title: Usefulness of multiparental populations of maize (Zea mays L.) for genome-based prediction.
abstract: The efficiency of marker-assisted prediction of phenotypes has been studied intensively for different types of plant breeding populations. However, one remaining question is how to incorporate and counterbalance information from biparental and multiparental populations into model training for genome-wide prediction. To address this question, we evaluated testcross performance of 1652 doubled-haploid maize (Zea mays L.) lines that were genotyped with 56,110 single nucleotide polymorphism markers and phenotyped for five agronomic traits in four to six European environments. The lines are arranged in two diverse half-sib panels representing two major European heterotic germplasm pools. The data set contains 10 related biparental dent families and 11 related biparental flint families generated from crosses of maize lines important for European maize breeding. With this new data set we analyzed genome-based best linear unbiased prediction in different validation schemes and compositions of estimation and test sets. Further, we theoretically and empirically investigated marker linkage phases across multiparental populations. In general, predictive abilities similar to or higher than those within biparental families could be achieved by combining several half-sib families in the estimation set. For the majority of families, 375 half-sib lines in the estimation set were sufficient to reach the same predictive performance of biomass yield as an estimation set of 50 full-sib lines. In contrast, prediction across heterotic pools was not possible for most cases. Our findings are important for experimental design in genome-based prediction as they provide guidelines for the genetic structure and required sample size of data sets used for model training.
authors.affiliation: Plant Breeding, Technische Universität München, 85354 Freising, Germany.
authors.forename: Christina
authors.initials: C
authors.lastname: Lehermeier
authors.affiliation: Plant Breeding, Technische Universität München, 85354 Freising, Germany.
authors.forename: Nicole
authors.initials: N
authors.lastname: Krämer
authors.affiliation: Plant Breeding, Technische Universität München, 85354 Freising, Germany.
authors.forename: Eva
authors.initials: E
authors.lastname: Bauer
authors.affiliation: INRA, UMR de Génétique Végétale, 91190 Gif-sur-Yvette, France.
authors.forename: Cyril
authors.initials: C
authors.lastname: Bauland
authors.affiliation: Limagrain Europe, 63720 Chappes, France.
authors.forename: Christian
authors.initials: C
authors.lastname: Camisan
authors.affiliation: Centro Investigacións Agrarias Mabegondo (CIAM), 15080 La Coruña, Spain.
authors.forename: Laura
authors.initials: L
authors.lastname: Campo
authors.affiliation: Limagrain Europe, 63720 Chappes, France.
authors.forename: Pascal
authors.initials: P
authors.lastname: Flament
authors.affiliation: Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany.
authors.forename: Albrecht E
authors.initials: AE
authors.lastname: Melchinger
authors.affiliation: Syngenta S.A.S., 31790 Saint-Sauveur, France.
authors.forename: Monica
authors.initials: M
authors.lastname: Menz
authors.affiliation: Syngenta S.A.S., 31790 Saint-Sauveur, France.
authors.forename: Nina
authors.initials: N
authors.lastname: Meyer
authors.affiliation: INRA, UMR de Génétique Végétale, 91190 Gif-sur-Yvette, France.
authors.forename: Laurence
authors.initials: L
authors.lastname: Moreau
authors.affiliation: Centro Investigacións Agrarias Mabegondo (CIAM), 15080 La Coruña, Spain.
authors.forename: Jesús
authors.initials: J
authors.lastname: Moreno-González
authors.affiliation: KWS SAAT AG, 37555 Einbeck, Germany.
authors.forename: Milena
authors.initials: M
authors.lastname: Ouzunova
authors.affiliation: Animal Breeding, Technische Universität München, 85354 Freising, Germany.
authors.forename: Hubert
authors.initials: H
authors.lastname: Pausch
authors.affiliation: Syngenta S.A.S., 31790 Saint-Sauveur, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Ranc
authors.affiliation: Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Schipprack
authors.affiliation: Plant Breeding, Technische Universität München, 85354 Freising, Germany.
authors.forename: Manfred
authors.initials: M
authors.lastname: Schönleben
authors.affiliation: Plant Breeding, Technische Universität München, 85354 Freising, Germany.
authors.forename: Hildrun
authors.initials: H
authors.lastname: Walter
authors.affiliation: INRA, UMR de Génétique Végétale, 91190 Gif-sur-Yvette, France.
authors.forename: Alain
authors.initials: A
authors.lastname: Charcosset
authors.affiliation: Plant Breeding, Technische Universität München, 85354 Freising, Germany chris.schoen@tum.de.
authors.forename: Chris-Carolin
authors.initials: CC
authors.lastname: Schön
mesh_terms: D018745:Genome, Plant; D006824:Hybridization, Genetic; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D003313:Zea mays / Q000235:genetics*
keywords: MPP; Multiparent Advanced Generation Inter-Cross (MAGIC); Multiparental populations; complex traits; genome-based prediction; genomic selection; high-density genotyping; linkage phases; maize breeding; mixed models