title: Linkage disequilibrium with linkage analysis of multiline crosses reveals different multiallelic QTL for hybrid performance in the flint and dent heterotic groups of maize.
abstract: Multiparental designs combined with dense genotyping of parents have been proposed as a way to increase the diversity and resolution of quantitative trait loci (QTL) mapping studies, using methods combining linkage disequilibrium information with linkage analysis (LDLA). Two new nested association mapping designs adapted to European conditions were derived from the complementary dent and flint heterotic groups of maize (Zea mays L.). Ten biparental dent families (N = 841) and 11 biparental flint families (N = 811) were genotyped with 56,110 single nucleotide polymorphism markers and evaluated as test crosses with the central line of the reciprocal design for biomass yield, plant height, and precocity. Alleles at candidate QTL were defined as (i) parental alleles, (ii) haplotypic identity by descent, and (iii) single-marker groupings. Between five and 16 QTL were detected depending on the model, trait, and genetic group considered. In the flint design, a major QTL (R(2) = 27%) with pleiotropic effects was detected on chromosome 10, whereas other QTL displayed milder effects (R(2) < 10%). On average, the LDLA models detected more QTL but generally explained lower percentages of variance, consistent with the fact that most QTL display complex allelic series. Only 15% of the QTL were common to the two designs. A joint analysis of the two designs detected between 15 and 21 QTL for the five traits. Of these, between 27 for silking date and 41% for tasseling date were significant in both groups. Favorable allelic effects detected in both groups open perspectives for improving biomass production.
authors.affiliation: Université Paris-Sud, Unité Mixte Unité Mixte/Unité Mixte de Recherche 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France.
authors.forename: Héloïse
authors.initials: H
authors.lastname: Giraud
authors.affiliation: Plant Breeding, Technische Universität München, D-85354 Freising, Germany.
authors.forename: Christina
authors.initials: C
authors.lastname: Lehermeier
authors.affiliation: Plant Breeding, Technische Universität München, D-85354 Freising, Germany.
authors.forename: Eva
authors.initials: E
authors.lastname: Bauer
authors.affiliation: Institut National de la Recherche Agronomique, Unité Mixte Unité Mixte/Unité Mixte de Recherche 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Falque
authors.affiliation: Institut National de la Recherche Agronomique, F-45075 Orléans, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Segura
authors.affiliation: Institut National de la Recherche Agronomique, Unité Mixte Unité Mixte/Unité Mixte de Recherche 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France.
authors.forename: Cyril
authors.initials: C
authors.lastname: Bauland
authors.affiliation: Limagrain Europe, F-63720 Chappes, France.
authors.forename: Christian
authors.initials: C
authors.lastname: Camisan
authors.affiliation: Centro Investigacións Agrarias Mabegondo, 15080 La Coruña, Spain.
authors.forename: Laura
authors.initials: L
authors.lastname: Campo
authors.affiliation: Kleinwanzlebener Saatzucht Saat AG, D-37555 Einbeck, Germany.
authors.forename: Nina
authors.initials: N
authors.lastname: Meyer
authors.affiliation: Syngenta Seeds, F-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, D-70593 Stuttgart, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Schipprack
authors.affiliation: Limagrain Europe, F-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, D-70593 Stuttgart, Germany.
authors.forename: Albrecht E
authors.initials: AE
authors.lastname: Melchinger
authors.affiliation: Syngenta Seeds, F-31790 Saint-Sauveur, France.
authors.forename: Monica
authors.initials: M
authors.lastname: Menz
authors.affiliation: Centro Investigacións Agrarias Mabegondo, 15080 La Coruña, Spain.
authors.forename: Jesús
authors.initials: J
authors.lastname: Moreno-González
authors.affiliation: Kleinwanzlebener Saatzucht Saat AG, D-37555 Einbeck, Germany.
authors.forename: Milena
authors.initials: M
authors.lastname: Ouzunova
authors.affiliation: Institut National de la Recherche Agronomique, Unité Mixte Unité Mixte/Unité Mixte de Recherche 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France.
authors.forename: Alain
authors.initials: A
authors.lastname: Charcosset
authors.affiliation: Plant Breeding, Technische Universität München, D-85354 Freising, Germany.
authors.forename: Chris-Carolin
authors.initials: CC
authors.lastname: Schön
authors.affiliation: Institut National de la Recherche Agronomique, Unité Mixte Unité Mixte/Unité Mixte de Recherche 8120 Génétique Végétale, F-91190 Gif-sur-Yvette, France moreau@moulon.inra.fr.
authors.forename: Laurence
authors.initials: L
authors.lastname: Moreau
mesh_terms: D000483:Alleles; D032461:Chromosomes, Plant; D016000:Cluster Analysis; D003433:Crosses, Genetic; D019143:Evolution, Molecular; D008040:Genetic Linkage; D005828:Genetics, Population; D018745:Genome, Plant; D006823:Hybrid Vigor; D006824:Hybridization, Genetic; D015810:Linkage Disequilibrium; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D003313:Zea mays / Q000235:genetics*
keywords: MPP; Multiparent Advanced Generation Inter-Cross (MAGIC); QTL detection; allelic series; linkage disequilibrium information with linkage analysis (LDLA); maize biomass production; multiparental families; multiparental populations