Transcriptome data from tomato parthenocarpic mutants lacking Tomato APETALA3 (TAP3)
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ABSTRACT:
ORGANISM(S): Solanum lycopersicum
PROVIDER: GSE179026 | GEO | 2022/05/18
REPOSITORIES: GEO
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Project description:We investigated the behavior of tomato mutants lacking transcription factors of SlIAA9, a key gene controlling parthenocarpy. To focus on the early stages of anthesis, ovary samples of MicroTom-J (MT-J) and the mutant at the three stages (bud, flowering, and after flowering) were collected.
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Project description:To evaluate the role of seeds in fruit quality, we induced parthenocarpy in tomato by regulating ovule-specific auxin synthesis or responsiveness using the INO promoter from A. thaliana, which is expressed in the outer layer of the integuments during early stages of ovule development. We compared these to fruit where the same coding regions were expressed from the DeFH9 promoter which is expressed in carpel tissues during early stages of ovule development. Expression of auxin synthesis or responsiveness genes by both of these promoters produced seedless parthenocarpic tomato fruit. We compared fruit samples using the Affymetrix tomato GeneChip (GPL4741) to determine how gene regulation and expression differed between wild-type and transgenic fruit. Keywords: genetic modification
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Project description:To evaluate the role of seeds in fruit quality, we induced parthenocarpy in tomato by regulating ovule-specific auxin synthesis or responsiveness using the INO promoter from A. thaliana, which is expressed in the outer layer of the integuments during early stages of ovule development. We compared these to fruit where the same coding regions were expressed from the DeFH9 promoter which is expressed in carpel tissues during early stages of ovule development. Expression of auxin synthesis or responsiveness genes by both of these promoters produced seedless parthenocarpic tomato fruit. We compared fruit samples using the Affymetrix tomato GeneChip (GPL4741) to determine how gene regulation and expression differed between wild-type and transgenic fruit. Experiment Overall Design: Wild-type fruit with seeds was compared with transgenic lines INO-IaaM, DefH9-IaaM, INO-RolB, and DefH9-RolB. To find genes with seed-specific expression, we also compared the control with wild-type fruit from which seeds had been manually removed. We had three biological replicates for each treatment and control except DefH9-RolB, for which only two replicates were available. Each CEL file from the microarray represents one plant from each line.
2009-09-15 | E-GEOD-14358 | biostudies-arrayexpress
Project description:Transcriptome data from tomato parthenocarpic mutants lacking Tomato APETALA3 (TAP3)
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Project description:Parthenocarpy—the production of seedless fruits without fertilization—is very useful for fruit cultivation. Among pear cultivars (Japanese, Chinese, and European pears and their interspecific hybrids) subjected to flower emasculation and left unpollinated, only some of the European pears had a stable and high degree of fruit set and fruit enlargement. Almost all the enlarged fruits formed no seeds. Comparison of fruits produced by using emasculation without pollination or with self-pollination ruled out the possibility of stenospermocarpy in these parthenocarpic pears. The results suggested that the abovementioned characteristics were inherited maternally by the next generation and that it should be possible to introduce parthenocarpy into Japanese pears. Neither Chinese nor Japanese pears treated with emasculation and no pollination showed consistently stable fruit set or fruit enlargement. In Chinese pears, these characteristics varied greatly from year to year, and in Japanese pears they were stable but weak. Although in each cultivar highly parthenocarpic fruits weighed slightly less than cross-pollinated ones, the cortexes of the emasculated fruits were enlarged and the fruits were not greatly inferior to those of cross-pollinated ones. By using a customized pear cDNA microarray, we compared the gene expression profiles of highly and weakly parthenocarpic cultivars before flowering. Expression of several phenylpropanoid-related genes and photosystem-related genes differed significantly between the two groups. Some of these genes were contained in the chloroplast genome. These results showed the unique mechanism of genetic parthenocarpy in pome fruits as opposed to non-pome fruits. The gene expression profiles between high and low parthenocarpy group before flowering were compared.
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Project description:Parthenocarpy—the production of seedless fruits without fertilization—is very useful for fruit cultivation. Among pear cultivars (Japanese, Chinese, and European pears and their interspecific hybrids) subjected to flower emasculation and left unpollinated, only some of the European pears had a stable and high degree of fruit set and fruit enlargement. Almost all the enlarged fruits formed no seeds. Comparison of fruits produced by using emasculation without pollination or with self-pollination ruled out the possibility of stenospermocarpy in these parthenocarpic pears. The results suggested that the abovementioned characteristics were inherited maternally by the next generation and that it should be possible to introduce parthenocarpy into Japanese pears. Neither Chinese nor Japanese pears treated with emasculation and no pollination showed consistently stable fruit set or fruit enlargement. In Chinese pears, these characteristics varied greatly from year to year, and in Japanese pears they were stable but weak. Although in each cultivar highly parthenocarpic fruits weighed slightly less than cross-pollinated ones, the cortexes of the emasculated fruits were enlarged and the fruits were not greatly inferior to those of cross-pollinated ones. By using a customized pear cDNA microarray, we compared the gene expression profiles of highly and weakly parthenocarpic cultivars before flowering. Expression of several phenylpropanoid-related genes and photosystem-related genes differed significantly between the two groups. Some of these genes were contained in the chloroplast genome. These results showed the unique mechanism of genetic parthenocarpy in pome fruits as opposed to non-pome fruits.
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Project description:MADS family genes in rice control flowering and inflorescence development. In the early flower stages of plant, MADS-box transcripion factors could form protein-protein interaction complexes with other floral homeotic genes and regulate the expression of downstram genes. OsMADS32 in rice is an important transcription factor in controlling flower development We used microarrays to detail the expression of downstream genes under the control of OsMADS32 during the early inflorescence stages in rice
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Project description:Gene-to-gene coexpression analysis is a powerful approach to infer function of uncharacterized genes. To perform non-targeted coexpression analysis of tomato genes, we collected a developmental gene expression dataset using various tissues of tomato plant. Expression data are collected from 24 different tissue types including root, hypocotyl, cotyledon, leaf at different stages, and fruit tissues at 4 different ripening stages from 4 different Solanum lycopersicum cultivars. Fruits were separated to the flesh and the peel. These two tissue types indeed showed remarkably different gene expression profiles. We also collected data from 4 different ripening stages (mature green, yellow, orange, and red) to detail the changes during ripening. By using this gene expression dataset, we calculated pair-wise Pearsonâs correlation coefficients, and performed network-based coexpression analysis. The analysis generated a number of coexpression modules, some of which showed an enrichment of genes associated with specific functional categories. This result will be useful in inferring functions of uncharacterized tomato genes, and in prioritizing genes for further experimental analysis. We used Affymetrix GeneChip Tomato genome Arrays to detail the global gene expression change using 24 different tomato tissue types (67 hybridizations). We collected gene expression data from 24 different tomato tissue types using 67 hybridizations. Root, hypocotyl, cotyledon, and leaf were sampled from 3-week-old or 5-weekâold plant of Solanum lycopersicum cultivar Micro-Tom. Fruit tissues were sampled from S. lycopersicum cultivars Micro-Tom, Anthocyanin fruit (Aft, LA1996), Line27859, and Momotaro 8 (Takii, Japan). From Micro-Tom fruit, the peel and the flesh were separately sampled from 4 different ripening stages: mature green (MG, approximately 30 day after anthesis), yellow (Y, approximately 35 days after anthesis), orange (O, approximately 38-40 days after anthesis), and red (R, approximately 45-48 days after anthesis). From fruits of Aft and Line27859, the peel and the flesh were sampled at mature green (MG, approximately 40 days after anthesis) and red (R, approximately 50-55 days after anthesis) stages. From Momotaro 8, the peel and the flesh were sampled at red (R, 50- approximately 50-55 days after anthesis) stages. For each tissue type, 2-4 biological replicates were made in RNA preparation.
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