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ABSTRACT:
PROVIDER: PRJNA777416 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:We demonstrated the manifestation of heterosis in hybrid maize embryo and endosperm tissue six days after fertilization in crosses of several inbred lines. Here we analyzed heterosis-associated gene expression pattern in these tissues of reciprocal crosses of two european maize inbred line combinations. Differences in gene expression were analyzed with custom microarrays by a combined approach of suppression subtractive hybridization and microarray hybridizations
2009-08-28 | GSE17821 | GEO
Project description:Many animal and plant species exhibit increased growth rates, reach larger sizes and, in the cases of crops and farm animals, produce higher yields when bred as hybrids between genetically differing strains, a phenomenon known as hybrid vigour or heterosis. Despite the importance of heterosis, and its extensive genetic analysis, there has been little understanding of its molecular basis. We aimed to determine whether characteristics of the leaf transcriptome, as an indicator of the innate functional genetic architecture of a plant line, could be used as markers to predict heterosis and the performance of hybrids, a methodology we term Association Transcriptomics. Relationships between transcript abundance of specific genes and the values of heterosis and heterosis-dependent traits were identified and mathematical models were constructed that relate gene expression characteristics in inbred lines of Arabidopsis thaliana and maize with vegetative biomass and for grain yield, respectively, in corresponding hybrids.
2011-12-23 | GSE19785 | GEO
Project description:We have used genome-wide proteomic profiling to examine leaves of hybrids for molecular phenotypes. Profiles of the proteome of maize leaves revealed hybrid-specific differences in the chloroplast and mitochondria; levels of their energy transduction complexes and ribosomes were selectively elevated 10-20% above mid-parent levels. Each of these protein machines is comprised of nuclear-encoded and organelle-encoded subunits and we refer to them as digenomic protein complexes. Expression heterosis of the organelle ribosome proteins was quantitatively predictive of growth heterosis in a set of hybrids. Ethylene biosynthetic enzyme levels were reduced in hybrids and an ethylene biosynthesis mutant in an inbred background partially phenocopied the molecular differences seen in hybrids indicating that reduced ethylene levels may play a role in maize heterosis.
2020-08-05 | MSV000085916 | MassIVE
Project description:Many animal and plant species exhibit increased growth rates, reach larger sizes and, in the cases of crops and farm animals, produce higher yields when bred as hybrids between genetically differing strains, a phenomenon known as hybrid vigour or heterosis. Despite the importance of heterosis, and its extensive genetic analysis, there has been little understanding of its molecular basis. We aimed to determine whether characteristics of the leaf transcriptome, as an indicator of the innate functional genetic architecture of a plant line, could be used as markers to predict heterosis and the performance of hybrids, a methodology we term Association Transcriptomics. Relationships between transcript abundance of specific genes and the values of heterosis and heterosis-dependent traits were identified and mathematical models were constructed that relate gene expression characteristics in inbred lines of Arabidopsis thaliana and maize with vegetative biomass and for grain yield, respectively, in corresponding hybrids. Plants used for transcriptome analysis were grown from seeds for 2 weeks. Aerial parts above the coleoptiles were excised, weighed and frozen in liquid nitrogen. All plants were harvested as close as practicable to the middle of the photoperiod. Plants used for transcriptome analysis were grown from seeds for 2 weeks. Maize seeds were first imbibed in distilled water for 2 days in glasshouse conditions to break dormancy, before transfer to peat and sand P7 pots. They were grown in long day glass house conditions (16 hours photoperiod) at 22 degrees Celsius. Aerial parts above the coleoptiles were excised, weighed and frozen in liquid nitrogen. All plants were harvested as close as practicable to the middle of the photoperiod. Plants for yield trials were grown in the field at Clayton, NC, U.S.A. in 2005. Forty plants of each hybrid were grown in duplicate 0.0007 hectare plots.
2011-12-23 | E-GEOD-19785 | biostudies-arrayexpress
Project description:The concurrent epigenetic changes during this period of remarkable improvement in maize grain yield remain unknown. Here, we performed MethylC-seq and RNA-seq on 4 related inbred lines with known pedigree information. Analysis of epigenetic changes over the course of historical maize breeding is a valuable new avenue in the exploration for crop improvement. These data lead us to suggest that novel epihaplotypes, in addition to DNA variation, are a substrate of selection during breeding, and that epigenetic variation between parents may also contribute to heterosis in hybrids. Xie, S; et al. 2013. Maize Genetics Conference Abstracts. 54:P326
2015-06-01 | E-MTAB-4238 | biostudies-arrayexpress
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: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
2008-02-22 | GSE10542 | GEO