Distribution of P1(D1) wart disease resistance in potato germplasm and GWAS identification of haplotype-specific SNP markers

Charlotte Prodhomme, Peter G. Vos, Maria João Paulo, Jasper E. Tammes, Richard G. F. Visser, Jack H. Vossen & Herman J. van Eck

Theoretical and Applied Genetics June 2020; vol 133: 1859–1871

Key message

A Genome-Wide Association Study using 330 commercial potato varieties identified haplotype specific SNP markers 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.

See https://link.springer.com/article/10.1007/s00122-020-03559-3

Figure 3: Genetic and physical maps comprising the Sen1 locus. a Consensus genetic map of the Sen1 haplotype in the combined AD and K × A validation populations (n = 77). The Glynne–Lemmerzahl phenotypic data were used to build the map. b Physical map of the chromosome 11 north arm adapted from Prodhomme et al. (2019). The KASP markers tested in this study are anchored on the right according to their physical position on DM v4.03 (Potato Genome Sequencing Consortium et al. 2011) and on the left are the NLR clusters according to Jupe et al. (2013). In grey are the markers designed in previous mapping studies: A Hehl et al. (1999), B Ballvora et al. (2011), C Obidiegwu et al. (2015), D Plich et al. (2018)