Genetic analysis of resistance of Solanum tuberosum L. to potato wart disease

Abstract

The obligate biotrophic soil-borne fungus Synchytrium endobioticum is the causal agent of potato wart disease and is classified as a quarantine pest by the European and Mediterranean Plant Protection Organization. It produces sporangia with several hundred motile zoospores which infect meristematic tissue of below-ground parts of the plants, like tubers, stolons and stems of the potato, causing yield losses of up to 50-100 %. Typical symptoms are the formation of cauliflower-like irregular galls on the below-ground parts of the plant. The thick-walled resting sporangia are able to survive in the soil for several decades. More than 40 different pathotypes of S. endobioticum have been described. Pathotypes 1, 2, 6 and 18 are the most common and most aggressive forms of the fungus in Europe. Chemical control is difficult because accessibility of winter sporangia is limited and chemicals cannot penetrate the thick walls of the sporangium. Chemicals reported to be effective against S. endobioticum have also been described as phytotoxic and harmful to the environment. Strict phytosanitary measures and breeding of resistant potato cultivars are currently the methods of choice to control the disease. Another difficulty is the phenotypic resistance assessment of potato cultivars. To determine the resistance approximately 20 tubers have to be inoculated per pathotype and genotype, which are then evaluated microscopically and assigned to different resistance classes, ranging from extremely resistant to extremely susceptible. These amounts of tubers become available only after several years within the breeding process. Molecular markers that could detect resistant genotypes early in the breeding process, independently of the availability of tubers, would greatly facilitate breeding of potato wart resistant cultivars. Several resistance loci have been identified on different potato chromosomes with different resistance loci dependent on the genetic background of the used plant material. One major resistance locus has been identified in almost all genetic studies on wart resistance: the Sen1 locus on chromosome 11. In this study, we generated a dihaploid potato population derived from a resistant tetraploid cultivar by a so-called prickle pollination with a wild potato species, Solanum phureja, which is known to possess high dihaploid induction ability, to analyze resistance against potato wart disease by reducing the genetic complexity implemented when working with tetraploid potato with its tetrasomic inheritance. Using genotyping data of a 12.8 k SNP array we could show that genetic analysis in dihaploids is much easier showing simpler segregation ratios in the progeny. Simultaneously the number of simplex markers is increased when compared to conventional crosses between two tetraploid genotypes. Putative introgressions of the pollinator genome in the dihaploid progeny were present in almost all genotypes and on almost all chromosomes. However, introgressions occurred as single events and did not disturb genetic analysis of the dihaploid genotypes. SNP marker data was used to generate 45 linkage maps, representing almost all of the 48 potato chromosomes. QTL mapping was performed for different phenotypic traits such as shoot length, number of nodes, number of tubers and tuber weight. QTL mapping revealed new quantitative trait loci but also confirmed already known QTLs described in the literature. Tubers of the dihaploid genotypes were tested for resistances to S. endobioticum pathotypes 6 and 18. Qualitative resistance mapping positioned the major resistance locus for both pathotypes on chromosome 11 in the Sen1 region. The development of additional molecular markers further improved the mapping resolution, narrowing the resistance locus to less than 800 kilobase pairs. Eight molecular markers were segregating without recombination to resistance in our population. Two markers showed high diagnostic values in a small association panel, consisting of 50 German and Polish potato varieties. The markers were diagnostic in 89.5 % of the cultivars for resistance to pathotype 18 and in 86.6 % of the cultivars for resistance for pathotype 6. The markers represent the first diagnostic markers for the pathotypes 18 and 6. Sequencing of different pathotypes of S. endobioticum was performed to develop molecular markers to allow differentiation of the pathotypes. However, sequencing revealed only a very low polymorphism rate between the pathotypes. Markers developed in this study, allowed the distinction between pathotypes 1, 2 and 6 and pathotypes 8 and 18.