E-GEOD-39894 - Comparative transcriptome analysis of responses to water deficit in Solanum lycopersicum and S. pimpinellifolium roots

Status
Released on 1 December 2013, last updated on 2 June 2014
Organism
S. lycopersicum, S. pimpinellifolium, Solanum lycopersicum, Solanum pimpinellifolium
Samples (46)
Array (1)
Protocols (7)
Description
Understanding the genetic basis of plants’ response to environmental stresses such as drought and salinity is vital for improving the future crop productivity and for deciphering the evolutionary mechanisms of adaptation and speciation. Here, we screened for genes and functional groups that are potentially involved in drought tolerance in tomato by comparing genome-wide transcriptome profiles of drought-sensitive S. lycopersicum and drought-tolerant S. pimpinellifolium populations under control and water deficit conditions. We also compared the transcriptome profiles from this study and a previous salt treatment study to investigate expression similarities and differences in gene expression patterns between water and salt stress responses, which are physiologically and biochemically similar. Stress-induced genes such as dehydration responsive element binding (DREB) protein, ABA-response element binding factor (AREB)-like protein, heat shock proteins, and chaperones were commonly up-regulated in S. lycopersicum and S. pimpinellifolium. Genes such as WRKY transcription factors and 1-aminocyclopropane-1-carboxylate (ACC) synthase exhibited striking differences in both the baseline expression under the control condition as well as expression changes in response to water deficit, suggesting that the two species have accumulated heritable differences in gene expression patterns. At the genome scale, there was a tendency that down-regulated genes in S. lycopersicum are more neutral or even up-regulated in S. pimpinellifolium, suggesting that S. pimpinellifolium may be able to maintain cellular activities during prolonged droughts. In comparison of water and salt stress responses, known stress-induced genes such as DREB protein, AREB-like protein, and nine-cis-epoxycarotenoid dioxygenase (NCED) were commonly up-regulated in response to these stresses. However, we also found fundamental differences between these stress responses in terms of genome-wide expression patterns, partly attributable to the difference in how these stresses were applied during the experiments. We compared Affymetrix microarray transcriptome profiles of root tissues from three natural populations each of S. lycopersicum and S. pimpinellifolium (3-4 individuals in each population as biological replicates under control (well-watered) and water deficit treatments.
Experiment type
transcription profiling by array 
Contacts
Takuya Nakazato <nakazato.takuya1@gmail.com>, Shirlean B Goodwin, Thomas R Sutter
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-39894.idf.txt
Sample and data relationshipE-GEOD-39894.sdrf.txt
Raw data (1)E-GEOD-39894.raw.1.zip
Processed data (1)E-GEOD-39894.processed.1.zip
Array designA-AFFY-87.adf.txt
Links