Morphological and Genetic Characterization of Fruit Abscission Zone in Muscadine
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ABSTRACT:
PROVIDER: PRJNA1081429 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28124938_1.fastq.gz | Fastqsanger.gz | |||
| SRR28124938_2.fastq.gz | Fastqsanger.gz | |||
| SRR28124939_1.fastq.gz | Fastqsanger.gz | |||
| SRR28124939_2.fastq.gz | Fastqsanger.gz | |||
| SRR28124940_1.fastq.gz | Fastqsanger.gz |
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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.
2024-10-23 | GSE259406 | GEO
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
Project description:Abscission is a cell separation process that takes place in particular positions of the plant body named abscission zones. In citrus, maturing fruits are shed through the calix abscission zone, which is composed by 10-15 cell layers located at the boundary between the calyx button and the fruit rind. In order to gain further insight into the molecular mechanisms involved in citrus fruit abscission, we used laser microdissection combined with microarray analysis to compare the global expression profiles of calyx abscission zone cells and adjacent fruit rind cells (control cells) at 0, 12 and 24 hours after the activation of the process with ethylene. Thus, this study allowed identifying a set of abscission zone-specifically expressed genes potentially involved in citrus fruit abscission.
2017-02-08 | E-MTAB-4538 | biostudies-arrayexpress
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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).
2010-07-03 | GSE22682 | GEO
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
Project description:Transcription profiling of the ethylene-induced abscission process in laminar abscission zone cells and petiolar cortical cells of debladed mature citrus leaf explants. Samples taken at 24h after ethylene treatment (10 ul/l) were compared.
2009-10-31 | E-MEXP-2018 | biostudies-arrayexpress
Project description:Citrus greening or huanglongbing (HLB) disease is caused by Candidatus liberibacter asiaticus (CLas) and associated with an increase in pre-harvest fruit drop, for which the molecular mechanisms remain unknown. In order to understand the molecular basis of the HLB-associated fruit abscission, by means of RNA-Sequencing analysis (RNA-Seq), transcriptomes in citrus calyx abscission zones were analyzed and compared among fruit dropped (D) or retained (R) from healthy (h) or HLB-diseased (d) trees upon shaking the trees. Cluster analysis based on the transcript reads indicates that dropped fruit from HLB-diseased trees (Dd) have largest distances from all other groups. Differentially expressed genes (DEGs) were identified between Dd and Rd, Dh and Rh, Rd and Rh, Dd and Dh. Wilcoxon test of the whole dataset of DEGs revealed that consistently up-regulated genes in Dd versus Rd and Dd versus Dh are in the functional categories of “secondary metabolism, lipid metabolism and hormone-ethylene and –jasmonate”; while those down-regulated genes didn’t show clear pattern of regulation. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses indicated that the significant biological processes or pathways involved in HLB-related fruit abscission were those related to defense response, secondary metabolism and hormone signaling. Among them, “response to chitin” was the most significant (p= 9.95E-13) biological process, and “jasmonic acid biosynthesis” was the most significant (p= 4.6E-5) pathway. Genes related to synthesis and signaling of ethylene (ET) and jasmonate (JA) were consistently up-regulated, while abscisic acid, auxin, brassinosteroid, cytokinin, and gibberellin were generally down-regulated in Dd; but not in Dh. Consistent with the transcriptomic data, fruit ethylene production was detected in two third of the Dd fruit, but none of Rd, Dh or Rh fruit. And, in agreement with the hormone expression profiles, substantial numbers of downstream JA/ET-responsive defense related genes were up-regulated in Dd, but not in Dh. Thirty representative DEGs covering categories of hormone, secondary metabolism, and JA/ET responsive defense responses were verified by qRT-PCR. The results indicate that HLB-associated pre-harvest fruit abscission is mediated by JA/ET signaling, which has been known to be triggered by infection of necrotrophic pathogens.
2018-01-13 | GSE101381 | GEO
Project description:Transcription profiling of the ethylene-induced abscission process in laminar abscission zone enriched tissues and petiole of debladed mature citrus leaf explants. Samples taken at 0, 6, 12, 24 and 36h after ethylene treatment (10 ul/l) were compared.
2008-12-31 | E-MEXP-1428 | biostudies-arrayexpress
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