Originally published as Genetics Published Articles Ahead of Print on June 18, 2008.

Genetics, Vol. 179, 1275-1283, July 2008, Copyright © 2008
doi:10.1534/genetics.108.088278

Comparison of Maize (Zea mays L.) F₁-Hybrid and Parental Inbred Line Primary Root Transcriptomes Suggests Organ-Specific Patterns of Nonadditive Gene Expression and Conserved Expression Trends

Nadine Hoecker^*, Barbara Keller, Nils Muthreich^*, Didier Chollet, Patrick Descombes, Hans-Peter Piepho and Frank Hochholdinger^*,1

^* Department of General Genetics, Center for Plant Molecular Biology, University of Tuebingen, 72076 Tuebingen, Germany, Institute for Crop Production and Grassland Research, University of Hohenheim, 70599 Stuttgart, Germany and Genomics Platform, National Center of Competence in Research Frontiers in Genetics, Centre Médical Universitaire, University of Genève, 1211 Genève 4, Switzerland

¹ Corresponding author: Center for Plant Molecular Biology (ZMBP), University of Tuebingen, Auf der Morgenstelle 28, 72076 Tuebingen, Germany.
E-mail: frank.hochholdinger{at}zmbp.uni-tuebingen.de

The phenomenon of heterosis describes the increased agronomic performance of heterozygous F₁ plants compared to their homozygous parental inbred plants. Heterosis is manifested during the early stages of root development in maize. The goal of this study was to identify nonadditive gene expression in primary roots of maize hybrids compared to the average expression levels of their parental inbred lines. To achieve this goal a two-step strategy was used. First, a microarray preselection of nonadditively expressed candidate genes was performed. Subsequently, gene expression levels in a subset of genes were determined via high-throughput quantitative real-time (qRT)–PCR experiments. Initial microarray experiments identified 1941 distinct microarray features that displayed nonadditive gene expression in at least 1 of the 12 analyzed hybrids compared to the midparent value of their parental inbred lines. Most nonadditively expressed genes were expressed between the parental values (>89%). Comparison of these 1941 genes with nonadditively expressed genes identified in maize shoot apical meristems via the same experimental procedure in the same genotypes revealed significantly less overlap than expected by pure chance. This finding suggests organ-specific patterns of nonadditively expressed genes. qRT–PCR analyses of 64 of the 1941 genes in four different hybrids revealed conserved patterns of nonadditively expressed genes in different hybrids. Subsequently, 22 of the 64 genes that displayed nonadditive expression in all four hybrids were analyzed in 12 hybrids that were generated from four inbred lines. Among those genes a superoxide dismutase 2 was expressed significantly above the midparent value in all 12 hybrids and might thus play a protective role in heterosis-related antioxidative defense in the primary root of maize hybrids. The findings of this study are consistent with the hypothesis that both global expression trends and the consistent differential expression of specific genes contribute to the organ-specific manifestation of heterosis.

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