title: A new test for family-based association mapping with inbred lines from plant breeding programs.
abstract: Association mapping holds great promise for the detection of quantitative trait loci (QTL) in plant breeding populations. The main objectives of this study were to (1) adapt the quantitative pedigree disequilibrium test to typical pedigrees of inbred lines produced in plant breeding programs, (2) compare the newly developed quantitative inbred pedigree disequilibrium test (QIPDT) with the commonly employed logistic regression ratio test (LRRT), with respect to the power and type I error rate of QTL detection, and (3) demonstrate the use of the QIPDT by applying it to flowering data of European elite maize inbreds. QIPDT and LRRT were compared based on computer simulations modeling 55 years of hybrid maize breeding in Central Europe. Furthermore, we applied QIPDT to a cross-section of 49 European elite maize inbred lines genotyped with 722 amplified fragment length polymorphism markers and phenotyped in four environments for days to anthesis. Compared to LRRT, the power to detect QTL was higher with QIPDT when using data collected routinely in plant breeding programs. Application of QIPDT to the 49 European maize inbreds resulted in a significant (P < 0.05) association located at a position for which a consensus QTL was detected in a previous study. The results of our study suggested that QIPDT is a promising QTL detection method for data collected routinely in plant breeding programs.
authors.affiliation: Institute for Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Stich
authors.forename: Albrecht E
authors.initials: AE
authors.lastname: Melchinger
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Piepho
authors.forename: Martin
authors.initials: M
authors.lastname: Heckenberger
authors.forename: Hans P
authors.initials: HP
authors.lastname: Maurer
authors.forename: Jochen C
authors.initials: JC
authors.lastname: Reif
mesh_terms: D001947:Breeding; D002874:Chromosome Mapping; D006824:Hybridization, Genetic; D015810:Linkage Disequilibrium; D010375:Pedigree; D010865:Pilot Projects; D040641:Quantitative Trait Loci; D003313:Zea mays / Q000235:genetics* / Q000254:growth & development