Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Olive (Olea europaea) cv.Kalamon: Control vs Salt-treated

ABSTRACT: A transcriptomics approach was used as a tool to unravel gene regulatory network underlying salinity response in a salt-tolerant olive cultivar (cv. Kalamon) by simulating as much as possible olive growing conditions in the field. A 135 day long salinity experiment was conducted using one year old trees exposed to NaCl stress for 90 days followed by 45 days of post-stress period. Total RNA was extracted from the root samples after 15, 45 and 90 days of NaCl-treated and un-treated olive trees as well as after 15 and 45 days of post-treatment period and used for microarray hybridizations using a loop design. Hierarchical clustering of differentially expressed transcripts revealed two major, distinct clusters. Despite the limited number of probe set, a transcriptional regulatory networks was constructed for the salt-tolerant cultivar. Five experimental time-points were analyzed: 15days stress, 45days stress, 90days stress, 15days post-stress and 45days post-stress. In each timepoint treated and untreated (control) samples were obtained. Dye swap hybridizations and 4 biological replicates were performed for each treatment/timepoint in a loop design experimental setup. Low-quality arrays were not included in the data analysis (36 arrays/samples submitted). Each sample included three spot replicates.

ORGANISM(S): Olea europaea

SUBMITTER: Maria Manioudaki

PROVIDER: E-GEOD-36196 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Comparative transcriptome analysis of two olive cultivars in response to NaCl-stress.

Bazakos Christos C Manioudaki Maria E ME Therios Ioannis I Voyiatzis Demetrios D Kafetzopoulos Dimitris D Awada Tala T Kalaitzis Panagiotis P

PloS one 20120830 8

<h4>Background</h4>Olive (Olea europaea L.) cultivation is rapidly expanding and low quality saline water is often used for irrigation. The molecular basis of salt tolerance in olive, though, has not yet been investigated at a system level. In this study a comparative transcriptomics approach was used as a tool to unravel gene regulatory networks underlying salinity response in olive trees by simulating as much as possible olive growing conditions in the field. Specifically, we investigated the ...[more]

PMID: 22952621

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Project description:Transcriptional variation, also called expression level polymorphism (ELP), contributes to intra-specific phenotypic variation in many organisms. Differentially expressed transcripts are typically enriched for stress-related genes, suggesting that differences in response to the environment are a particularly common point of divergence among gentoypes. Analysis of ELPs also has been suggested as a way to assess unintended consequences of transgene introduction; however, it is important that interpretation of transcriptional changes be performed within the context of potential fitness effects. In these studies we sought to examine differential gene expression in response to salinity for two widely used Arabidopsis thaliana ecotypes, Wassilewskija (Ws) and Columbia (Col), and a single gene mutation (glabrous, gl1-1) in the Col background (Col(gl)), in relation to genetic, phenotypic, and fitness differences. Growth analyses were performed with seedlings germinated on culture media and growth chamber-grown plants carried through the full life cycle. Transcriptome analyses were performed with salt treated and control growth-chamber grown plants six days post initiation of salt stress. Ws plants had the least salt injury and highest dry matter accumulation and seed production in salt stressed conditions. ELPs among genoytypes and in response to 100 mM NaCl were enriched for genes associated with response to stress, including stress-associated transcription factors, heat shock and redox metabolism genes, and R genes. Application of salt resulted in many more transcripts up- or down-regulated in Col and Ws than in Col(gl). Many of the transcripts influenced by salt in Col were already altered in gl1-1 plants in the absence of salt, although Col(gl) plants did not show any detectable signs of stress, or effects on fecundity in the absence of salt treatment. The majority of salt-induced transcriptional changes that occurred in Ws also occurred in Col, suggesting common salt stress responses in these two ecotypes. Many more genes were affected by salt in Col than Ws, however, possibly reflecting the greater salt injury observed for Col. There was minimal overlap between the transcripts that differed for Ws and Col prior to salt treatment and those that were subsequently affected by salt stress. Thus, many genes conferring comparative salt stress tolerance in Ws likely differ from those whose expression levels are modified in response to salt stress. These studies demonstrate transcriptional variation among Arabidopsis genotypes in response to salt stress. Greater transcriptome differences did not necessarily correspond with greater genetic difference or phenotypic differences in morphology, fecundity, and resistance to salt stress. These results suggest that depending on circumstance, transcriptional changes can reflect response to injury, facilitate adaptive expression of fitness-associated traits, or allow for phenotypic buffering to minimize the impact of genetic changes. Three Arabidopsis genotypes were grown in the growth chamber in the absence and presence of salt stress. Plants from 20 days after sowing (6 days after salt treatment) were used for RNA extraction and hybridization on Affymetrix microarrays. There were two biological replicates for each genotype and salt treatment combination.

Dataset Information

Olive (Olea europaea) cv.Kalamon: Control vs Salt-treated

Publications

Comparative transcriptome analysis of two olive cultivars in response to NaCl-stress.

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