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
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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