Modes of gene action observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents
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ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE3733 | GEO | 2005/12/06
SECONDARY ACCESSION(S): PRJNA104849
REPOSITORIES: GEO
Similar Datasets
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
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 The inbreds B73 (Schnable Lab Accession #660) and Mo17 (Schnable Lab Accession #2618) used in this study were derived by self-pollination from stocks originally obtained from Don Robertson (Iowa State University) and Mike Lee (Iowa State University), respectively. Mo17 was crossed as a female by B73 to generate the F1. Kernels from three different seed sources (ears) per genotype were used in the experimental design. Prior to microarray analyses genotypes were confirmed by genotyping DNA extracted from each seed source using co-dominant IDP genetic markers that distinguish B73 from Mo17 (Fu et al., in preparation). Ten biological replications of B73, Mo17, and their F1 (Mo17xB73) were grown under highly controlled conditions in a randomized complete block design. For each replication, the B73, Mo17, and F1 samples were hybridized to three two-color cDNA microarrays using a loop design such that each loop included all pairwise comparisons between genotypes. RNA pools for each genotype were alternately labeled providing dye balance within each loop. After hybridization, one biological replicate was removed due to poor quality. The final analysis incorporated 27 microarray slides (3 slides for each of nine high-quality biological replicates).
2010-06-26 | E-GEOD-4473 | biostudies-arrayexpress
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: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: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.
2012-01-01 | GSE27240 | GEO
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 Comparison of four inbred lines and the resulting twelve reciprocal hybrids. Samples from all 16 genotypes were paired on 85 arrays following a hybridization scheme including a dye-swap according to Keller et al. (2005). A tailor-made design was developed for this purpose using simulated annealing that was optimized for estimating non-additive effects while at the same time allowing estimation of additive effects with comparable precision. Optimizing precision for estimation of non-additivity required the design to be unbalanced with respect to the number of genotype pairings and the number of replications per genotype. Hence, two RNA samples were hybridized to each of the 85 microarray chips. Each RNA sample represented an independent biological replicate
2008-02-16 | E-GEOD-10539 | biostudies-arrayexpress
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
2010-06-26 | E-GEOD-4477 | biostudies-arrayexpress
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: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