Transcriptome analysis of tomato introgression line during fruit development.
Ontology highlight
ABSTRACT:
ORGANISM(S): Solanum lycopersicum
PROVIDER: GSE78260 | GEO | 2016/07/25
SECONDARY ACCESSION(S): PRJNA313105
REPOSITORIES: GEO
Similar Datasets
Project description:We performed transcriptome analyses throughout fruit development using the tomato cultivar M82 and its near-isogenic line IL8-3, with interesting and useful traits such as a high content of soluble solids. To identify genes that show differential expression between M82 and IL8-3 fruits, we used a custom microarray containing 43,803 tomato probes. Some genes, such as cell wall invertase and sucrose synthase genes, which are encoded by LIN6 (Solyc10g083290) and TOMSSF (Solyc12g009300) respectively, are well known to play a key role in the sink function of fruit. In this study, the levels of LIN6 and TOMSSF transcripts were higher in IL8-3 than in M82 fruit at 20 and 30 DAF, which are developmental stages for starch accumulation and increased hexose content, respectively, in IL8-3 fruit (Ikeda et al. 2013), and decreased to the level of M82 at ripening stage. Similar patterns were observed in many metabolites of glycolysis and the pentose phosphate pathway as well as metabolites in starch and sucrose metabolism. Gene expressions during fruit development were analyzed. Three biological replicates were prepared for each stage, and a total of 24 samples were analyzed.
2016-07-25 | E-GEOD-78260 | biostudies-arrayexpress
Project description:The fruit physiology of banana cultivars is poorly understood. To study the ripening of plantain, a high-throughput proteomics experiment was executed and compared to the better known Cavendish. The starch content in plantain was at the onset of ripening very high and decreased to undetectable levels. Multivariate analysis of the proteins was performed correlated to the starch dynamics. The drop in sucrose synthase and the raise of acid invertase during ripening indicated a change in the balance of the sucrose fate. During ripening, sugars may no longer be available for respiration since they are stored in the vacuoles, making citrate the preferred respiratory substrate. One isoform of alfa amylase acted during the early phases of starch breakdown while another acted during the later phases when the starch branches are simpler in structure. We found significant variety specific differences in granule-bound starch synthase, alpha- and beta amylases, cell wall invertase and sucrose synthase that corroborate the difference in starch content/structure between both bananas. Differences in small heat shock proteins and in the cell wall-modifying enzyme xyloglucan endotransglucosylase/hydrolase support respectively the presumed higher carotenoid content and the firmer fruit structure of plantains.
2020-06-08 | PXD013724 | Pride
Project description:Tomatoes are one of the valuable sources of antioxidants such as carotenes, ascorbic acid (AsA), and phenolic compounds (flavonoids and hydroxycinnamic acid derivatives). These secondary metabolites have been proved to be beneficial for humans and animals because their involvement in the prevention of many proliferative and degenerative diseases. The aim of this work is to gain greater insights in the genetic control of phenylpropanoid accumulation in tomato fruit by using genomics-based strategies. In order to identify QTLs controlling antioxidant accumulation in tomato fruit we carried out a comparative analysis of Solanum pennellii x S. lycopersicum cv. M82 introgression lines (ILs) over three year trials in greenhouse environment. Among all, IL7-3 showed higher fruit content of total phenolics and the HPLC-UV profile revealed that chlorogenic acid mainly accounted for the higher performance of this line. To investigate in details genetic mechanisms and candidate genes controlling phenols synthesis and accumulation in IL7-3 fruit we performed a comparative transcriptomic analysis in tomato pericarp. In particular, RNA was extracted from percarp of IL7-3 and M82 parental line and hybridized on a 90k Combimatrix TomatArray 1.0. The experiment was repeated over two consecutive years. The transcriptomic approach allowed to identify 291 differentially expressed transcripts, 149 showing up-rgulation and 142 down-regulation. The ethylene signaling pathway has been involved in the modulation of the level of total phenolics in ripe fruit. In particular, an Ethilene Responsive Factor 1 (ERF1) was functionally characterized by TILLING (Targeting Local Lesion IN Genomes) approach. The mutant line expressed lower accumulation of phenolics in the fruit and additional insights on the regulation of phenolics in tomato ripe fruit were provided. Comparative microarray analysis between a tomato introgression line (IL7-3) expressing higher level of fruit total phenolics and its parental cultivar M82 (reference) was performed. In particular, samples were generated by pooling red-ripe fruit from the same plant and discarding the seeds, jelly parenchyma, columella and placenta tissues. Three plant replica were used for each line (IL7-3 and M82) and the experiment was replicated over two consecutive years.
2013-02-13 | E-GEOD-37568 | 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:Tomatoes are one of the valuable sources of antioxidants such as carotenes, ascorbic acid (AsA), and phenolic compounds (flavonoids and hydroxycinnamic acid derivatives). These secondary metabolites have been proved to be beneficial for humans and animals because their involvement in the prevention of many proliferative and degenerative diseases. The aim of this work is to gain greater insights in the genetic control of phenylpropanoid accumulation in tomato fruit by using genomics-based strategies. In order to identify QTLs controlling antioxidant accumulation in tomato fruit we carried out a comparative analysis of Solanum pennellii x S. lycopersicum cv. M82 introgression lines (ILs) over three year trials in greenhouse environment. Among all, IL7-3 showed higher fruit content of total phenolics and the HPLC-UV profile revealed that chlorogenic acid mainly accounted for the higher performance of this line. To investigate in details genetic mechanisms and candidate genes controlling phenols synthesis and accumulation in IL7-3 fruit we performed a comparative transcriptomic analysis in tomato pericarp. In particular, RNA was extracted from percarp of IL7-3 and M82 parental line and hybridized on a 90k Combimatrix TomatArray 1.0. The experiment was repeated over two consecutive years. The transcriptomic approach allowed to identify 291 differentially expressed transcripts, 149 showing up-rgulation and 142 down-regulation. The ethylene signaling pathway has been involved in the modulation of the level of total phenolics in ripe fruit. In particular, an Ethilene Responsive Factor 1 (ERF1) was functionally characterized by TILLING (Targeting Local Lesion IN Genomes) approach. The mutant line expressed lower accumulation of phenolics in the fruit and additional insights on the regulation of phenolics in tomato ripe fruit were provided.
2013-02-13 | GSE37568 | GEO
Project description:Ascorbic acid (AsA), important for plant cell protection against oxidative stresses, is useful for human health. Among vegetables, tomato is the most important specie due to its significant consumption at worldwide level. Although AsA metabolism has been characterized in detail, the genetic mechanisms controlling AsA accumulation in tomatoes are poorly understood. We used an introgression line (IL 10-1) containing a QTL inducing a reduced AsA accumulation in the fruit and carried out a comparative transcriptomic analysis in fruit tissues using a parental cultivar (M82) with normal fruit AsA levels as a reference. We identified 233 differentially expressed genes, indicating that AsA accumulation in IL 10-1 reflects modification in the peroxisomal metabolism and reduced glutathione biosynthesis. Evidences coming from the experiment suggest that the lower AsA accumulation in IL10-1 fruit is mainly achieved by increasing ROS generation through a NAD+-dependent isocitrate dehydrogenase and promoting an increase in aminoacid catabolism, which is driven by a stress response and may lead to lower glutathione pool. Comparative microarray analysis between a tomato introgression line (IL10-1) expressing higher level of fruit ascorbic acid and its parental cultivar M82 (reference) was performed. In particular, samples were generated by pooling red-ripe fruit from the same plant and discarding the seeds, jelly parenchyma, columella and placenta tissues. Three plant replica were used for each line (IL10-1 and M82) and the experiment was replicated over two consecutive years.
2012-05-29 | E-GEOD-26962 | biostudies-arrayexpress
Project description:We sequenced mRNA from immature green (15 days after anthesis) and red (Breaker+10 days) tomato (Solanum lycopersicum) fruit tissues from plants over-expressing SlGLK1 and SlGLK2 and from control plants 'M82' to compare gene expression levels between transgenic fruit and the control. Note: Samples in SRA were assigned the same sample accession. This is incorrect as there are different samples, hence “Source Name” was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
2013-06-01 | E-MTAB-4819 | biostudies-arrayexpress
Project description:Photosynthesis is arguably the most important biological process on earth. In plants, energy harvested in photosynthesis is converted into sugar and starch, which are important products from species with agronomic interest. During the photosynthesis in the chloroplast, the intermediate carbon metabolites (triose phosphates) produced by the Calvin cycle can either be exported to the cytosol for sucrose synthesis or stay in the chloroplast for starch synthesis (formation). Two fructose-1,6-bisphosphatase (FBPase) enzymes, the chloroplastidial (cpFBPaseI) and the cytosolic (cyFBPase) isoforms, catalyse the first irreversible step during the conversion of triose phosphate to starch or sucrose, respectively. Recently, another cpFBPase isoform (cpFBPaseII) with unknown function was identified. It has been reported that the reduction of cyFBPase or cpFBPaseI activity leads to an alteration in starch and sucrose content. In our laboratory, Arabidopsis thaliana knock-out mutants for the cyFBPase and cpFBPaseI are now available. The objective this research project is to identify and functionally characterize genes differentially expressed in Arabidopsis thaliana knock-out mutants lacking FBPase genes. We make use of high throughput methodologies, such as the transcriptomic and proteomic analyses which represent invaluable tools to identify new loci responsible for agronomically important traits.
2012-05-04 | GSE32522 | GEO
Project description:Photosynthesis is arguably the most important biological process on earth. In plants, energy harvested in photosynthesis is converted into sugar and starch, which are important products from species with agronomic interest. During the photosynthesis in the chloroplast, the intermediate carbon metabolites (triose phosphates) produced by the Calvin cycle can either be exported to the cytosol for sucrose synthesis or stay in the chloroplast for starch synthesis (formation). Two fructose-1,6-bisphosphatase (FBPase) enzymes, the chloroplastidial (cpFBPaseI) and the cytosolic (cyFBPase) isoforms, catalyse the first irreversible step during the conversion of triose phosphate to starch or sucrose, respectively. Recently, another cpFBPase isoform (cpFBPaseII) with unknown function was identified. It has been reported that the reduction of cyFBPase or cpFBPaseI activity leads to an alteration in starch and sucrose content. In our laboratory, Arabidopsis thaliana knock-out mutants for the cyFBPase and cpFBPaseI are now available. The objective this research project is to identify and functionally characterize genes differentially expressed in Arabidopsis thaliana knock-out mutants lacking FBPase genes. We make use of high throughput methodologies, such as the transcriptomic and proteomic analyses which represent invaluable tools to identify new loci responsible for agronomically important traits. Three independent biological replicates were used for each type of sample. Three hybridizations were performed, representing the three independent biological replicates, being one of them a dye swap
2012-05-03 | E-GEOD-32522 | biostudies-arrayexpress
Project description:Transgenic tomato (Solanum lycopersicum) plants expressing a fragment of the SlSIOGDH gene encoding subunit E1 of the 2-oxoglutarate dehydrogenase protein complex in the antisense orientation and exhibiting considerable reductions in the activity of this enzyme exhibit a considerably reduced rate of respiration. They were, however, characterised by largely unaltered photosynthetic rates and fruit yield but a restricted leaf, stem and root growth rate. The lines displayed markedly altered metabolic profiles including changes in tricarboxylic acid cycle intermediates and in the majority of the amino acids without alterations in pyridine nucleotide content. Moreover, they displayed a generally accelerated development exhibiting early flowering, accelerated fruit ripening and a markedly earlier onset of leaf senescence. In addition, transcript and selective hormone profiling of gibberellins and ABA revealed changes only in the former coupled to changes in transcripts encoding enzymes of gibberellins biosynthesis. The data obtained are discussed in the context of the importance of this enzyme in both photosynthetic and respiratory metabolism as well as in programs of plant development connected to carbon nitrogen interactions. Three biological replicates per genotype were analysed. Genotypes analyzed were tomato var. M82 wild type plants grown under green house conditions with one 2-oxo-glutarate dehydrogenase antisense line grown under the same conditions.
2012-09-01 | E-GEOD-35618 | biostudies-arrayexpress