Transcriptome-wide analysis of epitranscriptome and translational efficiency associated with heterosis in maize
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ABSTRACT:
PROVIDER: PRJNA656105 | ENA |
REPOSITORIES: ENA
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Project description:Heterosis, also known as hybrid vigor, has been extensively utilized to increase productivity in crop, yet the underlying molecular mechanisms remain largely elusive. Recent studies have reported that in addition to mRNA transcription, epigenetic variations in DNA methylation, small RNAs and histone modifications also contribute to heterosis. However, the operative mode of post-transcriptional regulation on gene expression such as RNA m6A methylation and translational efficiency in heterosis has never been explored. In this study, we generated transcriptome-wide profiles of mRNA abundance, m6A methylation, and translational efficiency from the maize (Zea mays) F1 hybrid B73×Mo17 and its two parental lines B73 and Mo17 to ascertain contributions of each regulatory layer to heterosis at the seedling stage. We documented that although the global abundance and the distribution configuration of m6A maintained unchanged, a greater number of genes have gained m6A modification in hybrid compared to parent lines. m6A modification and translational efficiency exhibited greater variations between hybrid and parents as compared with observed variation of mRNA abundance. In hybrid, the vast majority of genes with m6A modification exhibited non-additive expression pattern, the percentage of which was exceedingly higher than that of differential genes at mRNA abundance and translation efficiency levels. Non-additive genes involved in different biological processes were hierarchically coordinated by discrete combinations of three regulatory layers. These findings suggest that transcriptional and post-transcriptional regulations on gene expression adopt divergent approaches to participate in the formation of heterosis in hybrid. Overall, the integrated multi-omics analysis provides a valuable portfolio for interpreting transcriptional and post-transcriptional regulation on gene expression in maize hybrid, and pave new avenues for exploring molecular mechanisms underlying hybrid vigor.
2021-04-13 | GSE155947 | GEO
Project description:Heterosis has been extensively utilized to increase productivity in crops, yet the underlying molecular mechanisms remain largely elusive. Here, we generated transcriptome-wide profiles of mRNA abundance, m6A methylation, and translational efficiency from the maize F1 hybrid B73×Mo17 and its two parental lines to ascertain the contribution of each regulatory layer to heterosis at the seedling stage. We documented that although the global abundance and distribution of m6A remained unchanged, a greater number of genes had gained an m6A modification in the hybrid. Superior variations were observed at the m6A modification and translational efficiency levels when compared with mRNA abundance between the hybrid and parents. In the hybrid, the vast majority of genes with m6A modification exhibited a non-additive expression pattern, the percentage of which was much higher than that at levels of mRNA abundance and translational efficiency. Non-additive genes involved in different biological processes were hierarchically coordinated by discrete combinations of three regulatory layers. These findings suggest that transcriptional and post-transcriptional regulation of gene expression make distinct contributions to heterosis in hybrid maize. Overall, this integrated multi-omics analysis provides a valuable portfolio for interpreting transcriptional and post-transcriptional regulation of gene expression in hybrid maize, and paves the way for exploring molecular mechanisms underlying hybrid vigor.
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Project description:This SuperSeries is composed of the following subset Series: GSE3733: Modes of gene action observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents GSE4473: Heterosis(II, Low scan) Keywords: SuperSeries Refer to individual Series
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Project description:Expression profiling analyses for 5 maize inbreds and 4 hybrids, chosen to represent diversity in genotypes and heterosis responses, revealed a correlation between genetic diversity and transcriptional variation. This is a companion dataset to an Affymetrix profiling experiment (GEO Series GSE10236). Keywords: Genotype comparison series Expression profiling was used to study gene expression in aerial tissue from 11-day seedlings of maize. Three biological replicates were performed for nine different genotypes; B37, B73, B84, Mo17, Oh43, B37xB73, B84xB73, Oh43xB73 and Oh43xMo17.
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Project description:This research reports the analysis of sRNAs in 14 and 7 inbred lines from a breeding population. We analyzed the contribution of sRNAs to the formation of heterosis via integrative association analysis with field data of 98 hybrids generated from the set of inbred lines. Our results indicate a contribution of sRNAs to heterosis. We were able to identify different sets of sRNAs associated with heterosis with distinct length and genome distribution patterns. Analysis of sRNA contribution to the formation of heterosis in maize by an association study in a breeding population.
2016-10-24 | E-GEOD-51662 | biostudies-arrayexpress
Project description:To date, the search for expression quantitative trait loci (eQTL) has centered entirely on transcription; variants with effects on mRNA translation have not been systematically studied. We tested the use of ribosomal association as proxy for translational efficiency of polymorphic mRNAs to develop a novel high throughput approach for translational cis-regulation in the human genome.
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