ABSTRACT: In this study expression levels of 732 genes were analyzed for European maize (Zea mays L.) inbred lines (4 Flint and 5 Dent) and nine corresponding hybrids by microarray analysis. The selection of the 732 genes was based on a previous study (Thiemann et al., Theor Appl Genet 2010, 120:401-413), which sequences were derived from the 46k microarray (platform GPL6438) (University of Arizona, USA). 558 of the 732 genes represented on the microarray were differentially expressed between the original 21 parental inbred lines and were correlated with at least one of the three characteristics MPH (mid-parent heterosis) and/or HP (hybrid performance) of the trait GY (grain yield) and/or HP of the trait grain dry matter content. Some of those correlated genes show overlapping correlations. The residual 174 non-correlated genes belong to the top 6 biological processes that were found to be enriched among the HP for GY-correlated genes (Thiemann et al., Theor Appl Genet 2010, 120:401M-bM-^@M-^S413). The aim of this study was the identification of the hybrid expression pattern of the subset of genes, which mid-parental expression levels were shown to be correlated with MPH for GY or showed no correlation. For the analysis total RNA of 7-day old seedlings was extracted and amino-allyl-labeled RNA was synthesized. The microarrays were scanned (AppliedPrecision ArrayWorx Scanner, Applied Precision Inc., USA) and data were evaluated using the Software GenePix Pro 4.0 (Molecular Devices, Sunnyvale, USA). Hybridizations were conducted between each pair of parental inbred lines and its corresponding hybrids. In total 4 biological replicates per genotype were analyzed. As a result 119 (22.9 %) of the 519 MPH for GY or non-correlated genes showed differential expression in at least one of the nine inbred-hybrid comparisons. These differentially expressed genes were further analyzed for hybrid expression, resulting in a mainly additive expression. Of all differential expression, additive expression of 86.21 % (with 13.79 % non-additive) of the MPH-correlated genes, and a slightly smaller contingent of 79.66 % (with 20.34 % non-additive) of the non-correlated genes was measured. Four biological replicates of each of the nine parental inbred lines (4 Flint: F012, F039, F047, L024; 5 Dent: S028, S036, P024, P033, P048) and of the nine corresponding hybrids (P033xF047, P048xF047, P024xF039, S036xL024, S028xL024, S028xF012, S028xF039, P024xF012, F012xF039) were grown under controlled conditions (25 M-BM-0C 16 h day, 21 M-BM-0C 8 h night, 70 % air humidity) for seven days in a climate chamber. Whole seedlings were frozen in liquid nitrogen and were finely pounded. Total RNA was extracted and then precipitated (4 M LiCl). Residual genomic DNA was hydrolyzed with DNaseI (Fermentas, St. Leon-Rot, Germany) and purified with the M-bM-^@M-^\NucleoSpin RNA Clean-up KitM-bM-^@M-^] (Macherey-Nagel, DM-CM-
