Ontology highlight
ABSTRACT:
PROVIDER: PRJEB89922 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| maize-final-ready.vcf.csi | Other | |||
| maize-final-ready.vcf.gz | Vcf |
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Similar Datasets
Project description:In this study, we grew three tetraploid alfalfa hybrids, two of which expressed heterosis for biomass yield in field experiments and a third that did not, and assessed global gene expression using Affymetrix Medicago GeneChip arrays. With these data, we tested the hypotheses that (i) more nonadditively expressed genes would be identified in heterotic than non-heterotic hybrids when hybrids were compared to their respective parents, (ii) more over- and under-dominant gene expression would be observed in heterotic than non-heterotic hybrids, and (iii) the two heterotic hybrids would have similar expression profiles.
2009-01-01 | E-MEXP-1579 | biostudies-arrayexpress
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:The behavior of transcriptomes and epigenomes in hybrids of heterotic parents is of fundamental interest. Here we report highly integrated maps of the epigenome, mRNA and small RNA transcriptomes of two rice subspecies and their reciprocal hybrids. We found that gene activity was correlated with DNA methylation and both active and repressive histone modifications in transcribed regions. Differential epigenetic modifications correlated with changes in transcript levels among hybrids and parental lines. Distinct patterns in gene expression and epigenetic modifications in reciprocal hybrids were observed. Through analyses of single nucleotide polymorphisms from our sequence data, we observed a high correlation of allelic bias of epigenetic modifications or gene expression in reciprocal hybrids with their differences in the parental lines. The abundance of distinct small RNA size classes differed between the parents and more small RNAs were down-regulated than up-regulated in the reciprocal hybrids. Together, our data reveals a comprehensive overview of transcriptional and epigenetic trends in heterotic rice crosses, and provides a very useful resource for the rice community.
2010-01-20 | GSE19602 | GEO
Project description:The improvement of breeding efficiencies for heterotic and climate-resilient crops can mitigate the food shortage crisis from overpopulation and climate change. Thus far, diverse molecular markers have been utilized for guiding field phenotypic selections, while the accurate predictions of complex heterotic traits are rarely reported. Here we present a practical metabolome-based prediction strategy for yield heterosis in rice. The dissection of population structures based on untargeted metabolite profiles, rather than the screening of predictive variables, was proved to be the initial critical step in multivariate modeling. Then the assessment of each predictive variable's contribution to predictive models was more precise according to all latent factors compared to the conventional first one. Metabolites belonging to specific pathways were tightly connected to yield heterosis, and the up-regulation of galactose metabolism represent robust yield heterosis for hybrids across different growth conditions. Our study demonstrates that metabolome-based predictive models with correctly dissected population structures and screened predictive variables can realize accurate prediction of yield heterosis and manifest great potential for establishing molecular marker-based precision breeding programs.
2019-12-10 | MTBLS742 | MetaboLights
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:Heterosis refers to the superior performance of the hybrid compared with its parental lines. Despite several genetic models and different molecular pathways proposed to explain heterosis, it remains unclear how cells integrate complementary gene expression, metabolic accumulation and/or hormone signaling to drive heterotic growth. In this work, using multiple omics combined with biochemical analyses, we showed an enhanced TORC1 signaling of the elite hybrid rice Shanyou 63 (SY63) relative to the parental lines, which was associated with accumulation of growth-promoting (translation, cell division) and energy metabolic (glycolysis and TCA) proteins energy metabolic activities, and superior growth of panicle meristem. Metabolism of nuclear-cytosolic acetyl-Coenzyme A was also enhanced in the hybrid, which paralleled with increases of histone H3 acetylation to selectively target growth-promoting and metabolic genes expression. Lysine acetylation of cellular proteins including TORC1, ribosomal proteins, and energy metabolic enzymes was also augmented and/or remodeled, potentially modulating their activities. The data revealed that the positive feedback loop between TOR-signaling, energy-producing metabolic activity, lysine acetylation, and growth-promoting gene expression is a mechanism underling the superior growth rate of the hybrid. The results implied that an enhanced activity in hybrids would drive and sustain the TOR signaling feedback loop to promote superior growth, which may represent a general mechanistic model for heterosis.
2023-10-24 | PXD035543 | Pride
Project description:Heterosis refers to the superior performance of the hybrid compared with its parental lines. Despite several genetic models and different molecular pathways proposed to explain heterosis, it remains unclear how hybrid cells integrate complementary gene expression, metabolic accumulation and/or hormone signaling to drive heterotic growth. In this work, using integrative omics combined with biochemical analyses, we uncovered an enhanced TORC1 signaling in the elite hybrid rice Shanyou 63 (SY63) relative to the parental lines, which was associated with accumulation of growth-promoting (translation, cell division) and energy metabolic (glycolysis and TCA) proteins, enhanced energy metabolic activities, increased histone H3 and cellular protein lysine acetylation, and superior growth of the panicle meristem. Metabolism of nuclear-cytosolic acetyl-Coenzyme A was also enhanced in the hybrid, which paralleled with increases of histone H3 acetylation to selectively target growth-promoting and metabolic genes expression. Lysine acetylation of cellular proteins including TORC1, ribosomal proteins, and energy metabolic enzymes was also augmented and/or remodeled, potentially modulating their activities. The data indicate that the positive feedback loop between TOR-signaling, energy-producing metabolic activity, lysine acetylation, and growth-promoting gene expression is a mechanism underling the superior growth rate of the hybrid. The results imply that any enhanced activity within the loop would drive and sustain the TOR signaling to promote superior growth of hybrids, which may represent a general mechanistic model for heterosis.
2023-10-24 | PXD035495 | Pride
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
2008-02-16 | GSE10539 | GEO
Project description:Heterosis (hybrid vigor) refers to the superior performance of hybrid progeny relative to their parents. Although widely exploited in agriculture, the mechanisms responsible for heterosis are not well understood. As a monoecious organism, a given maize plant can be used as both male and female parents of crosses. Regardless of the cross direction, the maize inbred lines B73 and Mo17 produce hybrids that substantially out-perform their parents. These reciprocal hybrids differ phenotypically from each other despite having identical nuclear genomes. Consistent with these phenotypic observations, 30-50% of genes were differentially expressed between these reciprocal hybrids. An eQTL experiment conducted to better understand the regulation of gene expression in inbred and hybrid lines detected ~4,000 eQTL associations. The majority of these eQTL act in trans to regulate expression of genes on other chromosomes. Surprisingly, many of the trans-eQTL, when heterozygous, differentially regulated transcript accumulation in a manner consistent with gene expression in the hybrid being regulated exclusively by the paternally transmitted allele. The design of the eQTL experiment controlled for cytoplasmic and maternal effects, suggesting that widespread paternal genomic imprinting contributes to the regulation of gene expression in maize hybrids. Keywords: eQTL, parent-of-origin GPL4521 - SAM1.2 (Reciprocal Hybrid Comparison): Six replications of B73xMo17 and Mo17xB73 were grown in growth chambers to tightly control environmental variation. Seeds from each genotype were taken from a single source (ear) for all six replications. Within each replication, genotypes were randomly assigned growth locations. Six healthy seedlings for each genotype and replication were harvested at two weeks of age. For each replication, B73xMo17 and Mo17xB73 were hybridized to the SAM1.2 microarray (GPL4521) using a randomized, alternate dye assignment. GPL3333 - SAM1.1 and GPL3538 - SAM3.0 (eQTL Experiment): Four biological replications of the RIL, B73xRIL, and Mo17xRIL cross-types were planted in growth chambers using seed from a single source for each genotype. Each RIL and its crosses onto B73 and Mo17 were planted using a split-plot design with RIL group (RIL and its cross onto B73 and Mo17) as the whole-plot treatment factor and cross-type (RIL, B73xRIL, and Mo17xRIL) as the split-plot treatment factor. The whole-plot portion of the experiment was designed as a randomized complete block design with four replications carried out on four separate occasions in the same environment. For the split-plot portion of the design, twelve seedlings of each RIL and its crosses were randomized within two adjacent flats in a growth chamber (six healthy seedlings per genotype were randomly chosen and pooled at harvest). For each replication, RIL, B73xRIL, and Mo17xRIL cross-types were hybridized to custom cDNA microarrays using a loop design such that each loop included all pairwise comparisons between the RIL and its crosses with B73 and Mo17. Four biological replications were hybridized to the SAM1.1 (GPL3333) array and two of the four biological replications were hybridized to SAM3.0 (GPL3538). RNA samples were alternately labeled to provide dye balance within each loop and replication. GPL8734 - Gene Expression between two maize reciprocal hybrids Heterosis refers to the enhanced agronomic performance of a hybrid relative to its (usually) inbred parents. We have previously documented widespread differences in gene expression in the B73xMo17 hybrid relative to its inbred parents B73 and Mo17 (Swanson, et al., 2006, PNAS). The reciprocal B73xMo17 and Mo17xB73 hybrids are both highly heterotic, but despite having identical nuclear genomes exhibit statistically significant differences in multiple traits. RNA-seq experiment was conducted to compare the gene expression globally between the two reciprocal hybrids. 1 samples from B73XMo17 and Mo17XB73 RNAs were extracted from a single replication of 14-day-old B73xMo17 and Mo17xB73 seedlings. RNAs were purified using DNaseI treatment followed by cleanup with the RNeasy Plant Mini Kit (Qiagen, Valencia, CA) as per manufacturer instructions. Sequencing library construction was completed using the Illumina mRNA-Seq sample preparation kit. Processed data file 'ZmB73_4a.53_filtered_genes.fasta' and its README file are linked below as supplementary files. The fasta file contains the gene model ID and corresponding sequence generated from maize genome project. This fasta file was used for the following samples: GSM418173, GSM418174, GSM420173, GSM420174, GSM422828, GSM422829.
2009-11-20 | E-GEOD-16136 | biostudies-arrayexpress
Project description:Heterosis is the phenomenon whereby the progeny of particular inbred lines have enhanced agronomic performance relative to both parents. Although several hypotheses have been proposed to explain this fundamental biological phenomenon, the responsible molecular mechanisms have not been determined. The maize inbred lines B73 and Mo17 produce a heterotic F1 hybrid. Global patterns of gene expression were compared in seedlings of these three genotypes using a microarray that contains 13,999 cDNAs. Using an estimated 15% false discovery rate as a cut-off, 1,367 ESTs (9.8%) were identified as being significantly differentially expressed among genotypes. All possible modes of gene action were observed, including additivity, high- and low-parent dominance, under-dominance, and over-dominance. The largest proportion of the ESTs (78%, 1,062/1,367) exhibited expression patterns that are not statistically distinguishable from additivity. Even so, 22% of the differentially regulated genes exhibited non-additive modes of gene expression. Classified on the basis of significant pair-wise comparisons of genotype means, 181 of these 305 genes exhibited high-parent dominance and 23 exhibited low-parent dominance. In addition, 44 genes exhibited under- or over-dominant gene action. These findings are consistent with the hypothesis that multiple molecular mechanisms contribute to heterosis, including over-dominance Keywords: Genotype Comparison
2008-06-19 | GSE4473 | GEO