Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents

ABSTRACT: The aim of the present study was to globally survey the transcriptome of the two inbred lines B73 and Mo17 in comparison to their reciprocal F1-progeny in an unbiased approach via RNA-seq using four biological replicates to increase the power for detecting differential expression while maintaining a low false discovery rate (FDR). For this purpose, primary roots of 3.5-d-old seedlings were surveyed, as young primary roots display a very simple structure. This stage was previously demonstrated to precede the first detectable developmental changes between inbred lines and hybrids during heterosis manifestation for numerous root-related traits (Hoecker et al. 2006). By choosing this particular stage, we intended to identify transcriptional patterns and regulators possibly determining the processes leading to heterosis for these early root system traits.

INSTRUMENT(S): Illumina Genome Analyzer IIx

ORGANISM(S): Zea mays

SUBMITTER: Patrick Schnable

PROVIDER: E-MTAB-4345 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents.

Paschold Anja A Jia Yi Y Marcon Caroline C Lund Steve S Larson Nick B NB Yeh Cheng-Ting CT Ossowski Stephan S Lanz Christa C Nettleton Dan D Schnable Patrick S PS Hochholdinger Frank F

Genome research 20121019 12

Typically, F(1)-hybrids are more vigorous than their homozygous, genetically distinct parents, a phenomenon known as heterosis. In the present study, the transcriptomes of the reciprocal maize (Zea mays L.) hybrids B73×Mo17 and Mo17×B73 and their parental inbred lines B73 and Mo17 were surveyed in primary roots, early in the developmental manifestation of heterotic root traits. The application of statistical methods and a suitable experimental design established that 34,233 (i.e., 86%) of all hi ...[more]

PMID: 23086286

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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

Dataset Information

Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents

Publications

Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents.

Similar Datasets

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