title: Validating the prediction accuracies of marker-assisted and genomic selection of Fusarium head blight resistance in wheat using an independent sample.
abstract: Compared with independent validation, cross-validation simultaneously sampling genotypes and environments provided similar estimates of accuracy for genomic selection, but inflated estimates for marker-assisted selection. Estimates of prediction accuracy of marker-assisted (MAS) and genomic selection (GS) require validations. The main goal of our study was to compare the prediction accuracies of MAS and GS validated in an independent sample with results obtained from fivefold cross-validation using genomic and phenotypic data for Fusarium head blight resistance in wheat. In addition, the applicability of the reliability criterion, a concept originally developed in the context of classic animal breeding and GS, was explored for MAS. We observed that prediction accuracies of MAS were overestimated by 127% using cross-validation sampling genotype and environments in contrast to independent validation. In contrast, prediction accuracies of GS determined in independent samples are similar to those estimated with cross-validation sampling genotype and environments. This can be explained by small population differentiation between the training and validation sets in our study. For European wheat breeding, which is so far characterized by a slow temporal dynamic in allele frequencies, this assumption seems to be realistic. Thus, GS models used to improve European wheat populations are expected to possess a long-lasting validity. Since quantitative trait loci information can be exploited more precisely if the predicted genotype is more related to the training population, the reliability criterion is also a valuable tool to judge the level of prediction accuracy of individual genotypes in MAS.
authors.affiliation: Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany.
authors.forename: Yong
authors.initials: Y
authors.lastname: Jiang
authors.affiliation: Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany.
authors.forename: Albert Wilhelm
authors.initials: AW
authors.lastname: Schulthess
authors.affiliation: Julius Kühn Institute, Brunswick, Germany.
authors.forename: Bernd
authors.initials: B
authors.lastname: Rodemann
authors.affiliation: Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany.
authors.forename: Jie
authors.initials: J
authors.lastname: Ling
authors.affiliation: TraitGenetics GmbH, Gatersleben, Germany.
authors.forename: Jörg
authors.initials: J
authors.lastname: Plieske
authors.affiliation: KWS LOCHOW GMBH, Bergen, Germany.
authors.forename: Sonja
authors.initials: S
authors.lastname: Kollers
authors.affiliation: KWS LOCHOW GMBH, Bergen, Germany.
authors.forename: Erhard
authors.initials: E
authors.lastname: Ebmeyer
authors.affiliation: KWS LOCHOW GMBH, Bergen, Germany.
authors.forename: Viktor
authors.initials: V
authors.lastname: Korzun
authors.affiliation: Syngenta France S.A.S., Orgerus, France.
authors.forename: Odile
authors.initials: O
authors.lastname: Argillier
authors.affiliation: Syngenta Seeds GmbH, Bad Salzuflen, Germany.
authors.forename: Gunther
authors.initials: G
authors.lastname: Stiewe
authors.affiliation: TraitGenetics GmbH, Gatersleben, Germany.
authors.forename: Martin W
authors.initials: MW
authors.lastname: Ganal
authors.affiliation: Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany.
authors.forename: Marion S
authors.initials: MS
authors.lastname: Röder
authors.affiliation: Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany. reif@ipk-gatersleben.de.
authors.forename: Jochen C
authors.initials: JC
authors.lastname: Reif
mesh_terms: D002874:Chromosome Mapping; D060467:Disease Resistance / Q000235:genetics*; D005670:Fusarium; D005787:Gene Frequency; D005819:Genetic Markers; D023281:Genomics / Q000379:methods*; D005838:Genotype; D008957:Models, Genetic; D010641:Phenotype; D000069600:Plant Breeding / Q000379:methods*; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D040641:Quantitative Trait Loci; D015203:Reproducibility of Results; D014908:Triticum / Q000235:genetics* / Q000382:microbiology
chemical_list: D005819:Genetic Markers