title: Genomic selection across multiple breeding cycles in applied bread wheat breeding.
abstract: We evaluated genomic selection across five breeding cycles of bread wheat breeding. Bias of within-cycle cross-validation and methods for improving the prediction accuracy were assessed. The prospect of genomic selection has been frequently shown by cross-validation studies using the same genetic material across multiple environments, but studies investigating genomic selection across multiple breeding cycles in applied bread wheat breeding are lacking. We estimated the prediction accuracy of grain yield, protein content and protein yield of 659 inbred lines across five independent breeding cycles and assessed the bias of within-cycle cross-validation. We investigated the influence of outliers on the prediction accuracy and predicted protein yield by its components traits. A high average heritability was estimated for protein content, followed by grain yield and protein yield. The bias of the prediction accuracy using populations from individual cycles using fivefold cross-validation was accordingly substantial for protein yield (17-712 %) and less pronounced for protein content (8-86 %). Cross-validation using the cycles as folds aimed to avoid this bias and reached a maximum prediction accuracy of [Formula: see text] = 0.51 for protein content, [Formula: see text] = 0.38 for grain yield and [Formula: see text] = 0.16 for protein yield. Dropping outlier cycles increased the prediction accuracy of grain yield to [Formula: see text] = 0.41 as estimated by cross-validation, while dropping outlier environments did not have a significant effect on the prediction accuracy. Independent validation suggests, on the other hand, that careful consideration is necessary before an outlier correction is undertaken, which removes lines from the training population. Predicting protein yield by multiplying genomic estimated breeding values of grain yield and protein content raised the prediction accuracy to [Formula: see text] = 0.19 for this derived trait.
authors.affiliation: Department for Agrobiotechnology (IFA-Tulln), Institute for Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430, Tulln, Austria.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Michel
authors.affiliation: Saatzucht Donau GesmbH. and CoKG, Saatzuchtstrasse 11, 2301, Probstdorf, Austria.
authors.forename: Christian
authors.initials: C
authors.lastname: Ametz
authors.affiliation: ProGen Seed A.Ş., Büyükdalyan Mah. 2. Küme evler Sok., No: 49, Antakya/Hatay, Turkey.
authors.forename: Huseyin
authors.initials: H
authors.lastname: Gungor
authors.affiliation: Probstdorfer Saatzucht Romania SRL, Str. Siriului Nr.20, sect. 1, Bucharest, Romania.
authors.forename: Doru
authors.initials: D
authors.lastname: Epure
authors.affiliation: Plant Breeding Division, Department of Crop Science, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 24, 3430, Tulln, Austria.
authors.forename: Heinrich
authors.initials: H
authors.lastname: Grausgruber
authors.affiliation: Saatzucht Donau GesmbH. and CoKG, Saatzuchtstrasse 11, 2301, Probstdorf, Austria.
authors.forename: Franziska
authors.initials: F
authors.lastname: Löschenberger
authors.affiliation: Department for Agrobiotechnology (IFA-Tulln), Institute for Biotechnology in Plant Production, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, 3430, Tulln, Austria. hermann.buerstmayr@boku.ac.at.
authors.forename: Hermann
authors.initials: H
authors.lastname: Buerstmayr
mesh_terms: D002523:Edible Grain / Q000737:chemistry; D018745:Genome, Plant; D005838:Genotype; D010641:Phenotype; D000069600:Plant Breeding; D010940:Plant Proteins / Q000737:chemistry; D019655:Quantitative Trait, Heritable; D012641:Selection, Genetic; D014908:Triticum / Q000235:genetics*
chemical_list: D010940:Plant Proteins