title: Relatedness severely impacts accuracy of marker-assisted selection for disease resistance in hybrid wheat.
abstract: The accuracy of genomic selection depends on the relatedness between the members of the set in which marker effects are estimated based on evaluation data and the types for which performance is predicted. Here, we investigate the impact of relatedness on the performance of marker-assisted selection for fungal disease resistance in hybrid wheat. A large and diverse mapping population of 1739 elite European winter wheat inbred lines and hybrids was evaluated for powdery mildew, leaf rust and stripe rust resistance in multi-location field trials and fingerprinted with 9 k and 90 k SNP arrays. Comparison of the accuracies of prediction achieved with data sets from the two marker arrays revealed a crucial role for a sufficiently high marker density in genome-wide association mapping. Cross-validation studies using test sets with varying degrees of relationship to the corresponding estimation sets revealed that close relatedness leads to a substantial increase in the proportion of total genotypic variance explained by the identified QTL and consequently to an overoptimistic judgment of the precision of marker-assisted selection.
authors.affiliation: State Plant Breeding Institute, University of Hohenheim, Stuttgart, Germany.
authors.forename: M
authors.initials: M
authors.lastname: Gowda
authors.affiliation: Department of Cytogenetics and Genome Analysis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
authors.forename: Y
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: State Plant Breeding Institute, University of Hohenheim, Stuttgart, Germany.
authors.forename: T
authors.initials: T
authors.lastname: Würschum
authors.affiliation: State Plant Breeding Institute, University of Hohenheim, Stuttgart, Germany.
authors.forename: C F H
authors.initials: CF
authors.lastname: Longin
authors.affiliation: State Plant Breeding Institute, University of Hohenheim, Stuttgart, Germany.
authors.forename: T
authors.initials: T
authors.lastname: Miedaner
authors.affiliation: KWS LOCHOW GmBH, Bergen, Germany.
authors.forename: E
authors.initials: E
authors.lastname: Ebmeyer
authors.affiliation: Nordsaat Saatzuchtgesellschaft mbH, Langenstein, Germany.
authors.forename: R
authors.initials: R
authors.lastname: Schachschneider
authors.affiliation: Lantmännen SW Seed Hadmersleben GmbH, Hadmersleben, Germany.
authors.forename: E
authors.initials: E
authors.lastname: Kazman
authors.affiliation: Limagrain GmbH, Peine-Rosenthal, Germany.
authors.forename: J
authors.initials: J
authors.lastname: Schacht
authors.affiliation: Limagrain GmbH, Peine-Rosenthal, Germany.
authors.forename: J-P
authors.initials: JP
authors.lastname: Martinant
authors.affiliation: Department of Cytogenetics and Genome Analysis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
authors.forename: M F
authors.initials: MF
authors.lastname: Mette
authors.affiliation: Department of Cytogenetics and Genome Analysis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
authors.forename: J C
authors.initials: JC
authors.lastname: Reif
mesh_terms: D001203:Ascomycota / Q000502:physiology; D001487:Basidiomycota / Q000502:physiology; D002874:Chromosome Mapping / Q000379:methods; D032461:Chromosomes, Plant / Q000235:genetics; D060467:Disease Resistance / Q000235:genetics*; D017343:Genes, Plant / Q000235:genetics; D005819:Genetic Markers / Q000235:genetics; D055106:Genome-Wide Association Study / Q000379:methods; D005838:Genotype; D054884:Host-Pathogen Interactions / Q000235:genetics; D006824:Hybridization, Genetic; D007178:Inbreeding; D010641:Phenotype; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics*; D015203:Reproducibility of Results; D014908:Triticum / Q000235:genetics* / Q000382:microbiology
chemical_list: D005819:Genetic Markers