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

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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.

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.