Molecular charcterisation of Tangerine2 Mutant
Ontology highlight
ABSTRACT:
ORGANISM(S): Solanum lycopersicum
PROVIDER: GSE91045 | GEO | 2018/12/01
REPOSITORIES: GEO
Similar Datasets
Project description:The High-β-Carotene (HBC) mutant identified from EMS mutagenized population of cultivar Arka Vikas and the biochemical studies revealed that mutant fruits contain four times higher level of β-Carotene in comparison to Wild type (cv. Arka Vikas). We have developed whole genome microarray expression profiling as a discovery platform to identify differentially expressed genes in fruits containing High-β-Carotene mutant in comparison to Wild type (cv. Arka Vikas). Tomato fruit tissue samples from different stages of fruit ripening like Mature green, Breaker, Turning and Ripening stages of High-β-Carotene (HBC) mutant and Wild type (cv. Arka VIkas) were used for microarray gene expression analysis. Carotenoid pathway analysis of both mutant and wild type reveals that the high expression of chromoplast specific lycopene- β-cyclase gene in the HBC mutant, which is involved in the conversion of lycopene to β-carotene, but in wild type the expression of this gene, was low. Four genes (PSY, PDS, CRTISO, CYCB) of the carotenoid pathway was quantified in the same RNA samples by real-time PCR, confirming that the variation of the gene expression in HBC mutant.
2017-12-01 | GSE90964 | GEO
Project description:Unripening mutant was identified from natural population of cv. Arka Vikas and the mutant was characterized with un ripened with light yellowish colour pericarp. Differential gene expression studies were carried out between unripening mutant and wild type using the whole genome microarray expression profiling as a discovery platform. Tomato fruit tissue samples from different stages of fruit ripening like Mature green, Breaker, Turning and Ripening stages of unripening mutant and wild type was used for microarray gene expression analysis. Carotenoid pathway analysis of both mutant and wild type reveals genes involved in the pathway altered in the unripening mutant. Four genes (PSY, PDS, CRTISO, CYCB) of the carotenoid pathway was quantified in the same RNA samples by real-time PCR, confirming that the variation of the gene expression in unripening mutant.
2018-12-01 | GSE92645 | GEO
Project description:The tomato MADS-box FRUITFULL (FUL) homologs, FUL1 and FUL2, interact with the main ripening regulator RIPENING INHIBITOR (RIN). To clarify their role in fruit ripening, we generated FUL1/FUL2-suppressed transgenic lines by RNAi. We found that five transgenic lines bearing fruits that did not ripen normally: lycopene accumulation and increase of ethylene production were severely inhibited. We then performed next generation RNA sequencing (RNA-Seq) analysis of the fruits of a FUL1/FUL2-suppressed line (TF18) with those of the wild type (Ailsa Craig cultivar; AC) and rin mutant. The comparison of RNA-Seq data among them indicated that FUL1/FUL2-suppression significantly affected the expression of a larger portion of ripening-induced and -repressed genes than the rin mutation did. Moreover, the effect of FUL1/FUL2-suppression was observed not only in the fruits harvested at the wild type ripening age [45 days after pollination (DAP)] but also in those at the pre-ripening age (35 DAP). This suggests that the FUL homologs play an essential role in the regulation of fruit development and ripening, the role which covers a wider range of biological processes than RIN does. Differentially expressed genes (DEGs) between the wild type and TF18 fruits included known ripening-related genes such as ACS2 and ACS4 involved in ethylene production and PSY1 in carotenoid biosynthesis, consistent with the phenotype of TF18 fruits described above. The DEGs also included many direct RIN target genes, which supports the hypothesis that the FUL homologs regulate fruit ripening in a form of MADS-box complex with RIN. mRNA profiles of wild type (Ailsa Craig cultivar), rin mutant and FUL1/FUL2-suppressed tomato fruits harvested at 35DAP and 45 DAP were generated by next generation sequencing, in triplicate, using Illumina Hiseq2000.
2014-06-23 | E-GEOD-49289 | biostudies-arrayexpress
Project description:The tomato MADS-box FRUITFULL (FUL) homologs, FUL1 and FUL2, interact with the main ripening regulator RIPENING INHIBITOR (RIN). To clarify their role in fruit ripening, we generated FUL1/FUL2-suppressed transgenic lines by RNAi. We found that five transgenic lines bearing fruits that did not ripen normally: lycopene accumulation and increase of ethylene production were severely inhibited. We then performed next generation RNA sequencing (RNA-Seq) analysis of the fruits of a FUL1/FUL2-suppressed line (TF18) with those of the wild type (Ailsa Craig cultivar; AC) and rin mutant. The comparison of RNA-Seq data among them indicated that FUL1/FUL2-suppression significantly affected the expression of a larger portion of ripening-induced and -repressed genes than the rin mutation did. Moreover, the effect of FUL1/FUL2-suppression was observed not only in the fruits harvested at the wild type ripening age [45 days after pollination (DAP)] but also in those at the pre-ripening age (35 DAP). This suggests that the FUL homologs play an essential role in the regulation of fruit development and ripening, the role which covers a wider range of biological processes than RIN does. Differentially expressed genes (DEGs) between the wild type and TF18 fruits included known ripening-related genes such as ACS2 and ACS4 involved in ethylene production and PSY1 in carotenoid biosynthesis, consistent with the phenotype of TF18 fruits described above. The DEGs also included many direct RIN target genes, which supports the hypothesis that the FUL homologs regulate fruit ripening in a form of MADS-box complex with RIN.
2014-06-23 | GSE49289 | 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 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:Phenotypes of the tomato (Solanum lycopersicum L.) high pigment-2dg (hp-2dg) mutant are caused by a mutation in the gene encoding DEETIOLATED1, a negative regulator of light signaling. Homozygous hp-2dg plants display a plethora of distinctive developmental and metabolic phenotypes in comparison to their normal isogenic counterparts. This mutant is however best known for the increased levels of lycopene and other plastid-accumulating functional metabolites. In this study we analyzed the transcriptional alterations in mature-green, breaker and early-red fruits of hp-2dg/hp-2dg plants in relation to their normal counterparts using microarray technology. Results show that a large portion of the genes that are affected by hp-2dg mutation, display a tendency for up- rather than down-regulation. Ontology assignment of these differentially regulated transcripts, revealed a consistent upregulation of those related to chloroplast biogenesis and photosynthesis in hp-2dg mutants throughout fruit ripening. A tendency of upregulation was also observed in structural genes involved in phytonutrient biosynthesis. However, this upregulation was not as consistent, positioning plastid biogenesis as an important determinant of phytonutrient overproduction in hp-2dg mutant fruits. Microscopic observations revealed a highly significant increase in chloroplasts size and number in pericarp cells of mature-green hp-2dg/hp-2dg fruits in comparison to their normal counterparts. This increase could be observed from early stages of fruit development. Therefore, the molecular trigger that drives phytonutrient overproduction in hp-2dg mutant fruits should be initially traced at early stages of fruit development. Keywords: Comparative Transcriptional Profiling of tomato fruit pericarp tissue
2007-10-08 | GSE6041 | GEO
Project description:Tomato fruit ripening is under the control of ethylene as well as a group of ethylene-independent transcription factors, including NON-RIPENING (NOR) and RIPENING INHIBITOR (RIN). During ripening, the linear carotene lycopene accumulates at the expense of cyclic carotenoids. Fruit-specific overexpression of LYCOPENE β-CYCLASE (LCYb) under the control of the PHYTOENE DESATURASE (PDS) promoter resulted in increased levels of β-carotene and ABA and in decreased ethylene levels. Genes regulated by ABA, or involved in its synthesis and signaling, were overexpressed, while those associated with ethylene and cell wall remodeling were repressed. In agreement with the transcriptional data, LCYb-overexpressing fruits exhibited increased density of cell wall material containing linear, under-methylated pectins and displayed an array of additional ripening phenotypes, including delayed softening, increased turgor, enhanced shelf life and a thicker cuticle with a higher content of cutin monomers and triterpenoids. The levels of several primary metabolites and phenylpropanoids also changed in the transgenics, which could be attributed to delayed fruit ripening and to ABA respectively. Network correlation analysis suggests that ABA, acting through NOR and RIN, is responsible for many of the above phenotypes. These data reinforce suggestions that ABA plays an important role in tomato fruit ripening and provide clues that fruit b-carotene, acting as a precursor for ABA, actively participates in controlling the ripening process rather than merely being an output thereof. Overexpression of a LCYb gene from Arabidopsis under the control of the ripening-associated PDS promoter leads to ripe tomato fruits accumulating high β-carotene levels. Using several independent transgenic lines, we conducted a system-wide study of the effect of increased β-carotene levels on tomato fruit ripening and shelf life. Our data suggest that β-carotene, acting through ABA, is involved in a regulatory loop within the network controlling tomato fruit ripening.
2020-01-01 | GSE108415 | GEO
Project description:Purpose: To identify genes regulated by SlDOF1 during fruit ripening, we performed RNAseq experiments with three biological replicates and compared the transcriptom profiles of SlDOF1-RNAi and wild-type fruit at breaker stage. Methods: Expression profiles of wild-type (wt) and SlDof1-RNAi fruits (SlDof-8-RNAi) at 38 days after poliation (dpa) were generated by deep sequencing with three replicates using Illumina HiSeqTM 2000. RNA-seq reads obtained from the replicate were further filtered and aligned against the whole tomato genome. Differential expressed genes between samples were defined by DESeq software using two separate models, based on PPEE > 0.05 and false discovery rate (FDR)<0.001. Quantitative RT–PCR was performed using SYBR Green assays. Results: A total of 1728 differentially expressed genes were identified in the SlDof1 RNAi fruit compared with the wild type and among them were a number of ripening-relate genes.
2020-12-01 | GSE119493 | GEO
Project description:By using parallel analysis of RNA ends (PARE) for global identification of miRNA targets and comparing four different stages of tomato fruit development we identified a large number of target genes of miRNAs. PARE libraries were produced, one each, for tomato fruits at 5 days after pollination, mature green fruit, Breaker fruit, and 7 days after Breaker stge fruits
2013-04-05 | E-GEOD-42661 | biostudies-arrayexpress
Project description:[original title] Understanding the complexity of fruit ripening by transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes A tomato MADS-box transcription factor, LeMADS-RIN, controls fruit ripening and mutation in this gene results in non-ripening phenotype of fruit. This mutation down-regulates certain ripening related ethylene responses, however, other ethylene responses are normal. A complete understanding of this mutation and its effect on fruit transcriptome during ripening is not clear. In this study, microarray analysis has been used to investigate the influence of rin mutation on fruit transcriptome at different stages of ripening. A total of 2,398 genes were found to be differentially expressed in wild type fruit pericarp, which on cluster analysis indicated a major shift in their expression profiles in rin mutant fruit. A total of 1,802 genes were found to be differentially expressed between wild type and rin mutant fruits and 17% of these genes encoded regulatory elements, suggesting that mutation in LeMADS-RIN results in disturbance in the regulatory transcriptional networks during ripening. Since LeMADS-RIN has been reported to bind to the CArG box of LeACS2 promoter, in-silico analysis of 51 putative promoter sequences of the genes, that showed ripening associated up-regulation in wild type but showed impairment in up-regulation in rin mutant fruit during ripening, were searched for presence of CArG box along with ethylene and auxin responsive elements. The study revealed that only 24 putative promoter sequences harbor LeMADS-RIN specific CArG box suggesting an alternative mode of regulation by LeMADS-RIN for CArG box deficient genes. Three chronological stages of tomato (Solanum lycopersicon) fruit ripening were compared between wild type and rin mutant
2012-02-29 | E-GEOD-20720 | biostudies-arrayexpress