Controlling important diseases in potato by cloning functional NB-LRR-type resistance genes

Lead Research Organisation: The James Hutton Institute
Department Name: Cell & Molecular Sciences

Abstract

Potato is one of the world's most important food crops, and production is threatened by several pests and pathogens that severely reduce crop yield and quality. These pathogens include late blight, the organism that caused the infamous Irish potato famine, soil-dwelling cyst nematodes that attack the roots, and a number of bacteria and viruses. Current control methods for many of these pathogens in most parts of the world are based mainly on the use of chemical sprays which are both environmentally hazardous and often ineffective. Moreover, some of these chemicals, for example nematicides, are being removed from use by EU legislation, severely limiting the ability of growers to control cyst nematodes. Modelling suggests that global potato production could increase by up to a third if the diseases that reduce yields could be controlled.

It is widely thought that the most promising and environmentally benign route for combating crop pests and diseases is by deployment of naturally-occurring plant resistance genes. In plants, including potato, disease resistance is typically controlled by resistance genes, known as 'R genes' that have a recognizable DNA 'domain' structure. In the plant innate immune system, the R proteins encoded by R genes provide resistance by recognising 'effector' molecules produced by the pathogen and then activating various defence processes. Hence R genes are key players in plant disease resistance, and they are effective towards diverse pathogens of all major types (oomycetes, fungi, viruses, nematodes and bacteria). We recently analysed the published potato genome and identified ~760 R genes using a novel technique we have developed for rapid isolation of all R genes from potato varieties or wild species. This new method, called RenSeq (R gene enrichment sequencing), takes advantage of recent developments in genome sequencing and in 'capturing' targeted DNA sequences from complex mixtures. Using this technique we can now sequence the R genes, which represent only about 0.24% of the DNA in the potato genome, from any potato or closely related plant in an efficient and cost effective manner. Moreover, given the appropriate sequence information, this method can be easily applied to other crop species.

This project makes use of the wide diversity of R genes present in wild potatoes and other Solanaceae. The main aims of this project are to combine the RenSeq method with the latest sequencing technologies to determine the R gene complements of selected Solanum species harbouring functionally effective resistances against one or more potato pathogen. We will use the sequence data generated to identify markers and gene candidates for functional resistances using an efficient genetic pooling approach. This will make use of existing crosses between resistant and susceptible plants to map the functional resistances to a chromosomal position in the plant genome. RenSeq will be deployed to sequence all R genes in the parents of crosses as well as pools of offspring plants that are resistant and susceptible. Comparing these sequence data using new bioinformatics approaches we will develop genetic markers that are within or immediately flanking the genes conferring resistance. Markers will be deployed via conventional plant breeding to select for resistance and candidate genes will be subjected to functional studies for potential future biotechnological deployment. A key aspect of this project is the partnership between the JHI, UoD and TSL, the plant genome sequencing expertise of TGAC as well as the link with Simplot, who will test resistance genes in field trials in the USA.

Technical Summary

We have developed RenSeq, an NB-LRR-specific enrichment and sequencing workflow that enables a detailed annotation of R genes in genome sequences and rapid mapping of resistances in segregating populations. The underlying principle for this project is RenSeq-based comparative bulked segregant analysis to reveal candidate R genes among closely-related paralogous and non-functional alleles.

RenSeq will be used to generate error corrected, long, R gene-specific sequences from parental plants (Objective 1). Up to 1.5 kb, highly accurate sequencing reads obtained by combining PacBio with MiSeq paired-end reads will be assembled to generate high-quality contigs that best describe the NB-LRRs in the resistant and susceptible parents, respectively, to enable discrimination between alleles and paralogs.

In Objective 2, shorter but highly accurate MiSeq-based RenSeq reads will be obtained from bulked resistant and bulked susceptible plants and compared to the parental NB-LRRs established in Objective 1. Candidate NB-LRRs are unique to the resistant parent as well as the resistant bulks and absent in the corresponding susceptible plants.

In Objective 3, transgenic potato lines expressing candidate R genes will be used to verify resistance to corresponding pathogens. In parallel, we will take advantage of on-going complementary research to identify and clone effectors from P. infestans, G. pallida and PVY. From these we will identify avirulence (Avr) genes matching the R genes in this study by co-infiltration with R gene candidates in the model Solanaceae N. benthamiana. Identification of avirulences will facilitate prediction of R genes durability. Markers will be developed from functional R genes to aid marker assistant selection in the JHI/MRS breeding programme.

In Objective 4, together with the industrial partner Simplot, we will test and combine R genes effective against late blight, PCN and PVY in selected US/UK potato cultivars using Golden Gate cloning.

Planned Impact

Who might benefit from this research?
The immediate beneficiaries of this research will include other academic researchers, as described in detail above. This project has been developed by the academic partners in collaboration with our commercial sponsor Simplot, who have a major investment in potato through ownership of various processed potato products. One of the main outputs of this project will be technical 'know-how' of how to efficiently isolate resistance gene repertoires from potato, which will be applicable to any plant. A second major output is a large amount of information about potato resistance genes, including some genes of known function that can be exploited via potato breeding as well as by biotechnological approaches. This project therefore will provide information, namely markers and functional resistances that will benefit those engaged in potato improvement, such as breeders and companies that generate varieties for the UK fresh and processed markets. JHI is ideally placed to exploit this link through its commercial arm, Mylnefield Research Services (MRS), which runs potato breeding programmes for all major national potato producers, enabling ready routes to translate research outcomes to UK industry. In the long term, breeding of other crop species will benefit from generic technologies developed in this proposal.

Our project is unusual in that our industrial partner is a US-based company that has extensive reach into the development of a diverse array of processed potato products. We believe that Simplot has a forward looking strategy for procuring improved raw material for their product range, and are not averse to the use of the latest technologies. We seek the best acceptable route to deploy resistances to important pathogens that will ultimately impact on food security as well as the sustainability of potato production. In the UK at the present time, this equates to conventional potato breeding. However, in the USA other options, including GM, are considered. We believe that the industrial link with Simplot will be very helpful for UK plant breeding and agriculture in the medium to long term. The public and stake holders will benefit from the availability of cultivars that are produced under more environmentally benign farming regimes which will require less pesticide input.

How will they benefit from this research?
In the shorter term potato breeders will have a much improved 'toolbox' for breeding varieties with improved resistances to pests and pathogens that impact on both UK production (e.g. blight, PCN) as well as those affecting countries to which UK, and Scotland, in particular, exports seed (e.g. viruses). JHI is well placed to efficiently exploit this information through its commercial arm, MRS, which operates multiple commercial breeding programmes with industrial partners. The availability of novel resistance genes and markers diagnostic for these genes will allow more rapid development of new resistant varieties. Moreover, varieties developed using these resources will combine resistances to more than one pathogen, something which has been hard to achieve to date.

Stakeholders, including the public and farmers will benefit from improved environmental conditions through reduced use of fungicides, nematicides and insecticides used to control blight, PCN and aphid vectors of viruses. The public will also benefit through availability of fresh produce and process products containing less chemical residues.

Publications

10 25 50

publication icon
He Q (2018) Plant pathogen effector utilizes host susceptibility factor NRL1 to degrade the immune regulator SWAP70. in Proceedings of the National Academy of Sciences of the United States of America

publication icon
Torrance L (2020) Natural resistance to Potato virus Y in Solanum tuberosum Group Phureja. in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

publication icon
Strachan SM (2019) Mapping the H2 resistance effective against Globodera pallida pathotype Pa1 in tetraploid potato. in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

 
Description This project commenced on the 1st of September 2014 and concluded on the 31st of August 2018.
Resources: We have designed NB-LRR gene specific bait libraries for RenSeq that encompasses the latest annotation of disease resistance genes from potato and tomato alongside functional genes from pepper and Nicotiana tobacco. The libraries are in the public domain: http://solanum.hutton.ac.uk/46220_probes_library.csv (Version 3.0) and http://solanum.hutton.ac.uk/renamed_FunctionalRefSequences.110mer.probes_KamilFiltered95.rmdup.0.91.fast a (version 4.0). In addition, we have utilised GenSeq, an enrichment strategy that targets established COS markers to aid the quick-mapping of new resistances (Chen et al., 2018; Strachan et al., 2019). The GenSeq probe library is also in the public domain http://solanum.hutton.ac.uk/GenSeq_filtered_probes.fasta.
We have screened diploid potato accessions from the Commonwealth Potato Collection for late blight resistant and identified novel sources of resistance in diverse wild species such as
Solanum bulbocastanum, S. capsicibaccatum, S. microdontum, S. mochiquense, S. okadae, S. pinnatisectum, S. polyadenium, S. tarijense, and S. verrucosum (Van Weymers et al., 2016).
Technology development:

To help prioritize novel resistances from resistant CPC accessions and to dismiss accessions that contain already characterized NB-LRRs, we have developed a diagnostic form of RenSeq, which is referred to as dRenSeq (Van Weymers et al., 2016). We have established dRenSeq on diploid species but also recently for tetraploid cultivars (Armstrong et al., 2019). For dRenSeq in tetraploid potatoes, we could demonstrate that the technology enables the parallel identification and sequence validation of multiple functional resistance genes effective against different pathogens (Armstrong et al., 2019). It is currently the only available tool to cost-effectively analyse multiple genotypes in crop breeding programs and to confirm transgene integrity in GM crops as shown for Simplot's Innate ® varieties. The sensitivity of dRenSeq, achieved through enrichment-based deep-sequencing, is sufficient to determine single sequence polymorphisms in NLRs within tetraploid varieties. This is a prerequisite to certifying deployment of functional genes rather than pseudogenised or less effective variants. PCR-based tests are typically unable to identify such variations without sequencing multiple cloned products. Similarly,
effector recognition studies are dependent on the discovery of cognate avirulence genes, limited by suitable expression systems that work in all host genotypes, and can suffer from a lack of specific plant responses. DRenSeq can be used for any crop where NLRs control diseases.
To identify candidate genes, we refined RenSeq to enable the targeted capture and PacBio-based sequencing of gene-sized DNA molecules of up to 7kb in length (Giolai et al., 2016).
We have shown recently that RenSeq-derived reads can be used for the design of highly-specific and transferrable markers such as KASP to track disease resistance genes in populations.
We developed PenSeq to enable the characterization of allelic diversity in pathogen effectors, enabling evolutionary and population genomic analyses of Phytophthora species. Furthermore, PenSeq enables the massively parallel identification of presence/absence variations and sequence polymorphisms in key pathogen genes, which is a prerequisite for the efficient deployment of host resistance genes (Thielliez et al., 2019 and Jouet et al., 2019)

Mapping/cloning of resistances:
DRenSeq established that the resistance QTL dPI09c in the B3 population, which was developed by CIP and thought to be free of any major R genes, is based on the resistance gene R8 (Jiang et al., 2018). We also identified and functionally confirmed R8-like variants.
We have mapped a novel late blight resistance from S. verrucosum to a 1 MB interval and successfully screened a BAC library for candidates (Chen et al., 2018).
The H2 resistance gene, introduced into cultivated potatoes from the wild diploid species Solanum multidissectum, confers a high level of resistance to the Pa1 pathotype of the potato cyst nematode Globodera pallida. A cross between tetraploid H2-containing breeding clone P55/7 and susceptible potato variety Picasso yielded an F1 population that segregated approximately 1:1 for the resistance phenotype, which is consistent with a single dominant gene in a simplex configuration. Using genome reduction methodologies RenSeq and GenSeq, the segregating F1 population enabled the genetic characterisation of the resistance through a bulked segregant analysis. A diagnostic RenSeq analysis of the parents confirmed that the resistance in P55/7 cannot be explained by previously characterised resistance genes. Only the variety Picasso contained functionally characterised disease resistance genes Rpi-R1, Rpi-R3a, Rpi-R3b variant, Gpa2 and Rx, which was independently confirmed through effector vacuum infiltration assays. RenSeq and GenSeq independently identified sequence polymorphisms linked to the H2 resistance on the top end of potato chromosome 5. Allele specific KASP markers further defined the locus containing the H2 gene to a 4.7Mb interval on the distal short arm of potato chromosome 5 and to positions that correspond to 1.4MB and 6.1MB in the potato reference genome. (Strachan et al., 2019). We have identified candidate genes through PacBio- based sequencing of gene-sized, NB-LRR gene enriched DNA molecules in collaboration with the Earlham Institute.
A new source of major gene resistance against Potato virus Y (PVY) was identified and genetically characterised in the progeny of two diploid potato populations of Solanum tuberosum Groups Phureja and Tuberosum. Phenotypic analysis revealed the resistance mechanism permitted a small amount of PVY replication in epidermal cells of inoculated leaves. The virus was confined to discrete local lesions and did not enter the vascular system, however, no hypersensitive response was visible. Detailed genotypic analysis located the resistance on chromosome 9 in the central region (at approx. 22 cM) not previously associated with PVY resistance. (Torrance et al., under revision for TAG)
In collaboration with Prof Xie Conghua (Wuhan, China) and Jin Liping (CAAS, Beijing) we fine mapped a novel PVY resistance gene (Cai et al., in preparation)
We have identified a novel resistance in Solanum bulbocastanum and mapped the resistance through RenSeq and GenSeq to chromosome 5 (manuscript in preparation).
We have adapted RenSeq to Receptor-like proteins and kinases (RLP/RLKs) and have shown that this approach is very powerful for the mapping of PRR receptors. In a proof of concept, we conducted enrichments of RLP/RLKs on the sequenced potato and tomato reference genomes and improved their annotations. A potato population that segregates for Inf1 and SCR74 recognition was used in a bulked segregant analysis. As expected, the position of the Inf1 receptor ELR was confirmed to be on LG12. However, we could also map the receptor for SCR74 recognition to the top end of chromosome 9 (Xia et al., under revision in New Phytologist).
Exploitation Route The commercial partner of this BBSRC IPA project, Simplot, has recently successfully applied for a deregulation of Innate ™ potatoes within the USA. The second generation of Innate will include late blight resistance genes and Simplot is seeking to 'future proof' these resistances with novel resistances that will arise through this project. We have identified potato cultivars with effective resistance against late blight which includes Rpi-blb2, R8, R9a, and Rpi-vnt1.3. These have been prioritised for a dRenSeq informed breeding approach through James Hutton Limited.
Sectors Agriculture, Food and Drink

 
Description This project builds on the previously established annotation of NB-LRR-like genes in potato (Jupe et al 2012 and 2013) and tomato (Andolfo 2014) that was used to establish RenSeq (Jupe et al 2013; 2014). RenSeq technology has proven a suitable tool for mapping and cloning NB-LRR genes and attracted substantial interest from the scientific community. Through RenSeq, we have mapped resistances against late blight (Chen et al., 2018), nematodes (Strachan et al., 2019) and Virus (Torrance et al., under revision for TAG). To help prioritize novel resistances and to dismiss CPC accessions that contain already characterized NB-LRRs, we have developed a diagnostic form of RenSeq, which is referred to as dRenSeq (Van Weymers et al., 2016). With the help of dRenSeq, we could demonstrate that an 'R gene free' source of late blight resistance, that behaved like a QTL in phenotypic screens was based on the presence of R8 (Rui et al., 2018). We have established dRenSeq on diploid species but also recently on tetraploid cultivars (Armstrong et al., 2019). The latter identified defeated late blight resistances as well as functional G. pallida and PVY resistance genes in, for example, the cultivar Picasso. We are using dRenSeq as a novel tool to evaluate breeding and pre-breeding material and for NB-LRR gene stacking. The data have been presented to the Industrial partner at progress meetings in 2014, 2015, 2016, 2017 and 2018 and Simplot has expressed a desire to characterise the top 30 US potato cultivars through dRenSeq. We have now sequenced over 30 US cultivars and 100 European/UK cultivars. By using dRenSeq in European/UK cultivars we could demonstrate the limited base of resistances that have been used in the potato breeding industry (R1-R3). However, we have also identified cultivars with broader resistances such as Rpi-blb2, R8, R9a, and Rpi-vnt1.3 (Armstrong et al., 2019). The technology is now used in potato breeding at James Hutton limited to direct parental selection in breeding programs that aim to combine multiple resistances. To identify candidate genes, we recently refined RenSeq to enable the targeted capture and PacBio-based sequencing of gene-sized DNA molecules of up to 7kb in length (Giolai et al., 2016). Additional projects that enrich related gene family members from host plants (RLP/RLKs) and pathogens (secreted proteins - PenSeq) have been setup in collaboration with colleagues in Wageningen, the USA, and China. In 2018 we also established RenSeq in Rice and mapped the source of a novel resistance from Zhonghua against free living nematodes (collaboration between JHI, University of St Andrews, France and Vietnam). The work has been represented at national and international conferences such as: Invited Speaker; Durham University (February 2016), Invited Speaker; National Institute of Biology, Ljubljana, Slovenia (June 2016); Selected Speaker; Plant Science Scotland PI meeting (June 2016), Selected Speaker; EAPR meeting (August 2016); Key Note Speaker; European Society of Nematology, Braga, Portugal (August 2016); Invited Speaker; Huazhong Agricultural University (HZAU), Wuhan, China (October 2016); Invited Speaker; Yunnan Academy of Agricultural Sciences, Yunnan, China (October 2016), Invited Speaker; Chinese Academy of Agricultural Sciences, Beijing, China (February 2017), Keynote Speaker /Chair 6th plant genomics & gene editing congress, Rotterdam (may 2018) Keynote Speaker EAPR meeting, Warnemuende, Germany (December 2018). A number of peer-reviewed publications have arisen thus far.
First Year Of Impact 2015
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description Policy document for 'knowledgescotland'
Geographic Reach National 
Policy Influence Type Citation in other policy documents
URL http://www.knowledgescotland.org/briefings.php?id=399
 
Description BBSRC - Subcontracting from the University of Dundee to the JHI
Amount £118,000 (GBP)
Funding ID BB/N009967/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2016 
End 03/2019
 
Description BBSRC - subcontract
Amount £1 (GBP)
Funding ID BB/P019595/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2018 
End 02/2020
 
Description COST ACTION
Amount € 2,330 (EUR)
Funding ID COST-STSM-FA1208-21999 
Organisation European Commission 
Department Horizon 2020
Sector Public
Country European Union (EU)
Start 04/2015 
End 04/2015
 
Description Innovate UK
Amount £1,320,000 (GBP)
Funding ID Innovate UK MCAP2 
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 06/2017 
End 05/2020
 
Title GenSeq enrichment tool 
Description A new, enrichment-sequencing based approach to map novel traits in potato. The manuscript detailing the technology has been accepted for publication in the journal Theoretical and Applied Genetics (TAG) 2018 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? Yes  
Impact Publication 
URL http://solanum.hutton.ac.uk
 
Title PenSeq 
Description We have developed pathogenicity factor target enrichment and sequencing (PenhSeq) to include P. infestans and P. capsici secreted proteins and RXLR effectors, to facilitate the massively parallel elucidation of polymorphisms in effectors and known avirulence determinants. Results: Target enrichment sequencing of 579 P. infestans and 574 P. capsici genes was conducted in parallel for twelve isolates, six from each species, and included the reference isolates T30-4 for P. infestans and LT1534 for P. capsici. Under high-stringent mapping conditions PenSeq reads displayed a higher than 50 % on-target rate and over 87 % of all targeted genes from the reference genomes were fully represented. PenSeq revealed presence/absence variations and sequence polymorphisms for known Avr genes across different pathogen genotypes. Hybridization of P. infestans and P. capsici-derived baits identified 30 additional RXLR effectors in novel parts of the T30-4 genome. A subsequent de novo annotation identified 1367 putative RXLR-containing regions of which 631 displayed evidence of expression in at least three publically available RNAseq datasets. Conclusions: PenSeq enables the massively parallel sequence polymorphism study of effectors, facilitating the molecular characterization of Phytophthora isolates for population studies. The technology provides a novel diagnostic tool to predict the efficacy of host resistances in the face of pathogen population shifts. A high number of novel RXLR candidates were identified through PenSeq and a de novo analysis. 
Type Of Material Technology assay or reagent 
Year Produced 2016 
Provided To Others? Yes  
Impact Predicting the durability of deployed resistances by studying the diversity of P. infestans effectors including Avr genes. Thielez et al., 2019 and Jouette et al., 2018 
URL https://www.ncbi.nlm.nih.gov/pubmed/30288743
 
Title dRenSeq - a new tool for potato disease resistance breedings 
Description We can identify and validate the sequence of all currently known NB-LRRs genes in potato wild accessions and cultivars. We are using the technoloyg (dRenSeq) as part of breeding efforts to identify the best complementary parents for disease resistance gene stacking. 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? Yes  
Impact We are using the technology at James Hutton Limited and have had requests from companies SIMPLOT, Agrico, Syngenta and Solana for potential collaborations. The manuscript detailing the approach is currently under review in Nature Biotechnology 
 
Title NB-LRR gene browser for potato 
Description Potato gene browser with the latest annotation tracks for NB-LRR genes 
Type Of Material Database/Collection of data 
Year Produced 2013 
Provided To Others? Yes  
Impact The presented NB-LRR gene annotation is seen as the international standard for potato 
URL http://solanum.hutton.ac.uk
 
Title SolArray 
Description This website describes the results of microarray experiments in Potato. Sequence ID's are based on the gene and transcript IDs from the PGSC DM assembly annotation (v4.03). The microarray probes are from the Potato 60K Agilent array, and were designed to the PSGC transcripts. You can use a probe ID from the Potato 60K Agilent Microarray chip or a PGSC gene ID or transcript ID in the search forms below. Alternatively you can use the BLAST utility to search your own DNA or protein sequences against the PGSC transcripts to find related sequences. Finally the transcripts have been annotated using the top BLAST hit found in the Tomato (ITAG) and Arabidopsis thaliana (TAIR) predicted peptides, and you can use the keyword search form to filter the transcripts for terms of interest. 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact Hormone-specific marker genes have been developed for potato and are currently being used in fundamental and applied research studies. 
URL https://ics.hutton.ac.uk/solarray/
 
Description Chinese Academy of Agricultural Sciences 
Organisation Chinese Academy of Agricultural Sciences
Country China 
Sector Academic/University 
PI Contribution RenSeq and dRenSeq analysis on late blight resistant chinese potato cultivars
Collaborator Contribution Providing plant material and DNA, phenotyping populations, effector recognition studies
Impact We have submitted a grant proposal under the ASTIP programme
Start Year 2017
 
Description Compass: COMbat crop diseases through PAthogen informed Selection of resistance gene Stacks in resilient varieties and their deployment in changing environments 
Organisation University of Wageningen
Country Netherlands 
Sector Academic/University 
PI Contribution We have jointly prepared and submitted an application for EU H2020; Proposal in the framework of H2020 research programme; SFS-03-2016: Testing and breeding for sustainability and resilience in crops
Collaborator Contribution Leading the European consortium
Impact Exchange of plant material and genetic resources
Start Year 2016
 
Description LB diversity in the US 
Organisation Cornell University
Country United States 
Sector Academic/University 
PI Contribution We have been studying the diversity of P. infestans effectors on a molecular level using PenSeq. We have focused the research on typical genotypes (e.g. US23 and US24) from the US.
Collaborator Contribution Christine Smart and Niklaus Gruenwald have sent us well characterised isolates and DNA and helped with the interpretation of results.
Impact Grant applications to the BBSRC and USDA, Support of a PhD student in the US through the data that we generated
Start Year 2016
 
Description Potato in China 
Organisation Huazhong Agricultural University
Country China 
Sector Academic/University 
PI Contribution dRenSeq analysis revealed that quantitative resistance to late blight in segregating population is based on R8. We have shared the probe library design for RenSeq with partners in China. In addition we mapped a novel PVY resistance with RenSeq to the bottom end of LG9
Collaborator Contribution Phenotyping of potato populations that segregate for LB and PVY resistances
Impact Preparation of manuscripts detailing dRenSeq and mapping of PVY resistance
Start Year 2014
 
Description SGC ODA GCRF - Vietnam Zhonghua rice 
Organisation University of St Andrews
Country United Kingdom 
Sector Academic/University 
PI Contribution We developed RenSeq for Rice and mapped. Through RenSeq we achieved the mapping and marker development for the Zhonghua source of resistance to root-knot nematodes in rice. The collaboration includes partners in France and Vietnam.
Collaborator Contribution Crossing of rice, phenotypic analysis of segregants and establishment of bulks for bulked segregant analysis.
Impact Map position for Zhongua-based disease resistance in rice towards root-knot nematodes.
Start Year 2018
 
Description Tomato resistance to LB 
Organisation French National Institute of Agricultural Research
Country France 
Sector Public 
PI Contribution Hosted a PhD student for training purposes funded through COST ACTION SUSTAIN. Shared P. infestans RXRL libraries
Collaborator Contribution Characterised PH2 and PH3 segregating populations; Identified tomato 'specific' RXLRs from P. infestans isolates that preferential infect tomato rather than potato
Impact COST ACTION STSM funding for PhD student
Start Year 2014
 
Description Verticillium nonalfalfae and mechanisms of hop (Humulus lupulus L.) resistance to verticillium wilt 
Organisation University of Ljubljana
Country Slovenia 
Sector Academic/University 
PI Contribution Effector co-localization studies in Nicotiana benthamina and setting up yeast-two-hybrid approach to identify interacting host genes
Collaborator Contribution Identification of candidate effectors from Verticillium that cause hyper-virulence in hop
Impact Successful COST Action STSM application
Start Year 2016
 
Title R8 Universal marker 
Description RenSeq derived markers that are universally transferrable between potato varieties have been developed for R8 and are used in commercial breeding activities. 
IP Reference  
Protection Protection not required
Year Protection Granted 2018
Licensed Commercial In Confidence
Impact Disease resistance breeding and stacking is supported through the markers
 
Description : Keynote Speaker /Chair 6th plant genomics & gene editing congress, Rotterdam 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Keynote Speaker /Chair 6th plant genomics & gene editing congress, Rotterdam
Year(s) Of Engagement Activity 2018
 
Description Article in Holyrood current affairs magazine 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Policymakers/politicians
Results and Impact Article about the positive impact of genome sequencing for crop protection
Year(s) Of Engagement Activity 2017
URL http://www.holyrood.com
 
Description BSPP outreach event: The plant Doctor, Edinburgh 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Engaging with the public at the Edinburgh International Science Festival

Raising public awareness about plant pathology and the impact on food crops
Year(s) Of Engagement Activity 2014
URL http://www.bspp.org.uk/outreach/article.php?id=91
 
Description EPSO Agricultural Technologies Working Group member 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact As part of the EPSO working group on Agricultural Technology, we have writen responses to the ECJ ruling on CRISP/CAS9 and distributed this to policy makers and the members of EPSO
Year(s) Of Engagement Activity 2018,2019
URL https://epsoweb.org/working-groups/agricultural-technologies/
 
Description Fascination of Plants Days 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Display of wild potato species and explaining the cloning of disease resistance genes
Year(s) Of Engagement Activity 2017
URL http://www.hutton.ac.uk/events/fascination-plants-day-0
 
Description Invited Keynote speaker at EAPE meeting, Warnemuende, Germany 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Keynote speaker on potato disease resistance at EAPR meeting
Year(s) Of Engagement Activity 2018
URL https://www.potatopro.com/potato-conferences-tradeshows/19th-joint-meeting-eapr-section-'breeding-va...
 
Description Invited Speaker (COST ACTION SUSTAIN, FA1208; Wageningen, The Netherlands) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I gave a talk at the workshop Pathogen-Informed Crop Improvement describing our RenSeq approach and the use of effectors in the search for host and non-host resistance. Following the meeting we hosted a student from Wageningen at our lab to apply RenSeq to RLP and RLK-like sequences. We successfully mapped a novel PRR receptor to LG9.
Year(s) Of Engagement Activity 2015
 
Description Invited Speaker at the opening of a research facility at ZARI Zambia 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact I was invited to present our work at the opening of a new research facility at ZARI in Zambia. Subsequently, I have been advising students on research projects.
Year(s) Of Engagement Activity 2015
 
Description Invited Speaker; Chinese Academy of Agricultural Sciences, Beijing, China 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited Speaker; Chinese Academy of Agricultural Sciences, Beijing, China - this was a workshop to identify collaborations between CAAS and UK institutes (JHI, CEH). We have prepared a joint project proposal on potato and late blight resistance
Year(s) Of Engagement Activity 2016
 
Description Invited Speaker; Huazhong Agricultural University (HZAU), Wuhan, China 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited Speaker; Huazhong Agricultural University (HZAU), Wuhan, China. This workshop was part of an appointment as a 'high end foreign expert' and is relevant to host and non-host resistances. Future project for potato crop protections were discussed
Year(s) Of Engagement Activity 2016
 
Description Invited Speaker; National Institute of Biology, Ljubljana, Slovenia 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Invited Presentation
Year(s) Of Engagement Activity 2016
 
Description Invited Speaker; Yunnan Academy of Agricultural Sciences, Yunnan, China 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Invited Speaker; Yunnan Academy of Agricultural Sciences, Yunnan, China
This invitation had arisen after the Sino-Scottish workshop. The main purpose was to discuss late blight resistance and breeding from a commercial prospective
Year(s) Of Engagement Activity 2016
 
Description Invited Visit to Wuhan Huazhong Agricultural University 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact As part of the 'High-End Foreign Recruitment program' in China, I was invited to visit the Huazhong Agricultural University for one week and gave formal presentations as well as workshops. I am involved in the Co-supervision of a PhD student who is working on late blight resistance. We have now used RenSeq to fine-map this resistance to LG9 alongside a novel PVY resistance.
Year(s) Of Engagement Activity 2015
 
Description Invited speaker at IPK Germany 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Katie Baker visited IPK Gatersleben and gave a talk on the genetic work done in our group. Following the talk she had detailed discussion with Marco Pellino and Jonathan Brassac about RenSeq.
Year(s) Of Engagement Activity 2015
 
Description Invited speaker to International Workshop on Potato Quantitative Traits: Genetic Analysis and Perspectives (October 14-16, 2014 at Huazhong Agricultural University, Wuhan, China) 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The feasibility of joint PhD studentships is currently being discussed as part of a wider UK-China network.

We are most likely receiving a PhD student from Wuhan University to explore effector recognition in Solanaceae plants and also to learn RenSeq technology.
Year(s) Of Engagement Activity 2014
 
Description Key Note Speaker; European Society of Nematology, Braga, Portugal 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Key Note Speaker; I highlighted the importance of using effectors to characterise non-host and host resistance and introduced target enrichment approaches such as PathSeq and RenSeq. I had requests now for collaborations and developing similar approaches for various plant/pathogens.
Year(s) Of Engagement Activity 2016
URL https://www.esn-online.org
 
Description OMGN meeting in Norwich 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact We presented data relevant to the non-host grant as well as RenSeq technology and established a collaboration with Wageningen University. Known late blight resistance genes were sent to us as a consequence. The possibility to adapt RenSeq technology to pathogen effectors and plant pattern recognising receptors are being explored.

We have agreed to host a scientist from Wagening to establish an enrichment for plant pattern recognising receptors
Year(s) Of Engagement Activity 2012,2014
URL http://omgn.org/
 
Description Potatoes in Practise 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact We had a display of the Commonwealth Potato Collection and introduced the concept of dRenSeq as a new breeding tool
Year(s) Of Engagement Activity 2017
URL http://www.hutton.ac.uk/events/potatoes-practice-2017
 
Description Presentation at Durham University 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact I was invited to Durham University to present our work on potato as part of the University's effort on Crop Protection
Year(s) Of Engagement Activity 2016
 
Description Presentation at SLU Sweden 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact I visited SLU Alnarp, Sweden to conduct a VIVA of a PhD student. I was invited to present our work at the University during a seminar.
Year(s) Of Engagement Activity 2016
 
Description Royal Highland Show 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact We presented at the Royal Highland Show the impact of disease resistance breeding in potato as a consequence of the Irish potato famine.
We had on display heritage potato cultivars grown during the time of the famine (Lumper, Pink Fir Apple, Skerry Blue), current potato cultivars (Maris Piper, King Edward and Maris Piper) and wild potato species (S. verrucosum, S. polyadenium and S. bulbocastanum) with novel resistances. In addition, we had information about each cultivars in respect to the R genes that they contained (or lacked) as established through dRenSeq.
Year(s) Of Engagement Activity 2017
URL http://www.hutton.ac.uk/news/hutton-science-show-royal-highland-show
 
Description Royal Highland Show 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact We displayed dRenSeq technology and the impact of disease resistance gene deployment in potato cultivars since the early 1800.
Year(s) Of Engagement Activity 2017
URL https://www.royalhighlandshow.org
 
Description Selected Speaker and Organiser; UK-China Workshop, Dundee 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact As part of Potato in Practise, we had organised a Sino-Scotland workshop specifically focused on potato and potato diseases/resistances
Year(s) Of Engagement Activity 2016
 
Description Selected Speaker; EAPR meeting; Dundee 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Selected Speaker at European Association for Potato Research (EAPR) Pathology & Pests Section
Year(s) Of Engagement Activity 2016
URL http://eaprpathology2016.webarchive.hutton.ac.uk
 
Description Selected Speaker; Plant Science Scotland PI meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact This was a gathering of PI from Scotland that are engaged in Plant Sciences. The scope was to establish further links between Institutes
Year(s) Of Engagement Activity 2016
 
Description Street food 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact dRenSeq technology in plants and CPC wild potato species
Year(s) Of Engagement Activity 2017
URL http://www.dundeesciencecentre.org.uk/local/events/event.php?eventgroupID=202&categoryID=10
 
Description Teaching (University of Dundee) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact I gave a 2 hour tutorial about modern genetics with a focus on utilising next-generation sequencing technology
Year(s) Of Engagement Activity 2015