title: Association mapping in an elite maize breeding population.
abstract: Association mapping (AM) is a powerful approach to dissect the genetic architecture of quantitative traits. The main goal of our study was to empirically compare several statistical methods of AM using data of an elite maize breeding program with respect to QTL detection power and possibility to correct for population stratification. These models were based on the inclusion of cofactors (Model A), cofactors and population effect (Model B), and SNP effects nested within populations (Model C). A total of 930 testcross progenies of an elite maize breeding population were field-evaluated for grain yield and grain moisture in multi-location trials and fingerprinted with 425 SNP markers. For grain yield, population stratification was effectively controlled by Model A. For grain moisture with a high ratio of variance among versus within populations, Model B should be applied in order to avoid potential false positives. Model C revealed large differences among allele substitution effects for trait-associated SNPs across multiple plant breeding populations. This heterogeneous SNP allele substitution effects have a severe impact for genomic selection studies, where SNP effects are often assumed to be independent of the genetic background.
authors.affiliation: State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany.
authors.forename: Wenxin
authors.initials: W
authors.lastname: Liu
authors.forename: Manje
authors.initials: M
authors.lastname: Gowda
authors.forename: Jana
authors.initials: J
authors.lastname: Steinhoff
authors.forename: Hans Peter
authors.initials: HP
authors.lastname: Maurer
authors.forename: Tobias
authors.initials: T
authors.lastname: Würschum
authors.forename: Carl Friedrich Horst
authors.initials: CF
authors.lastname: Longin
authors.forename: Frédéric
authors.initials: F
authors.lastname: Cossic
authors.forename: Jochen Christoph
authors.initials: JC
authors.lastname: Reif
mesh_terms: D001947:Breeding; D056726:Genetic Association Studies; D005838:Genotype; D015810:Linkage Disequilibrium; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D003313:Zea mays / Q000235:genetics* / Q000502:physiology