Distribution of P1(D1) wart disease resistance in potato germplasm and GWAS identification of haplotype-specific SNP markers
Autor: | Herman J. van Eck, Charlotte Prodhomme, Maria João Paulo, Peter G. Vos, Jack H. Vossen, Richard G. F. Visser, Jasper E. Tammes |
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Jazyk: | angličtina |
Rok vydání: | 2020 |
Předmět: |
0106 biological sciences
Genetic Markers Linkage disequilibrium Synchytrium endobioticum Quantitative Trait Loci Locus (genetics) Single-nucleotide polymorphism Genome-wide association study Quantitative trait locus Genes Plant 01 natural sciences Identity by descent Polymorphism Single Nucleotide Chromosomes Plant Linkage Disequilibrium 03 medical and health sciences Laboratorium voor Plantenveredeling Genetics Life Science Genetic Association Studies 030304 developmental biology Disease Resistance Plant Diseases Solanum tuberosum 0303 health sciences biology Haplotype General Medicine biology.organism_classification PE&RC Plant Breeding Chytridiomycota Phenotype Biometris Haplotypes Original Article EPS Agronomy and Crop Science 010606 plant biology & botany Biotechnology Microsatellite Repeats |
Zdroj: | TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik Theoretical and Applied Genetics, 133, 1859-1871 Theoretical and Applied Genetics 133 (2020) |
ISSN: | 0040-5752 |
Popis: | Key messageA Genome-Wide Association Study using 330 commercial potato varieties identified haplotype specific SNP markers associated with pathotype 1(D1) wart disease resistance.AbstractSynchytrium endobioticumis 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 toSen1were 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 chromosome11, at the position of the previously identifiedSen1locus. 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 ofSen1, founders could not be traced because of a lack of identity by descent and because of the decay of linkage disequilibrium betweenSen1and flanking SNP markers.Sen1appeared 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. |
Databáze: | OpenAIRE |
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