Multiple-Line Cross Quantitative Trait Locus Mapping in European Elite Maize

Multiple-line cross quantitative trait locus (QTL) mapping is considered a promising tool to detect QTL with high power and substantial accuracy. The main goal of this study was to investigate the benefits of combined QTL analysis by applying two biometrical models compared to single-population analyses. For the combined QTL analysis we used a biometrical model that assumes allele substitution effects specific for every biparental population (disconnected model). We also applied a biometrical model that assumes allele substitution effects specific for every parent (connected model). Six testcross populations of maize (Zea mays L.) derived from a diallel cross of four parents were tested in 10 Italian environments in 2007 for grain yield and grain moisture. The 788 genotypes were fingerprinted with 857 single nucleotide polymorphism (SNP) markers. Our findings clearly underline the potential to improve the power to detect QTL and the resolution to localize the QTL in the genome by switching from single population QTL mapping toward joint QTL analysis across populations. The disconnected model outperformed the connected model with regard to the power to detect QTL. Consequently, our results suggest that the disconnected model is the model of choice for multiple-line cross QTL mapping in elite maize germplasm.