investigated by Dr Emma Tilston, who continues to build EMR s capability in soil science research. Sample of phase III mushroom compost being taken to determine the effect of nutritional supplements on Agaricus bosporus gene expression The potential of precision irrigation to improve mushroom yields and quality and reduce the impact of bacterial blotch disease is being investigated by Prof. Ralph Noble in a new Innovate UK project, led by G s Fresh. Most aspects of mushroom cultivation are precisely controlled, but the decision to apply water is subjective, depending on visual observation of the crop and feel of the casing, while the moisture status of the underlying compost remains unknown. Precise, sensor controlled irrigation to the two substrate layers in mushroom cultivation will lead to improved yields of higher quality, with less crop and water wastage. Manipulating the cropping substrate by adding nutritional supplements can also improve mushroom quality and Dr Kerry Burton s experiments have shown that both the cap whiteness and density of Agaricus mushrooms can also be influenced by the straw and manure components of the cropping substrate. Increased cap density not only improves quality as firmer textured mushrooms are produced, but reduces picking cost, a major cost component of mushroom production. The mechanism of how the nutritional supplements can improve mushroom yields is being analysed by gene expression analysis using microarrays.