Durable resistance to early blight disease in potato
Early blight caused by Alternaria solani is an important disease of potato and on the rise. In contrast to other important potato diseases no true resistance is available to early blight in the current potato cultivars grown all over the world. So far, the only way to control the disease is to frequently apply fungicides, which is obviously not sustainable, especially since fungicide-resistant strains are emerging. Fortunately, in a recent small-scale screen, we identified genetic resistance to Alternaria in the collection of wild Solanum species at Plant Breeding (WUR). Here, we propose to jump start the development of a potato cultivar with a natural genetic resistance to early blight. We will screen the entire wild Solanum collection with our reliable disease assay to identify promising sources of resistance and subject them to crosses. By focusing on species that are sexually compatible with cultivated potato, this project will yield pre-breeding material that can be used to breed early blight-resistant potato cultivars. In addition, crosses with susceptible wild Solanum genotypes will allow detailed study of the genetic basis of early blight resistance. We will use innovative technologies to sequence the genomes of the most promising wild Solanum species and to develop molecular markers linked to resistance. The available sequence information will also enable to fine-tune the action of the responsible resistance genes by using gene editing technologies, should they become available. The results from this project will enable the partners (some of whom who are not a member of HIP) to develop potato cultivars that are truly resistant to early blight.
The project contributes to priorities 44 (Generieke sleuteltechnologieën ten behoeve van het ontwikkelen van kennis, concepten en ondersteunende technologieën), since state-of-the art key technologies are exploited, such as long read genome sequencing, Agriseq, transcriptomics, big data. We will sequence the genomes of wild potato species using the latest long-read sequencing technology. The data will be used to prepare high-quality genome assemblies of wild potato species for which a genome is currently unavailable. In case of single-gene resistance, we will develop molecular markers through bulked-segregant analysis (BSA), using short-read sequencing data from bulks of susceptible and resistant progeny as well as parents. Markers for QTL analysis will be developed using ‘Agriseq’, a technology based on Ion Torrent sequencing and multiplex PCR, targeting known polymorphic regions from potato (using primers developed at Plant Breeding). Finally, comparative genomics using genomic data from resistant and susceptible genotypes, combined with transcriptomic data, will be used to predict and to prioritize candidate resistance genes.
By sharing pre-breeding material, molecular markers and genomes with the companies that are involved in the project, it will become feasible to develop an early blight-resistant potato and the breeding programmes of the users will be accelerated. Overall the available genome sequences will be of use to other projects in the future.
The project also contributes to Mission A priority 4 (Gezonde, weerbare bodem, planten en teeltsystemen, bestand tegen zowel abiotische (klimaatbestendig) als biotische stress) as the early blight disease is expected to become a more common problem in potato cultivation in the future, due to a changing climate that is more favourable for disease development (increased occurrence of drought stress, higher temperatures and overhead irrigation). Breeding for a potato cultivar with resistance to early blight is important to be able to cope with this predicted consequence of climate change. By introducing natural resistance to early blight in potato, fungicide use can be reduced and the development of fungicide resistant Alternaria can be avoided. Healthy plants and reduced yield losses due the disease will result in improved efficiency and a reduction of input and land required for potato production. The results from this project can be applied to achieve a more sustainable potato production chain with less environmental impact.
The goal of this project is to deliver the necessary material and data to breed an early-blight resistant potato. In order to achieve this, we screen the collection of wild Solanum species at Plant Breeding (WUR) that contains approximately 600 genotypes and 130 different species in the first year of the project. This screen will result in the identification of Solanum species with resistance to early blight.
In the first and second year of the project, we will attempt crosses between resistant genotypes and S. tuberosum, to get information about crossability with cultivated potato and to produce pre-breeding material. We will also perform disease tests on progeny of crosses between resistant and susceptible genotypes to study the inheritance.
In the second year, we will select the most promising resistant genotypes for further studies. We will perform genome sequencing and initiate genetic mapping studies. Depending on the type of resistance that is identified, we will perform QTL mapping or fine-mapping studies in the third year. These studies will yield molecular markers that can be used in breeding for resistance.
In the final year of the project, we will look at candidate resistance genes predicted in the identified resistance regions. The candidate genes will be cloned and their role in resistance will be studied using transient assays and transgenics. This study will yield candidate genes for the development of potato cultivars with resistance to early blight.
A project meeting was held on 23 September 2021, with a presentation of the first results, and a short report was sent to the four participating companies.