Maize (Zea mays L.) serves as model plant for heterosis research and is the crop where hybrid breeding was pioneered. We analyzed genomic and phenotypic data of 1254 hybrids of a typical maize hybrid breeding program based on the important Dent 3 Flint heterotic pattern. Our main objectives were to investigate genome properties of the parental lines (e.g., allele frequencies, linkage disequilibrium, and phases) and examine the prospects of genomic prediction of hybrid performance. We found high consistency of linkage phases and large differences in allele frequencies between the Dent and Flint heterotic groups in pericentromeric regions. These results can be explained by the Hill-Robertson effect and support the hypothesis of differential fixation of alleles due to pseudooverdominance in these regions. In pericentromeric regions we also found indications for consistent marker-QTL linkage between heterotic groups. With prediction methods GBLUP and BayesB, the cross-validation prediction accuracy ranged from 0.75 to 0.92 for grain yield and from 0.59 to 0.95 for grain moisture. The prediction accuracy of untested hybrids was highest, if both parents were parents of other hybrids in the training set, and lowest, if none of them were involved in any training set hybrid. Optimizing the composition of the training set in terms of number of lines and hybrids per line could further increase prediction accuracy. We conclude that genomic prediction facilitates a paradigm shift in hybrid breeding by focusing on the performance of experimental hybrids rather than the performance of parental lines in testcrosses.H YBRID breeding was pioneered in maize (Shull 1908) and plays an ever increasing role in other globally important field (Duvick 1999) and vegetable crops (Silva Dias 2010). Maize has also served as a model species for research in heterosis, the phenomenon behind the success of hybrid varieties, for which the genetic mechanisms have been elusive (Duvick 1999;Lippman and Zamir 2006). In recent years, evidence emerged for the importance of (pseudo-)overdominance in the manifestation of heterosis in maize (Lippman and Zamir 2006;Schön et al. 2010) and the particular role of the centromeres in this process (Gore et al. 2009;McMullen et al. 2009). Today, the availability of high-density marker data and whole-genome regression methods developed in the context of genomic prediction (Meuwissen et al. 2001) allows us to revisit this hypothesis by studying key genome properties such as allele frequencies and linkage phases.Consistency of linkage phases between quantitative trait loci (QTL) and markers is a key prerequisite for pooling of diverse breeds and germplams to increase sample size for genetic studies and transferability of their results to different populations (De Roos et al. 2008). Weber et al. (2012) used whole-genome estimates of marker effects of several cattle breeds to investigate across-breed marker-QTL linkage phase consistency. Such a study is still missing for maize and other important crops. For o...