Molecular analysis of heterosis in alfalfa
Ontology highlight
ABSTRACT:
ORGANISM(S): Medicago sativa Sinorhizobium meliloti Medicago truncatula
PROVIDER: GSE25034 | GEO | 2010/12/29
SECONDARY ACCESSION(S): PRJNA134769
REPOSITORIES: GEO
Similar Datasets
Project description:The aim of the experiment was to investigate the transcriptome changes in a double hybrid of alfala. The transcriptomes of a double hybrid (B2xB5) was compared to the two parental lines. 9 samples were used in the experiment, 3 biologcal replicates of the double hybrid and two parental lines.
2010-12-29 | E-GEOD-25034 | biostudies-arrayexpress
Project description:This experiment involves RNAseq data on 3 parental lines and 2 hybrid crosses. The parents: inbred lines B104 and Mo17, and the GA20OX transgenic line in B104 background. The hybrid crosses: B104 x Mo17, GA20OX x Mo17.
2021-11-17 | E-MTAB-11102 | biostudies-arrayexpress
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. The majority of differentially expressed genes in each of the different hybrids exhibited additive expression patterns, and ~25% exhibited statistically significant non-additive expression profiles. Among the non-additive profiles, ~80% exhibited hybrid expression levels between the parental levels, ~20% exhibited hybrid expression levels at the parental levels and ~1% exhibited hybrid levels outside the parental range. These findings indicate that the frequencies of additive and non-additive expression patterns are very similar across a range of hybrid lines. Keywords: Genotype comparison series
2008-01-26 | GSE10236 | GEO
Project description:Heterosis is most frequently manifested as the superior performance of a hybrid than either parent, especially under stress conditions. Nitric oxide (NO) is a well-known gaseous signaling molecule that acts as a functional component during plant growth, development, and defense responses. In this study, the Brassica napus L. hybrid (F1, NJ4375 × MB1942) showed significant heterosis under salt stress, during both the germination and post-germination periods. These were in parallel with the changes in redox and ion homeostasis. The stimulation of endogenous NO was more pronounced in hybrid plants, compared to parental lines, which might be mediated by nitrate reductase. Proteomic and biochemical analysis further revealed that protein abundance related to several metabolic processes, including the chlorophyll biosynthesis, the proline metabolism, and the tricarboxylic acid cycle metabolism pathway, were greatly suppressed by salt stress in the two parental lines, respect to those in hybrid. Above responses in hybrid plants were intensified by a NO-releasing compound, but abolished by a NO scavenger, both of which were matched with the changes in chlorophyll and proline contents. Taken together, we proposed that heterosis derived from F1 hybridization in salt stress tolerance might be mediated by NO-dependent activation of defense responses and metabolic processes.
2021-03-30 | PXD023601 | 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: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:Loop-design (triangle design with the comparison of each triplet: hybrid + parent 1 and parent 2) and pairwise design (hybrid + parent 1, hybrid + parent 2) were used in the experiment.<br> Four inbred lines and their four inter-pool hybrids were hybridized respectively in two-colour chips experiments. <br> The objective of our study was to:(i) identify differentially expressed genes in relation to heterosis for plant height, (ii) relate gene expression patterns to the dominance and overdominance hypothesis, (iii) determine the consistency of expression patterns between inbred parent - hybrid triplets also in view of differing degrees of relatedness of triplets, and to (iv) validate consistently differentially expressed genes between hybrids and their parental inbreds by real-time (qRT) PCR.
2006-08-17 | E-MEXP-764 | 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:Although heterosis has significantly contributed to increases in worldwide crop production, the molecular mechanisms regulating this phenomenon are still unknown. In the present study, we used a comparative proteomic approach to explore hybrid vigor via the proteome of both the popcorn L54 ♀ and P8 ♂ genotypes and the resultant UENF/UEM01 hybrid cross. To analyze the differentially abundant proteins involved in heterosis, we used the primary roots of these genotypes to analyze growth parameters and extract proteins. The results of the growth parameter analysis showed that the mid- and best-parent heterosis were positive for root length and root dry matter but negative for root fresh matter, seedling fresh matter, and protein content. The comparative proteomic analysis identified 1343 proteins in the primary roots of hybrid UENF/UEM01 and its parental lines; 220 proteins were differentially regulated in terms of protein abundance. A total of 62 regulated proteins were classified as non-additive, of which 53.2% were classified as high-parent abundance (+), 17.8% as above high-parent abundance (+ +), 16.1% as below low-parent abundance (- -), and 12.9% as low-parent abundance (-). A total of 22 biological processes were associated with non-additive proteins; processes involving translation, ribosome biogenesis, and energy-related metabolism represented 45.2% of the non-additive proteins. Our results suggest that heterosis in the popcorn hybrid UENF/UEM01 at an early stage of plant development is associated with an up-regulation of proteins related to synthesis and energy metabolism
2018-05-17 | PXD009436 | Pride
Project description:Combining dissimilar parents often leads to increased vigor in the hybrid offspring. “Heterosis” describes both this behavior and its underlying Mendelian and non-Mendelian interactions [1], although its molecular basis remains largely unknown. Recent comparisons of small RNA (sRNA) profiles from parents and their heterotic progeny identified correlations between interparental 24-nucleotide (24-nt) RNA variation and non-additive 24-nt RNA changes in the resulting hybrid [2,3]. 24-nt RNAs guide de novo cytosine methylation, and several proteins are required for their biogenesis, including a Snf2-like ATPase: required to maintain repression1 (RMR1) [4]. We found height variation between heterotic hybrids +/- RMR1 activity, implicating a role for RMR1 in heterosis. Based on the published correlations mentioned above [2,3], we hypothesized that RMR1-loss reduces parental sRNAs, altering their relative ratios and changing the sRNA profiles in the resulting hybrid from those of a standard hybrid (from +RMR1 parents). To probe this hypothesis, we profiled sRNAs from parents and hybrids +/- RMR1 function, limiting the parental diversity to only portions of chromosomes 6 and 9. Our analysis will address how RMR1 loss changes hybrid sRNAs in the presence and absence of underlying genetic variation and help to determine how this loss results in different phenotypic outcomes from heterotic crosses. 1. Shull (1948) Genetics 2. Groszmann et al (2011) PNAS 3. Barber et al (2012) PNAS 4. Hale et al (2007) PLoS Biology
2014-06-04 | GSE52103 | GEO