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Browse CitrusPLEX Experiment Data

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Transcriptional Analysis of Rind Separation in Mandarin Oranges
Livia Tommasini, University of California, Riverside, Department of Botany and Plant Science, Riverside, California (liviat@ucr.edu)
Experiment design (16 hybridizations)
genetic line
•Clementine Nules •Lee X Nova
developmental stage name
•before rind separation •at rind separation •after rind separation

This experiment has been imported by PLEXdb from NCBI GEO (GSE15886)

Series_summary:
In mandarin (Citrus reticulata Blanco), rind sep...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Transcriptional Analysis of Rind Separation in Mandarin Oranges
Accession No: CT3
Microarray: Citrus
Visibility: public
Experiment Type:
Experiment Factor(s):
genetic line
•Clementine Nules   •Lee X Nova
developmental stage name
•before rind separation   •at rind separation   •after rind separation
Quality Control:
Treatment summary:
 genetic line  developmental stage name  # replicates
 Clementine Nules  before rind separation  3
 Clementine Nules  at rind separation  3
 Clementine Nules  after rind separation  1
 Lee X Nova  before rind separation  3
 Lee X Nova  at rind separation  3
 Lee X Nova  after rind separation  3
Total hybridizations: 16
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE15886)

Series_summary:
In mandarin (Citrus reticulata Blanco), rind separation is an essential trait for marketing, as it confers easy-peeling, an inheritable trait whose genetic basis has not yet been characterized. To this end, we used the 30 K Affymetrix Citrus GeneChip to compare gene expression in albedo tissues of an easy-peeling genotype (Clementine Nules) to a less easy-peeling hybrid genotype (Lee x Nova, USDA 88-2) at three time points: before, at and after the onset of rind separation. A high percent of genes were detected reliably by the chip (76.1 %), and Principal Component Analysis (PCA) based on these genes showed that three replicates were well clustered, indicating the reliability of the data set. Functional analysis of genes showing >5-fold difference in expression between Clementine Nules and Lee x Nova across three developmental points suggested that the transcriptome of the two varieties diverges as the maturation process advances. A pectin methylesterase was expressed at levels more than 100-fold higher in Clementine Nules than in Lee x Nova at all three time points and two genes encoding for pectinases were more than 10-fold higher in Clementine Nules than in Lee x Nova during the last sampling time. Different hydrolases, a glucanase and a carbohydrate kinase were higher in Nules than in Lee x Nova. Higher expression of two cellulose synthases, an expansin and an aquaporin was observed in the easy peel genotype Clementine Nules. The difference between Clementine Nules and Lee x Nova at the transcript level suggests that three main molecular mechanisms are involved in the easy peeling trait: 1) lower cell adhesion, 2) pronounced degradation of albedo cell wall polysaccharides, and 3) high and extended cell expansion rate of the rind.

Series_overall_design:
We used the 30 K Affymetrix Citrus GeneChip to compare gene expression in albedo tissues of an easy-peeling genotype (Clementine Nules) to a less easy-peeling hybrid genotype (Lee x Nova, USDA 88-2) at three time points (16 arrays): before, at and after the onset of rind separation.
Publication: none
Created: 2011-05-23 15:50:43
Last Update: 2011-05-24 10:33:47
Released: 2011-05-24
GEO Accession GSE15886
Submitter: PLEXdb Curator
Name: Livia Tommasini
Institution: University of California, Riverside, Department of Botany and Plant Science, Riverside, California
Head of Laboratory: Timothy J Close
email(s):
Homepage:

 
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