E-MTAB-4837
Ontology highlight
ABSTRACT:
PROVIDER: E-MTAB-4837 | ExpressionAtlas | 2019-05-14
REPOSITORIES: ExpressionAtlas
Similar Datasets
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
2009-08-31 | GSE14358 | GEO
Project description:To investigate the effects of transgenic lines L6 and L7 tomato fruits on total expression profile of MCF-7 breast cancer cells, we treated MCF-7 cells with 1 ug/ml of tomato fruit extract for 24 hours and compare it with wild type tomato fruit extract Objectives for this study included the identification of genes that were up or down-regulated at the transcriptional level in MCF-7 cells treated with transgenic lines L6 and L7 tomatofruit extract and compare it to wild type tomato fruit extract.
2017-06-12 | GSE94548 | GEO
Project description:Transcriptome analysis of 7 tissues of commercial tomato (S. lycopersicum cv MoneyMaker) and its wild red-fruited ancestor (S. pimpinellifolium LA0722) genotypes performed to assess expression level of tomato transcriptome and to aid whole genome annotation. Sequencing of fruit at 3 different developmental stages will help to assess gene regulation through ripening.
2012-05-08 | GSE33507 | GEO
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:Background: Fruit color is an important quality trait for nutrition value in tomato (Solanum lycopersicum) and has attracted huge attention for a long time. In order to dissect the yellow-fruit color of a novel tomato mutant n3122, we compared the dynamic transcriptome of the fruit pericarps from the mutant n3122 and its wild type red-fruited tomato cultivar M82. Results: The transcriptomes of fruits from M82 35 DPA (Days Post Anthesis), M82 47 DPA, M82 54 DPA, n3122 35 DPA, n3122 47 DPA, n3122 54 DPA and n3122 60 DPA were sequenced using an Illumina Hiseq 2000 sequencing platform. A total of 5568 differentially expressed genes (DEGs) were commonly identified in the four pairwise comparisons of M82_35 DPA vs n3122_35 DPA, M82_47 DPA vs n3122_47 DPA, M82_54 DPA vs n3122_54 DPA and M82_47 DPA vs n3122_60 DPA. Further Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that carotenoids biosynthesis, ethylene biosynthesis and signaling transduction, and transcription factors associated fruit ripening were different between M82 and n3122 which might be the underlying mechanisms for the yellow-fruit color of tomato. Conclusions: This research provided a global data set of dynamic transcriptomic changes during fruit development and ripening for the wild type red-fruited tomato cultivar M82 and its yellow-fruited mutant n3122, and offered a base for elucidating the molecular mechanisms underlying tomato red/yellow fruit color mutation.
2017-04-10 | GSE73908 | GEO
Project description:Anthocyanins are high value plant antioxidants which are not present in the fruits of cultivated tomato. However, both the dominant gene Anthocyanin fruit (Aft) and the recessive gene atroviolacea (atv), introgressed into domesticated tomato from two different wild Solanum species, stimulate a limited anthocyanin pigmentation. Surprisingly, double mutant Aft/Aft atv/atv tomatoes are characterised by the presence of anthocyanins in the fruit peel, resulting in intensely purple pigmented fruit. We carried out a transcript profiling analysis using GeneChip® Tomato Genome Arrays, in order to identify differentially expressed genes when comparing wild type, Aft/Aft, atv/atv, and Aft/Aft atv/atv fruits. The expression pattern of several genes involved in the anthocyanin pathway was analyzed in detail. Among the fruit peel-associated differentially expressed transcripts, genes involved in phenylpropanoid pathway, cell wall composition, biotic and abiotic stress responses, sugar and hormone metabolism were overrepresented in Aft/Aft atv/atv. Transcriptomic analysis thus revealed that the activation of anthocyanin synthesis in tomato fruit was accompanied by a complex remodulation of gene expression, likely affecting important agronomic and merceological traits.
2010-07-31 | GSE19792 | GEO
Project description:An Ac/Ds transposon tagged mutant population was screened for changes in visible fruit phenotypes. One line showed orange, yellow sectors in the fruit and was named Orange ripening (Orr), its transposase free offspring showed Mendelian segregation yielding red, yellow and orange fruit bearing plants in a ratio of 1:2:1. Crossing the an orange fruit plant line to the wild-type yielded only plants bearing yellow fruit. A cross between the yellow fruit bearing progeny yielded 26 plants having red and 17 plants having yellow fruit, suggesting an over-dominant allele. Using inverse PCR analysis showed an insertion in the putative subunit M of the tomato Ndh complex. Subsequently, an Orr Ds transposon excision line was recovered which only showed red pigmented fruit. Here, we describe microarray profiling of tomato fruits from wild-type, heterozygous and homozygous Orr insertion plants and from fruits harvested from the Orr excision line. Keywords: mutant wild type
2010-06-05 | GSE22110 | GEO
Project description:Anthocyanins are high value plant antioxidants which are not present in the fruits of cultivated tomato. However, both the dominant gene Anthocyanin fruit (Aft) and the recessive gene atroviolacea (atv), introgressed into domesticated tomato from two different wild Solanum species, stimulate a limited anthocyanin pigmentation. Surprisingly, double mutant Aft/Aft atv/atv tomatoes are characterised by the presence of anthocyanins in the fruit peel, resulting in intensely purple pigmented fruit. We carried out a transcript profiling analysis using GeneChip® Tomato Genome Arrays, in order to identify differentially expressed genes when comparing wild type, Aft/Aft, atv/atv, and Aft/Aft atv/atv fruits. The expression pattern of several genes involved in the anthocyanin pathway was analyzed in detail. Among the fruit peel-associated differentially expressed transcripts, genes involved in phenylpropanoid pathway, cell wall composition, biotic and abiotic stress responses, sugar and hormone metabolism were overrepresented in Aft/Aft atv/atv. Transcriptomic analysis thus revealed that the activation of anthocyanin synthesis in tomato fruit was accompanied by a complex remodulation of gene expression, likely affecting important agronomic and merceological traits. Wild type (Cv. Ailsa Craig, accession number LA2838A), Aft/Aft (accession number LA1996), atv/atv (accession number LA0797) and double mutant (Aft/Aft atv/atv) were grown during the winter season in a controlled heated greenhouse. Fruits were collected at mature green, turning red and red stages of development. The transcriptional profile in Aft/Aft, atv/atv, and Aft/Aft atv/atv fruits when compared to the wild type was analyzed using the GeneChip® Tomato Genome Array.
2010-07-30 | E-GEOD-19792 | biostudies-arrayexpress
Project description:An Ac/Ds transposon tagged mutant population was screened for changes in visible fruit phenotypes. One line showed orange, yellow sectors in the fruit and was named Orange ripening (Orr), its transposase free offspring showed Mendelian segregation yielding red, yellow and orange fruit bearing plants in a ratio of 1:2:1. Crossing the an orange fruit plant line to the wild-type yielded only plants bearing yellow fruit. A cross between the yellow fruit bearing progeny yielded 26 plants having red and 17 plants having yellow fruit, suggesting an over-dominant allele. Using inverse PCR analysis showed an insertion in the putative subunit M of the tomato Ndh complex. Subsequently, an Orr Ds transposon excision line was recovered which only showed red pigmented fruit. Here, we describe microarray profiling of tomato fruits from wild-type, heterozygous and homozygous Orr insertion plants and from fruits harvested from the Orr excision line. Keywords: mutant wild type Tomato fruits were harvested at breaker stage using wild-type, ORR homozygouse and heterozygous lines as well as Orr excision lines. To investigate the expression changes in the ORR mutants, wildtype and ORR mutant line fruits were harvested at the breaker stage and subjected to Affymetrix microarray profiling
2010-06-16 | E-GEOD-22110 | biostudies-arrayexpress
Project description:Purpose: The goals of this study was to provide genome-wide data to investigate the molecular mechanism of ABA regulation in many ripening related biological processes, including fruit color variation, antioxidant capacity, flavonoids biosynthesis and photosynthesis. Methods:By applying the next generation sequencing technology, we conducted a comparative analysis of exogenous ABA and NDGA effects on tomato fruit maturation. Results:The high throughput sequencing results showed that 25728 genes expressed across all three samples, and 10388 of them were identified as significantly differently expressed genes (DEGs). Exogenous ABA was found to enhance the transcription of genes in pigments metabolism, including carotenoids biosynthesis and chlorophyll degradation, whereas NDGA treatment inhibited these progresses. The results also revealed the crucial role of ABA in flavonoids synthesis and regulation of antioxidant system. Intriguingly, we also found that an inhibition of endogenous ABA significantly enhanced the transcriptional abundance of genes involved in fruit photosynthesis. Conclusions:next-generation sequencing enabled us to characterize the transcriptomes of tomato fruit treated with ABA and NDGA. By comparing these transcriptomes with control respectively, we observed that ABA could accelerate fruit maturation by positively regulating many genes related to ripening processes. Our study have turned spotlight on the pathways of fruit pigmentation, including carotenoid biosynthesis and chlorophyll metabolism. Exogenous ABA was able to up-regulate many genes in relation to the carotenoids accumulation and chlorophyll breakdown, thus promoting the color transition of tomato fruit. In addition, ABA has the potential to improve the genes related to antioxidant capacity, such as SODs, CATs, APXs, GSTs, GPXs, TrXs and PrxRs. Besides, the expression changes of genes involved in flavonoids biosynthesis after ABA exposure was striking, suggesting ABA could enhance the defense response by producing more secondary metabolite in tomato fruit. Moreover, the sequencing results also implied high level of ABA could negatively affect photosynthesis of tomato fruit, which needs more investigations to explore the interaction between ABA and photosynthesis in the future.
2017-02-09 | GSE63521 | GEO