Distribution of P1(D1) wart disease resistance in potato germplasm and GWAS identification of haplotype-specific SNP mar
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ORIGINAL ARTICLE
Distribution of P1(D1) wart disease resistance in potato germplasm and GWAS identification of haplotype‑specific SNP markers Charlotte Prodhomme1 · Peter G. Vos1,3 · Maria João Paulo2 · Jasper E. Tammes1,4 · Richard G. F. Visser1 · Jack H. Vossen1 · Herman J. van Eck1 Received: 10 September 2019 / Accepted: 28 January 2020 © The Author(s) 2020
Abstract Key message A Genome-Wide Association Study using 330 commercial potato varieties identified haplotype specific SNPmarkers associated with pathotype 1(D1) wart disease resistance. Abstract 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.
Introduction Communicated by Albrecht E. Melchinger. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00122-020-03559-3) contains supplementary material, which is available to authorized users. * Herman J. van Eck [email protected] 1
Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
2
Biometris, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Present Address: HZPC Research B.V., Roptawei 4, 9123 JB Metslawier, The Netherlands
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Present Address: Averis Seeds B.V., Valtherblokken Z40, 7876 TC Valthermond, The Netherlands
Potato wart disease, caused by Synchytrium endobioticum, induces the formation of galls on tubers of potato (Solanum tuberosum). The pathogen bel
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