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| Status |
Public on Feb 21, 2018 |
| Title |
Expression data from leaflets of domesticated tomato and wild-related Solanum pennellii plants subjected to water stress |
| Platform organism |
Solanum lycopersicum |
| Sample organisms |
Solanum lycopersicum; Solanum pennellii |
| Experiment type |
Expression profiling by array
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| Summary |
Transcriptomics study which main goal is to elucidate the programme of gene expression triggered by water stress in leaflets of the drought-tolerant wild-related tomato Solanum pennellii (acc. PE47) compared with domesticated tomato (S. lycopersicum, cv. P73).
In this study we used S. lycopersicum (Sl) (cv. P73) and S. pennellii (Sp) (acc. PE47) species displaying remarkable divergences regarding drought tolerance, to investigate the physiological and molecular responses in leaves of plants grown without stress (control) and after four days of water withholding (water stress, WS), when plant water loss was significant but leaves did not show visual dehydration symptoms yet. Significant physiological differences between species were found, showing Sp leaves higher ability to avoid water loss. Leaf transcriptomic analysis showed important constitutive expression differences between Sp and Sl, including genes with unknown function. In relation to the genes specifically induced by drought in Sp, those linked to stomatal closure, cell wall and primary carbohydrate metabolism and, specially, nitrogen metabolism were identified. Thus, genes linked to NH4+ assimilation, GOGAT/GS cycle and the GDH- and GABA-shunt were specifically induced by water stress in leaves of Sp. Our results showed also the up-regulation in Sp of genes involved in JA biosynthesis pathway, which were induced in both conditions, whereas genes involved in ET biosynthesis were specifically induced under WS. Regarding ET signaling, ERF genes were up-regulated by WS in Sp, hinting at the importance of these transcriptional regulators in the drought response of Sp.
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| Overall design |
Domesticated tomato (cv. P73) and wild-related tomato S. pennellii (acc. PE47) plants were cultivated by pairs in pots with substrate. Eighteen pots with plants having 2-3 full-developed leaves for domesticated tomato, and 3-4 full-developed leaves for wild-related tomato were selected (18 P73 plants and 18 PE47 plants in total). Nine couples divided into three biological replicates were maintained in standard culture conditions (control) while the other nine, also divided into three biological replicates, were subjected to water stress treatment by withholding watering during four days (water stress, WS). RNA isolated from leaflets coming from three individual pooled plants (biological replicates) was used in hybridization to one chip, resulting in total 12 chips: three replicates of P73 control, three replicates of PE47 control, three replicates of P73 WS and three replicates of PE47 WS. The biotinilated cRNA was hybridized to GeneChip® Tomato Genome Array of Affymetrix interrogating 10209 sequences. The intensity value of each probe in the array were processed and normalized according to the Robust Multichip Average (RMA) method to obtain an individual intensity value for each probeset. First filtering, normalization and second filtering of probes yield a final list of 5050 sequences (working list). A statistical analysis based in multiple test corrections was performed using the FDR test on the working list. Genes with an FDR < 0.05 and a fold change (ratio value) of ≥ 2.0 when comparing genotypes in the same experimental condition were identified as differentially expressed genes. A final list of 535 genes was accomplished with the above conditions. The annotation of probe sets was obtained from Affymetrix and loaded in the Partek Genomics Suite software (Partek Incorporated, St. Louis, USA). For the functional study of DEGs MapMan software was used (http://mapman.gabipd.org). The Slyc_AFFY_SGN_BUILD2_070709 database was loaded and used for this functional analysis. The statistical analysis followed was of Willcoxon Rank Sum test with Benjamini-Hochberg correction.
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| Contributor(s) |
Albaladejo I, Egea I, Meco V, Sevilla A, Bolarin MC, Flores FB |
| Citation(s) |
29434236 |
| Submission date |
Mar 27, 2017 |
| Last update date |
Feb 21, 2018 |
| Contact name |
Francisco Borja Flores |
| E-mail(s) |
borjaflores@cebas.csic.es
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| Organization name |
CEBAS-CSIC
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| Department |
Stress Biology and Plant Pathology
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| Lab |
Abiotic Stress, Production and Quality
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| Street address |
P.O. Box 164
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| City |
Espinardo - Murcia |
| State/province |
Murcia |
| ZIP/Postal code |
30100 |
| Country |
Spain |
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| Platforms (1) |
| GPL4741 |
[Tomato] Affymetrix Tomato Genome Array |
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| Samples (12)
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| GSM2550523 |
Tomato (S. lycopersicum) cv. P73, control condition, rep. 1 |
| GSM2550524 |
Tomato (S. lycopersicum) cv. P73, control condition, rep. 2 |
| GSM2550525 |
Tomato (S. lycopersicum) cv. P73, control condition, rep. 3 |
| GSM2550526 |
Tomato (S. lycopersicum) cv. P73, water stress condition, rep. 1 |
| GSM2550527 |
Tomato (S. lycopersicum) cv. P73, water stress condition, rep. 2 |
| GSM2550528 |
Tomato (S. lycopersicum) cv. P73, water stress condition, rep. 3 |
| GSM2550529 |
S. pennellii acc. PE47, control condition, rep. 1 |
| GSM2550530 |
S. pennellii acc. PE47, control condition, rep. 2 |
| GSM2550531 |
S. pennellii acc. PE47, control condition, rep. 3 |
| GSM2550532 |
S. pennellii acc. PE47, water stress condition, rep. 1 |
| GSM2550533 |
S. pennellii acc. PE47, water stress condition, rep. 2 |
| GSM2550534 |
S. pennellii acc. PE47, water stress condition, rep. 3 |
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| Relations |
| BioProject |
PRJNA380579 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE97045_RAW.tar |
11.9 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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