title: Mixed model approaches for the identification of QTLs within a maize hybrid breeding program.
abstract: Two outlines for mixed model based approaches to quantitative trait locus (QTL) mapping in existing maize hybrid selection programs are presented: a restricted maximum likelihood (REML) and a Bayesian Markov Chain Monte Carlo (MCMC) approach. The methods use the in-silico-mapping procedure developed by Parisseaux and Bernardo (2004) as a starting point. The original single-point approach is extended to a multi-point approach that facilitates interval mapping procedures. For computational and conceptual reasons, we partition the full set of relationships from founders to parents of hybrids into two types of relations by defining so-called intermediate founders. QTL effects are defined in terms of those intermediate founders. Marker based identity by descent relationships between intermediate founders define structuring matrices for the QTL effects that change along the genome. The dimension of the vector of QTL effects is reduced by the fact that there are fewer intermediate founders than parents. Furthermore, additional reduction in the number of QTL effects follows from the identification of founder groups by various algorithms. As a result, we obtain a powerful mixed model based statistical framework to identify QTLs in genetic backgrounds relevant to the elite germplasm of a commercial breeding program. The identification of such QTLs will provide the foundation for effective marker assisted and genome wide selection strategies. Analyses of an example data set show that QTLs are primarily identified in different heterotic groups and point to complementation of additive QTL effects as an important factor in hybrid performance.
authors.affiliation: Biometris, Wageningen UR, PO Box 100, 6700 AC Wageningen, The Netherlands. fred.vaneeuwijk@wur.nl
authors.forename: Fred A
authors.initials: FA
authors.lastname: van Eeuwijk
authors.forename: Martin
authors.initials: M
authors.lastname: Boer
authors.forename: L Radu
authors.initials: LR
authors.lastname: Totir
authors.forename: Marco
authors.initials: M
authors.lastname: Bink
authors.forename: Deanne
authors.initials: D
authors.lastname: Wright
authors.forename: Christopher R
authors.initials: CR
authors.lastname: Winkler
authors.forename: Dean
authors.initials: D
authors.lastname: Podlich
authors.forename: Keith
authors.initials: K
authors.lastname: Boldman
authors.forename: Andy
authors.initials: A
authors.lastname: Baumgarten
authors.forename: Matt
authors.initials: M
authors.lastname: Smalley
authors.forename: Martin
authors.initials: M
authors.lastname: Arbelbide
authors.forename: Cajo J F
authors.initials: CJ
authors.lastname: ter Braak
authors.forename: Mark
authors.initials: M
authors.lastname: Cooper
mesh_terms: D001499:Bayes Theorem; D002874:Chromosome Mapping; D008040:Genetic Linkage; D005819:Genetic Markers; D006824:Hybridization, Genetic; D008390:Markov Chains; D008957:Models, Genetic; D040641:Quantitative Trait Loci; D003313:Zea mays / Q000235:genetics*
chemical_list: D005819:Genetic Markers