Project description:The phenomenon of heterosis describes the increased agronomic performance of heterozygous F1-plants compared to their homozygous parental inbred plants. Heterosis is already manifested during the early stages of root development in maize. The goal of this study was to identify non-additive 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 selected. First, a microarray preselection of non-additively expressed candidate genes was performed. Subsequently, gene expression levels in a subset of genes were determined via high throughput qRT-PCR experiments. Initial microarray experiments identified 1941 non-redundant genes which displayed non-additive gene expression in at least one of the twelve analyzed hybrids compared to the midparent value of their parental inbred lines. Comparison of these 1941 genes with non-additively 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 supporting. This supports the notion of organ specific patterns of non-additively expressed genes. qRT-PCR analyses of 64 of the 1941 non-additively expressed genes in four different hybrids revealed that the majority of non-additively expressed genes were expressed between the high and low parent expression values and only a small fraction of genes was expressed below low or above high parent levels. Subsequently, 22 of the 64 genes that displayed non-additive expression in all four hybrids were analyzed in twelve hybrids that were generated from four inbred lines. Among those genes a superoxide dismutase 2 was expressed significantly above the midparent value in all twelve hybrids and might thus play a protective role in antioxidative defense in the primary root of maize hybrids. These findings are consistent with the hypothesis that global expression trends but also the consistent differential expression of key genes might be relevant during the organ-specific manifestation of heterosis. Keywords: Comparative genomic hybridization Comparison of four inbred lines and the resulting twelve reciprocal hybrids. Samples from all 16 genotypes were paired on 85 arrays following a hybridization scheme including a dye-swap according to Keller et al. (2005). A tailor-made design was developed for this purpose using simulated annealing that was optimized for estimating non-additive effects while at the same time allowing estimation of additive effects with comparable precision. Optimizing precision for estimation of non-additivity required the design to be unbalanced with respect to the number of genotype pairings and the number of replications per genotype. Hence, two RNA samples were hybridized to each of the 85 microarray chips. Each RNA sample represented an independent biological replicate

Project description:The phenomenon of heterosis describes the increased agronomic performance of heterozygous F1-plants compared to their homozygous parental inbred plants. Heterosis is already manifested during the early stages of root development in maize. The goal of this study was to identify non-additive 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 selected. First, a microarray preselection of non-additively expressed candidate genes was performed. Subsequently, gene expression levels in a subset of genes were determined via high throughput qRT-PCR experiments. Initial microarray experiments identified 1941 non-redundant genes which displayed non-additive gene expression in at least one of the twelve analyzed hybrids compared to the midparent value of their parental inbred lines. Comparison of these 1941 genes with non-additively 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 supporting. This supports the notion of organ specific patterns of non-additively expressed genes. qRT-PCR analyses of 64 of the 1941 non-additively expressed genes in four different hybrids revealed that the majority of non-additively expressed genes were expressed between the high and low parent expression values and only a small fraction of genes was expressed below low or above high parent levels. Subsequently, 22 of the 64 genes that displayed non-additive expression in all four hybrids were analyzed in twelve hybrids that were generated from four inbred lines. Among those genes a superoxide dismutase 2 was expressed significantly above the midparent value in all twelve hybrids and might thus play a protective role in antioxidative defense in the primary root of maize hybrids. These findings are consistent with the hypothesis that global expression trends but also the consistent differential expression of key genes might be relevant during the organ-specific manifestation of heterosis. Keywords: Comparative genomic hybridization

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Salvelinus Microarray experiment: cross-specific transcriptome in hybrids

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