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Transcriptomic identification of candidate genes involved in sunflower responses to chilling and salt stresses based on cDNA microarray analysis.

Fernandez P, Di Rienzo J, Fernandez L, Hopp HE, Paniego N, Heinz RA - BMC Plant Biol. (2008)

Bottom Line: Microarray profiling of chilling and NaCl-treated sunflower leaves revealed dynamic changes in transcript abundance, including transcription factors, defense/stress related proteins, and effectors of homeostasis, all of which highlight the complexity of both stress responses.This study not only allowed the identification of common transcriptional changes to both stress conditions but also lead to the detection of stress-specific genes not previously reported in sunflower.This is the first organ-specific cDNA fluorescence microarray study addressing a simultaneous evaluation of concerted transcriptional changes in response to chilling and salinity stress in cultivated sunflower.

View Article: PubMed Central - HTML - PubMed

Affiliation: Instituto de Biotecnología, CICVyA, INTA Castelar, Las Cabañas y Los Reseros, (B1712WAA) Castelar, Provincia de Buenos Aires, Argentina. pfernandez@cnia.inta.gov.ar

ABSTRACT

Background: Considering that sunflower production is expanding to arid regions, tolerance to abiotic stresses as drought, low temperatures and salinity arises as one of the main constrains nowadays. Differential organ-specific sunflower ESTs (expressed sequence tags) were previously generated by a subtractive hybridization method that included a considerable number of putative abiotic stress associated sequences. The objective of this work is to analyze concerted gene expression profiles of organ-specific ESTs by fluorescence microarray assay, in response to high sodium chloride concentration and chilling treatments with the aim to identify and follow up candidate genes for early responses to abiotic stress in sunflower.

Results: Abiotic-related expressed genes were the target of this characterization through a gene expression analysis using an organ-specific cDNA fluorescence microarray approach in response to high salinity and low temperatures. The experiment included three independent replicates from leaf samples. We analyzed 317 unigenes previously isolated from differential organ-specific cDNA libraries from leaf, stem and flower at R1 and R4 developmental stage. A statistical analysis based on mean comparison by ANOVA and ordination by Principal Component Analysis allowed the detection of 80 candidate genes for either salinity and/or chilling stresses. Out of them, 50 genes were up or down regulated under both stresses, supporting common regulatory mechanisms and general responses to chilling and salinity. Interestingly 15 and 12 sequences were up regulated or down regulated specifically in one stress but not in the other, respectively. These genes are potentially involved in different regulatory mechanisms including transcription/translation/protein degradation/protein folding/ROS production or ROS-scavenging. Differential gene expression patterns were confirmed by qRT-PCR for 12.5% of the microarray candidate sequences.

Conclusion: Eighty genes isolated from organ-specific cDNA libraries were identified as candidate genes for sunflower early response to low temperatures and salinity. Microarray profiling of chilling and NaCl-treated sunflower leaves revealed dynamic changes in transcript abundance, including transcription factors, defense/stress related proteins, and effectors of homeostasis, all of which highlight the complexity of both stress responses. This study not only allowed the identification of common transcriptional changes to both stress conditions but also lead to the detection of stress-specific genes not previously reported in sunflower. This is the first organ-specific cDNA fluorescence microarray study addressing a simultaneous evaluation of concerted transcriptional changes in response to chilling and salinity stress in cultivated sunflower.

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Profile of gene expression by putative functional category. The number and direction of transcriptional changes of the 80 differential genes under cold and salinity stresses are presented by functional categories.
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Figure 5: Profile of gene expression by putative functional category. The number and direction of transcriptional changes of the 80 differential genes under cold and salinity stresses are presented by functional categories.

Mentions: The 80 sequences that showed changes in transcriptional levels in response to salt and cold conditions were classified by putative functionality according to best hits on sequence similarity analysis based on BLAST algorithms and GO terminology (see Additional file 1) [64]. Gene expression profile by clustering analysis using heatmap representation (see Additional file 3) allowed the detection of gene patterns among treatments (chilling, salinity and control) confirmed by individual gene transcription profiles (see Additional file 2). Out of the 80 candidate, 50 genes were either up or down regulated under both abiotic stresses, thus supporting common regulatory mechanisms and general responses to low temperature and salinity. Fifteen and 12 sequences were either up or down-regulated respectively in a stress-specific manner under chilling or salinity. Finally, 3 genes showed inverted pattern of expression (F171, T107, E502) [GenBank: BU671987] [GenBank: BU671799] [GenBank: BU671910] and 39 differential ESTs correspond to genes with unknown predicted function [64]. The number of genes that were either up or down regulated under salt or chilling stresses are showed in Figure 5 grouped by assigned molecular and/or processes function. Changes in transcriptional patterns in response to chilling and salinity stresses are discussed below according to their predicted functionality classes (see Additional file 1) based on the Gene Ontology [65]. Those accessions without GO-term association were included in a particular category by means of a manual procedure.


Transcriptomic identification of candidate genes involved in sunflower responses to chilling and salt stresses based on cDNA microarray analysis.

Fernandez P, Di Rienzo J, Fernandez L, Hopp HE, Paniego N, Heinz RA - BMC Plant Biol. (2008)

Profile of gene expression by putative functional category. The number and direction of transcriptional changes of the 80 differential genes under cold and salinity stresses are presented by functional categories.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2265713&req=5

Figure 5: Profile of gene expression by putative functional category. The number and direction of transcriptional changes of the 80 differential genes under cold and salinity stresses are presented by functional categories.
Mentions: The 80 sequences that showed changes in transcriptional levels in response to salt and cold conditions were classified by putative functionality according to best hits on sequence similarity analysis based on BLAST algorithms and GO terminology (see Additional file 1) [64]. Gene expression profile by clustering analysis using heatmap representation (see Additional file 3) allowed the detection of gene patterns among treatments (chilling, salinity and control) confirmed by individual gene transcription profiles (see Additional file 2). Out of the 80 candidate, 50 genes were either up or down regulated under both abiotic stresses, thus supporting common regulatory mechanisms and general responses to low temperature and salinity. Fifteen and 12 sequences were either up or down-regulated respectively in a stress-specific manner under chilling or salinity. Finally, 3 genes showed inverted pattern of expression (F171, T107, E502) [GenBank: BU671987] [GenBank: BU671799] [GenBank: BU671910] and 39 differential ESTs correspond to genes with unknown predicted function [64]. The number of genes that were either up or down regulated under salt or chilling stresses are showed in Figure 5 grouped by assigned molecular and/or processes function. Changes in transcriptional patterns in response to chilling and salinity stresses are discussed below according to their predicted functionality classes (see Additional file 1) based on the Gene Ontology [65]. Those accessions without GO-term association were included in a particular category by means of a manual procedure.

Bottom Line: Microarray profiling of chilling and NaCl-treated sunflower leaves revealed dynamic changes in transcript abundance, including transcription factors, defense/stress related proteins, and effectors of homeostasis, all of which highlight the complexity of both stress responses.This study not only allowed the identification of common transcriptional changes to both stress conditions but also lead to the detection of stress-specific genes not previously reported in sunflower.This is the first organ-specific cDNA fluorescence microarray study addressing a simultaneous evaluation of concerted transcriptional changes in response to chilling and salinity stress in cultivated sunflower.

View Article: PubMed Central - HTML - PubMed

Affiliation: Instituto de Biotecnología, CICVyA, INTA Castelar, Las Cabañas y Los Reseros, (B1712WAA) Castelar, Provincia de Buenos Aires, Argentina. pfernandez@cnia.inta.gov.ar

ABSTRACT

Background: Considering that sunflower production is expanding to arid regions, tolerance to abiotic stresses as drought, low temperatures and salinity arises as one of the main constrains nowadays. Differential organ-specific sunflower ESTs (expressed sequence tags) were previously generated by a subtractive hybridization method that included a considerable number of putative abiotic stress associated sequences. The objective of this work is to analyze concerted gene expression profiles of organ-specific ESTs by fluorescence microarray assay, in response to high sodium chloride concentration and chilling treatments with the aim to identify and follow up candidate genes for early responses to abiotic stress in sunflower.

Results: Abiotic-related expressed genes were the target of this characterization through a gene expression analysis using an organ-specific cDNA fluorescence microarray approach in response to high salinity and low temperatures. The experiment included three independent replicates from leaf samples. We analyzed 317 unigenes previously isolated from differential organ-specific cDNA libraries from leaf, stem and flower at R1 and R4 developmental stage. A statistical analysis based on mean comparison by ANOVA and ordination by Principal Component Analysis allowed the detection of 80 candidate genes for either salinity and/or chilling stresses. Out of them, 50 genes were up or down regulated under both stresses, supporting common regulatory mechanisms and general responses to chilling and salinity. Interestingly 15 and 12 sequences were up regulated or down regulated specifically in one stress but not in the other, respectively. These genes are potentially involved in different regulatory mechanisms including transcription/translation/protein degradation/protein folding/ROS production or ROS-scavenging. Differential gene expression patterns were confirmed by qRT-PCR for 12.5% of the microarray candidate sequences.

Conclusion: Eighty genes isolated from organ-specific cDNA libraries were identified as candidate genes for sunflower early response to low temperatures and salinity. Microarray profiling of chilling and NaCl-treated sunflower leaves revealed dynamic changes in transcript abundance, including transcription factors, defense/stress related proteins, and effectors of homeostasis, all of which highlight the complexity of both stress responses. This study not only allowed the identification of common transcriptional changes to both stress conditions but also lead to the detection of stress-specific genes not previously reported in sunflower. This is the first organ-specific cDNA fluorescence microarray study addressing a simultaneous evaluation of concerted transcriptional changes in response to chilling and salinity stress in cultivated sunflower.

Show MeSH
Related in: MedlinePlus