Digital gene expression analysis of 5 rice samples
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ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE27240 | GEO | 2012/01/01
SECONDARY ACCESSION(S): PRJNA137495
REPOSITORIES: GEO
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Project description:To study the function of chromatin regulators in hybrid gene expression, the histone deacetylase gene OsHDT1 was over-expressed or inactivated by RNAi in an elite rice parent. Digital analysis of gene expression using high throughput sequencing technology revealed several differential gene expression patterns in the hybrid, including additivity, nonadditivity and overdominance, etc. Alteration of OsHDT1 levels affected many genes specifically in the hybrid. In addition, we show that increased OsHDT1 could suppress overdominance gene expression, providing evidence of overdominance gene action in heterosis. These results not only support the overdominance hypothesis to explain heterosis, but also provide evidence that variation in the levels of single trans-acting regulatory proteins such as chromatin factors is important to establish differential gene expression pattern in the hybrid. High throughput sequencing technology was used to analyse gene differencial expression of 15 days old rice seedling of 5 samples, MH63(MH), ZS97(ZS), SY63(SY,hybrids of MH and ZS), overexpression of OsHDT1 in SY(FU), RNAi of OsHDT1 in SY(FR).
2012-01-01 | E-GEOD-27240 | biostudies-arrayexpress
Project description:Based our serial analysis of gene expression (SAGE) data from an elite Chinese super-hybrid rice (LYP9) and its parental cultivars (93-11 and PA64s) in three major tissue types at three different developmental stages, we obtained a much more comprehensive view of genes that related to rice heterosis and analyzed the potential effects of gene-expression difference on the heterosis of rice.These heterotic expression genes among different genotypes provided new avenues for exploring the molecular mechanisms underlying heterosis, including variable gene expression patterns. Keywords: Heterosis study by SAGE
2007-06-08 | GSE8048 | GEO
Project description:Although utilization of heterosis has largely improved the yield of many crops worldwide, the underlying molecular mechanism of heterosis, particularly for allopolyploids, remains unclear. Here, we compared epigenome and transcriptome data of an elite hybrid and its parental lines in three assessed tissues (seedling, flower bud, and silique) to explore their contribution to heterosis in allopolyploid B. napus. Transcriptome analysis illustrated that a small proportion of non-additive genes in the hybrid compared with its parents, as well as parental expression level dominance, might have a significant effect on heterosis. We identified histone modification (H3K4me3 and H3K27me3) variation between the parents and hybrid, most of which resulted from the differences between parents. H3K4me3 variations were positively correlated with gene expression differences among the hybrid and its parents. Furthermore, H3K4me3 and H3K27me3 were rather stable in hybridization and were mainly inherited additively in the B. napus hybrid. Together, our data revealed that transcriptome reprogramming and histone modification remodeling in the hybrid could serve as valuable resources for better understanding heterosis in allopolyploid crops.
2023-07-18 | GSE218592 | GEO
Project description:Based our serial analysis of gene expression (SAGE) data from an elite Chinese super-hybrid rice (LYP9) and its parental cultivars (93-11 and PA64s) in three major tissue types at three different developmental stages, we obtained a much more comprehensive view of genes that related to rice heterosis and analyzed the potential effects of gene-expression difference on the heterosis of rice.These heterotic expression genes among different genotypes provided new avenues for exploring the molecular mechanisms underlying heterosis, including variable gene expression patterns. Keywords: Heterosis study by SAGE We constructed nine SAGE libraries parallelly, including root at the first tillering stage, leaf at the milky stage of rice grain maturation, and panicle at the pollen-maturing stage of hybrid rice (LYP9) and its paternal lines (9311, PA64s).
2007-06-07 | E-GEOD-8048 | biostudies-arrayexpress
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:Non-additive gene regulation has been recently suggested as an important factor promoting phenotypic variation and plasticity. In order to obtain a description of gene expression status at an early stage of ear development in a maize (Zea mays L.) F1 hybrid as relative to its parental inbreds, we compared gene expression profiles in immature ears of elite inbred lines B73 and H99 to one of their F1 hybrids (B73xH99) using cDNA microarray technology. Results show several genes expressed at a significantly different level between both inbred lines and their hybrid. In addition, gene expression non-additivity in the hybrid was detected on a broad scale, consisting of both dominance and over-dominance components, indicating that complex non-additive interactions at the molecular level exist in the developing ear of the studied maize hybrid. Non-additively regulated genes belong to a wide range of molecular functions, indicating that several regulatory and metabolic patterns are possibly affected during ear development in the investigated hybrid. We discuss the possibility that observed gene expression non-additivity in immature ear might be an early molecular manifestation of hybrid vigor, the most exploited factor for maize agronomic improvement.
2007-10-01 | GSE2771 | GEO
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:Non-additive gene regulation has been recently suggested as an important factor promoting phenotypic variation and plasticity. In order to obtain a description of gene expression status at an early stage of ear development in a maize (Zea mays L.) F1 hybrid as relative to its parental inbreds, we compared gene expression profiles in immature ears of elite inbred lines B73 and H99 to one of their F1 hybrids (B73xH99) using cDNA microarray technology. Results show several genes expressed at a significantly different level between both inbred lines and their hybrid. In addition, gene expression non-additivity in the hybrid was detected on a broad scale, consisting of both dominance and over-dominance components, indicating that complex non-additive interactions at the molecular level exist in the developing ear of the studied maize hybrid. Non-additively regulated genes belong to a wide range of molecular functions, indicating that several regulatory and metabolic patterns are possibly affected during ear development in the investigated hybrid. We discuss the possibility that observed gene expression non-additivity in immature ear might be an early molecular manifestation of hybrid vigor, the most exploited factor for maize agronomic improvement. We directly contrasted both B73 and H99 inbred lines vs. their F1 heterotic hybrid transcriptomes in immature ear. Our experimental design consisted of 10 cDNA microarray hybridizations, 5 for each combination of hybrid vs. inbred genotypes, involving 20 separate labeling reactions. Labeling dyes were swapped in two of the five replicates for each combination. In each hybridization, control channel was assigned to the F1 hybrid, and differences in transcriptional levels between B73 and H99 were inferred using the hybrid as a common reference sample in an indirect experimental design. To take in account variability in transcript population among individuals, total RNA coming from different isolations, each collected on multiple individuals, were mixed before poly(A+) RNA purification. All hybridizations on microarray slides were then performed using cDNA independently labeled from the poly(A+) RNA purification product for each genotype. Base-two logarithms of expression ratios were subjected to one-class response significance analysis in SAM v. 2.20 software [Tusher et al. 2001]. For each EST the estimates of additive parameter "a" and dominance parameter "d" (middle-parent heterosis) were obtained as a = (L2 – L1)/2 d = (L1 + L2)/2 (where L1 and L2 are mean base-two logarithms of expression ratios of F1 vs. B73 and F1 vs. H99, respectively). Positive values of "a" indicate expression values bigger in B73 than in H99. The dominance/additivity ratio (d/|a|) was also calculated [Falconer 1989]. Evaluation of statistical significance of parameters was done by calculating standard errors of the estimates "a" and "d" as standard errors of linear functions of the means. Significance testing was done correspondingly, using an F-test for linear contrasts. P-values for the families of tests corresponding to each parameter were subjected to global error analyses using a method based on fitting mixture distribution [Allison et al. 2002], allowing to estimate the false discovery rates (FDR) and false negative rates (FNR). Confidence intervals for d/|a| ratios were obtained by Fieller’s method [Piepho and Emrich 2005], allowing to classify the genes into different dominance type classes.
2007-10-01 | E-GEOD-2771 | 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
2005-12-06 | GSE3733 | GEO