Abstract
Key messageA Genome-Wide Association Study using 330 commercial potato varieties identified haplotype specific SNPmarkers associated with pathotype 1(D1) wart disease resistance.Synchytrium endobioticum is a soilborne obligate biotrophic fungus responsible for wart disease. Growing resistant varieties is the most effective way to manage the disease. This paper addresses the challenge to apply molecular markers in potato breeding. Although markers linked to Sen1 were published before, the identification of haplotype-specific single-nucleotide polymorphisms may result in marker assays with high diagnostic value. To identify hs-SNP markers, we performed a genome-wide association study (GWAS) in a panel of 330 potato varieties representative of the commercial potato gene pool. SNP markers significantly associated with pathotype 1 resistance were identified on chromosome 11, at the position of the previously identified Sen1 locus. Haplotype specificity of the SNP markers was examined through the analysis of false positives and false negatives and validated in two independent full-sib populations. This paper illustrates why it is not always feasible to design markers without false positives and false negatives for marker-assisted selection. In the case of Sen1, founders could not be traced because of a lack of identity by descent and because of the decay of linkage disequilibrium between Sen1 and flanking SNP markers. Sen1 appeared to be the main source of pathotype 1 resistance in potato varieties, but it does not explain all the resistance observed. Recombination and introgression breeding may have introduced new, albeit rare haplotypes involved in pathotype 1 resistance. The GWAS approach, in such case, is instrumental to identify SNPs with the best possible diagnostic value for marker-assisted breeding.
Highlights
Potato wart disease, caused by Synchytrium endobioticum, induces the formation of galls on tubers of potato (Solanum tuberosum)
A principal coordinate analysis and a STRUCTURE analysis were performed on a random subset of 1000 SNPs (Fig. 1)
Because the population structure correlated with P1 resistance, we applied a principal coordinate analysis (PCoA) correction in our genome-wide association study (GWAS) model to correct for the structure confounding effect
Summary
Potato wart disease, caused by Synchytrium endobioticum, induces the formation of galls on tubers of potato (Solanum tuberosum). The pathogen belongs to the phylum of the Chytridiomycota, one of the early diverging fungal lineages It is an obligate biotrophic soilborne fungus producing winter spores presumably after a sexual phase of its life cycle. The yield losses can reach 50 to 100%, and no fungicides are available against this pathogen It has the status of a quarantine disease. When the presence of the fungus is recorded in a field, no potato can be cultivated until soil tests become negative for the presence of sporangia (EPPO 1990) For these reasons, breeding for varieties resistant to the potato wart disease is essential, especially in Europe where the presence of the pathogen has been recorded in many countries (Obidiegwu et al 2014)
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