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Expression profiling of tomato pre-abscission pedicels

ABSTRACT: Organ abscission is a general activity found in plants and its regulation is an important agronomical concern because the trait directly affects the harvesting efficiency of fruits or grains and the yields. Generally, abscission takes place at a specialized cell layer, which is called abscission zones (AZs). So far, investigations on organ abscission have been focused mainly on the cell activities during organ detachment. By contrast, little attention has been paid to the properties of AZ cells at the pre-abscission stage. The pre-abscission cells are at a turning point for initiating abscission; until an abscission initiating signal is provided, the AZ cells keep their physiological state, while once the signal occurs, the cells immediately change their state into the onset of abscission. In this study, to screen the genes involved in the regulation of abscission at the pre-abscission state, we investigated the gene expression profiles of tomato flower pedicels at anthesis. The screening revealed many genes that characterize cell identities in each pedicel region.

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE39519 | GEO | 2012/07/20

SECONDARY ACCESSION(S): PRJNA171014

REPOSITORIES: GEO

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Expression profiling of tomato pre-abscission pedicels

Project description:Organ abscission is a general activity found in plants and its regulation is an important agronomical concern because the trait directly affects the harvesting efficiency of fruits or grains and the yields. Generally, abscission takes place at a specialized cell layer, which is called abscission zones (AZs). So far, investigations on organ abscission have been focused mainly on the cell activities during organ detachment. By contrast, little attention has been paid to the properties of AZ cells at the pre-abscission stage. The pre-abscission cells are at a turning point for initiating abscission; until an abscission initiating signal is provided, the AZ cells keep their physiological state, while once the signal occurs, the cells immediately change their state into the onset of abscission. In this study, to screen the genes involved in the regulation of abscission at the pre-abscission state, we investigated the gene expression profiles of tomato flower pedicels at anthesis. The screening revealed many genes that characterize cell identities in each pedicel region. We harvested tomato flower pedicels at the anthesis stage and divided them into three parts: the abscission zone (AZ) and the flanking proximal- (Prox) and distal- (Dis) regions. RNA was isolated and subjected to DNA microarray analyses. Experiments were performed three times with independently prepared samples.

2012-07-19 | E-GEOD-39519 | biostudies-arrayexpress

Global gene expression analysis in the pedicel abscission zone of tomato flowers by DNA microarray

2010-07-03 | GSE22682 | GEO

Global gene expression analysis in the pedicel abscission zone of tomato flowers by DNA microarray

Project description:In tomato, the mutants that lack the abscission zone (AZ) within pedicels are called a ‘jointless’ and are agronomically significant in that they increase the tomato fruit yield for industrial processing. We have employed DNA microarray expression analysis to identify genes with the potential to play a role in development of the pedicel abscission zone of tomato, and identified several classes of differentially regulated genes between pedicels of the AZ-forming line (wild-type) and pedicels of the non AZ-forming lines (jointless mutant and MC-suppressed transformant). Tomato flower pedicels were harvested at anthesis stage from the AZ-forming line (wild-type) and the non AZ-forming lines (jointless mutant and MC-suppressed transformant), and subjected to DNA microarray analyses. Experiments were performed twice with independently prepared samples.

2010-07-03 | E-GEOD-22682 | biostudies-arrayexpress

Transcriptome Analysis using customized AZ microarray on Flower pedicel Abscission and non abscission zones in Tomato (Solanum lycopersicum c.v New Yorker) Plants.

Project description:To extend our previous knowledge from our gene expression studies on Flower pedicel Abscission zone using Affymetrix microarray chip we have employed whole transcriptome analysis by NGS as a discovery platform to identify and add the transcripts to pre-existing database. We designed the Customized AZ Microarray chip with the transcripts obtained from NGS (includes novel transcripts), pre existing Agilent probes, and some additional transcripts from previous databases. The flower pedicel AZ tissue and non abscission(NAZ) pedicel tissues was sampled at six time points (0, 4, 8, 12, 16 and 20 h), following flower removal, and analyzed for their gene expression profiles using the customized AZ microarray.

2017-01-19 | GSE64221 | GEO

Transcriptome analysis using customized AZ microarray on tomato Flower Abscission zone of transgeneic line TAPG::antisense TPRPgene

Project description:To extend our previous knowledge from our gene expression studies on Flower pedicel Abscission zone using Affymetrix microarray chip we have employed whole transcriptome analysis by NGS as a discovery platform to identify and add the transcripts to pre-existing database. We designed the Customized AZ Microarray chip with the transcripts obtained from NGS (includes novel transcripts), pre existing Agilent probes, and some additional transcripts from previous databases. we developed transgenic lines by antisense silenciencing the genes, which are expressed in the AZ to study the functional role in abscission process. In the current stuty we silenced TPRP gene by antisense technology under abscisson promoter (TAPG::antsisense TPRP). The flower pedicel AZ tissue tissue was sampled at six time points (0, 4, 8, 12, 16 and 20 h), following flower removal, and analyzed for their gene expression profiles using the customized AZ microarray.

2018-01-01 | GSE64606 | GEO

Transcriptome analysis using customized AZ microarray on tomato Flower Abscission zone of transgeneic line TAPG::antisense KD gene

Project description:To extend our previous knowledge from our gene expression studies on Flower pedicel Abscission zone using Affymetrix microarray chip we have employed whole transcriptome analysis by NGS as a discovery platform to identify and add the transcripts to pre-existing database. We designed the Customized AZ Microarray chip with the transcripts obtained from NGS (includes novel transcripts), pre existing Agilent probes, and some additional transcripts from previous databases. We developed transgenic lines by antisense silencing the genes, which are expressed in the AZ to study the functional role in abscission process. In the current stuty we silenced KD gene by antisense technology under abscisson promoter (TAPG::antsisense KD). The flower pedicel AZ tissue tissue was sampled at six time points (0, 4, 8, 12, 16 and 20 h), following flower removal, and analyzed for their gene expression profiles using the customized AZ microarray.

2018-01-01 | GSE64564 | GEO

Early fruit abscission is associated with the IAA14/SLR-ARF7 signaling cascade in pedicels of self-abscising apple

Project description:The self-abscising characteristic of fruit is a prominent trait for labor-saving cultivation in apple (Malus × domestica). Up to 30 days after full bloom, early abscission leaves only central fruit in a cluster, while four lateral fruits are abscised. Since fruit abscission is possibly induced during earlier phases of fruit development, samples were collected at full bloom and 10 days after full bloom. Comparative analysis between central and lateral pedicels in self-abscising apple can be used to identify the genes that trigger the abscission mechanism, as the destinies of the pedicels in a cluster are obvious. Transcriptome analysis was performed using RNA-Seq to compare expression profiles between the surviving central pedicel to be survived and abscised lateral pedicel to be abscised from self-abscising apple. A total of 797,647 ESTs were assembled into 65,876 contigs which were annotated and analyzed with using Blast2GO. A total of 1,585 differentially expressed genes in central and lateral pedicels were identified using the NOISeq software. , and these genes were were characterized using the MapMan ontology software. Transcription factors involved in vascular bundle differentiation functioned in the central pedicel, while the signaling cascade of IAA14/SLR-ARF7, which progressed during lateral root emergence from primary roots, operated in lateral pedicels. Future studies should explore associations between the mechanisms of lateral root emergence and pedicel abscission during early phases of fruit development, as well as the interconnection among hormones.

2017-08-05 | GSE60091 | GEO

Oil Palm Fruit Abscission Zone Transcriptome

Project description:To determine the mechanisms of fleshy fruit abscission of the monocot oil palm (Elaeis guineensis Jacq.) compared with other abscission systems, we performed multi-scale comparative transcriptome analyses on fruit targeting the developing primary AZ and adjacent tissues. Combining between-tissue developmental comparisons with exogenous ethylene treatments, and naturally occurring abscission in the field, RNAseq analysis revealed a robust core set of 168 genes with differentially regulated expression, spatially associated with the ripe fruit AZ, and temporally restricted to the abscission timing. The expression of a set of candidate genes was validated by qRT-PCR in the fruit AZ of a natural oil palm variant with blocked fruit abscission, which provides evidence for their functions during abscission. Our results substantiate the conservation of gene function between dicot dry fruit dehiscence and monocot fleshy fruit abscission. The study also revealed major metabolic transitions occur in the AZ during abscission, including key senescence marker genes and transcriptional regulators, in addition to genes involved in nutrient recycling and reallocation, alternative routes for energy supply and adaptation to oxidative stress. The study provides the first reference transcriptome of a monocot fleshy fruit abscission zone and provides insight into the mechanisms underlying abscission by identifying key genes with functional roles and processes, including metabolic transitions, cell wall modifications, signalling, stress adaptations and transcriptional regulation, that occur during ripe fruit abscission of the monocot oil palm. The transcriptome data comprises an original reference and resource useful towards understanding the evolutionary basis of this fundamental plant process.

2021-02-08 | GSE166314 | GEO

NGS and Transcriptome Analyses using AZ customized microarray on Flower Abscission zone in Tomato (Solanum lycopersicum) Plants

Project description:To extend our previous knowledge from our gene expression studies on Flower Abscission zone using Affymetrix microarray chip we have employed whole transcriptome analysis by NGS as a discovery platform to identify and add the transcripts to pre-existing database. We designed the Customized AZ Microarray chip with the transcripts obtained from NGS (includes novel transcripts), pre existing Agilent probes, and some additional transcripts from previous databases. The flower AZ tissue was sampled at five time points (0, 2, 4, 8, and 14 h), following flower removal and analyzed for their gene expression profiles using the customized AZ microarray.

2017-01-19 | GSE45355 | GEO

Morphological and Genetic Characterization of Fruit Abscission Zone in Muscadine

Project description:Muscadines face limitations to fresh market production due to high manual labor costs. Mechanical harvesting holds promise for reducing the costs associated with muscadine production but requires cultivars with easily detached berries at maturity. This study aimed to determine muscadine fruit and pedicel characteristics influencing fruit detachment force and to unravel the genes, hormones, and regulatory networks governing muscadine abscission. We characterized the fruit detachment force of muscadine berries across eighteen genotypes and at four developmental stages. Following this, we performed a transcriptome analysis using the mature pedicel tissue of two genotypes, a genotype with high fruit detachment force at maturity and a genotype with low fruit detachment force at maturity, to identify differentially expressed and uniquely expressed genes contributing to fruit detachment. We found that pedicel length, pedicel-fruit junction area, and fruit diameter were all positively correlated with fruit detachment force. This study also identifies novel candidate genes, transcription factor families, and pathways associated with muscadine fruit abscission. These findings provide valuable knowledge on the progression of fruit abscission and insights for reducing fruit detachment force, particularly in developing machine-harvestable muscadine cultivars and fostering sustainability and efficiency in muscadine production.

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