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The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE.

Molina C, Zaman-Allah M, Khan F, Fatnassi N, Horres R, Rotter B, Steinhauer D, Amenc L, Drevon JJ, Winter P, Kahl G - BMC Plant Biol. (2011)

Bottom Line: From several filtered pathways, here we focus exemplarily on transcripts associated with the generation and scavenging of reactive oxygen species (ROS), as well as on transcripts involved in Na+ homeostasis.Newly identified transcript isoforms are potential targets for breeding novel cultivars with high salinity tolerance.We demonstrate that these targets can be integrated into breeding schemes by micro-arrays and RT-PCR assays downstream of the generation of 26 bp tags by SuperSAGE.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular BioSciences, Biocenter, Johann Wolfgang Goethe University, Max-von-Laue-Str, 9, D-60439 Frankfurt am Main, Germany. carlos.molina@dijon.inra.fr

ABSTRACT

Background: The combination of high-throughput transcript profiling and next-generation sequencing technologies is a prerequisite for genome-wide comprehensive transcriptome analysis. Our recent innovation of deepSuperSAGE is based on an advanced SuperSAGE protocol and its combination with massively parallel pyrosequencing on Roche's 454 sequencing platform. As a demonstration of the power of this combination, we have chosen the salt stress transcriptomes of roots and nodules of the third most important legume crop chickpea (Cicer arietinum L.). While our report is more technology-oriented, it nevertheless addresses a major world-wide problem for crops generally: high salinity. Together with low temperatures and water stress, high salinity is responsible for crop losses of millions of tons of various legume (and other) crops. Continuously deteriorating environmental conditions will combine with salinity stress to further compromise crop yields. As a good example for such stress-exposed crop plants, we started to characterize salt stress responses of chickpeas on the transcriptome level.

Results: We used deepSuperSAGE to detect early global transcriptome changes in salt-stressed chickpea. The salt stress responses of 86,919 transcripts representing 17,918 unique 26 bp deepSuperSAGE tags (UniTags) from roots of the salt-tolerant variety INRAT-93 two hours after treatment with 25 mM NaCl were characterized. Additionally, the expression of 57,281 transcripts representing 13,115 UniTags was monitored in nodules of the same plants. From a total of 144,200 analyzed 26 bp tags in roots and nodules together, 21,401 unique transcripts were identified. Of these, only 363 and 106 specific transcripts, respectively, were commonly up- or down-regulated (>3.0-fold) under salt stress in both organs, witnessing a differential organ-specific response to stress.Profiting from recent pioneer works on massive cDNA sequencing in chickpea, more than 9,400 UniTags were able to be linked to UniProt entries. Additionally, gene ontology (GO) categories over-representation analysis enabled to filter out enriched biological processes among the differentially expressed UniTags. Subsequently, the gathered information was further cross-checked with stress-related pathways. From several filtered pathways, here we focus exemplarily on transcripts associated with the generation and scavenging of reactive oxygen species (ROS), as well as on transcripts involved in Na+ homeostasis. Although both processes are already very well characterized in other plants, the information generated in the present work is of high value. Information on expression profiles and sequence similarity for several hundreds of transcripts of potential interest is now available.

Conclusions: This report demonstrates, that the combination of the high-throughput transcriptome profiling technology SuperSAGE with one of the next-generation sequencing platforms allows deep insights into the first molecular reactions of a plant exposed to salinity. Cross validation with recent reports enriched the information about the salt stress dynamics of more than 9,000 chickpea ESTs, and enlarged their pool of alternative transcripts isoforms. As an example for the high resolution of the employed technology that we coin deepSuperSAGE, we demonstrate that ROS-scavenging and -generating pathways undergo strong global transcriptome changes in chickpea roots and nodules already 2 hours after onset of moderate salt stress (25 mM NaCl). Additionally, a set of more than 15 candidate transcripts are proposed to be potential components of the salt overly sensitive (SOS) pathway in chickpea. Newly identified transcript isoforms are potential targets for breeding novel cultivars with high salinity tolerance. We demonstrate that these targets can be integrated into breeding schemes by micro-arrays and RT-PCR assays downstream of the generation of 26 bp tags by SuperSAGE.

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In situ localization of ascorbate peroxidase APX transcript isoforms in chickpea root nodules. In situ localization of APX1 (upper panel) and APX2 (lower panel, bar: 500 μm). Corresponding cDNAs were derived from RACE amplifications using UniTags as starting sequences. A) Control without reverse transcription B) Nodules from non-stressed plants C) Nodules from plants after a 2 h exposure to 25 mM NaCl Abbreviations: see figure 6
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Figure 7: In situ localization of ascorbate peroxidase APX transcript isoforms in chickpea root nodules. In situ localization of APX1 (upper panel) and APX2 (lower panel, bar: 500 μm). Corresponding cDNAs were derived from RACE amplifications using UniTags as starting sequences. A) Control without reverse transcription B) Nodules from non-stressed plants C) Nodules from plants after a 2 h exposure to 25 mM NaCl Abbreviations: see figure 6

Mentions: Transcripts from the ascorbate peroxydase 1 (APX1) gene were detected mostly in the inner cortex and less in the outer cortex of control nodules (non-exposed to salinity) (Figure 6). Two hours after exposure to 25 mM NaCl, the transcripts accumulated to high levels in the outer cortex (Figure 7). Note, that the negative controls did not show any fluorescent signal. In contrast, only few transcripts from the APX2 gene appear in control root nodules, whereas the number of transcripts highly increased both in the inner and the outer cortex after exposure to salinity (Figure 7).


The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE.

Molina C, Zaman-Allah M, Khan F, Fatnassi N, Horres R, Rotter B, Steinhauer D, Amenc L, Drevon JJ, Winter P, Kahl G - BMC Plant Biol. (2011)

In situ localization of ascorbate peroxidase APX transcript isoforms in chickpea root nodules. In situ localization of APX1 (upper panel) and APX2 (lower panel, bar: 500 μm). Corresponding cDNAs were derived from RACE amplifications using UniTags as starting sequences. A) Control without reverse transcription B) Nodules from non-stressed plants C) Nodules from plants after a 2 h exposure to 25 mM NaCl Abbreviations: see figure 6
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3045889&req=5

Figure 7: In situ localization of ascorbate peroxidase APX transcript isoforms in chickpea root nodules. In situ localization of APX1 (upper panel) and APX2 (lower panel, bar: 500 μm). Corresponding cDNAs were derived from RACE amplifications using UniTags as starting sequences. A) Control without reverse transcription B) Nodules from non-stressed plants C) Nodules from plants after a 2 h exposure to 25 mM NaCl Abbreviations: see figure 6
Mentions: Transcripts from the ascorbate peroxydase 1 (APX1) gene were detected mostly in the inner cortex and less in the outer cortex of control nodules (non-exposed to salinity) (Figure 6). Two hours after exposure to 25 mM NaCl, the transcripts accumulated to high levels in the outer cortex (Figure 7). Note, that the negative controls did not show any fluorescent signal. In contrast, only few transcripts from the APX2 gene appear in control root nodules, whereas the number of transcripts highly increased both in the inner and the outer cortex after exposure to salinity (Figure 7).

Bottom Line: From several filtered pathways, here we focus exemplarily on transcripts associated with the generation and scavenging of reactive oxygen species (ROS), as well as on transcripts involved in Na+ homeostasis.Newly identified transcript isoforms are potential targets for breeding novel cultivars with high salinity tolerance.We demonstrate that these targets can be integrated into breeding schemes by micro-arrays and RT-PCR assays downstream of the generation of 26 bp tags by SuperSAGE.

View Article: PubMed Central - HTML - PubMed

Affiliation: Molecular BioSciences, Biocenter, Johann Wolfgang Goethe University, Max-von-Laue-Str, 9, D-60439 Frankfurt am Main, Germany. carlos.molina@dijon.inra.fr

ABSTRACT

Background: The combination of high-throughput transcript profiling and next-generation sequencing technologies is a prerequisite for genome-wide comprehensive transcriptome analysis. Our recent innovation of deepSuperSAGE is based on an advanced SuperSAGE protocol and its combination with massively parallel pyrosequencing on Roche's 454 sequencing platform. As a demonstration of the power of this combination, we have chosen the salt stress transcriptomes of roots and nodules of the third most important legume crop chickpea (Cicer arietinum L.). While our report is more technology-oriented, it nevertheless addresses a major world-wide problem for crops generally: high salinity. Together with low temperatures and water stress, high salinity is responsible for crop losses of millions of tons of various legume (and other) crops. Continuously deteriorating environmental conditions will combine with salinity stress to further compromise crop yields. As a good example for such stress-exposed crop plants, we started to characterize salt stress responses of chickpeas on the transcriptome level.

Results: We used deepSuperSAGE to detect early global transcriptome changes in salt-stressed chickpea. The salt stress responses of 86,919 transcripts representing 17,918 unique 26 bp deepSuperSAGE tags (UniTags) from roots of the salt-tolerant variety INRAT-93 two hours after treatment with 25 mM NaCl were characterized. Additionally, the expression of 57,281 transcripts representing 13,115 UniTags was monitored in nodules of the same plants. From a total of 144,200 analyzed 26 bp tags in roots and nodules together, 21,401 unique transcripts were identified. Of these, only 363 and 106 specific transcripts, respectively, were commonly up- or down-regulated (>3.0-fold) under salt stress in both organs, witnessing a differential organ-specific response to stress.Profiting from recent pioneer works on massive cDNA sequencing in chickpea, more than 9,400 UniTags were able to be linked to UniProt entries. Additionally, gene ontology (GO) categories over-representation analysis enabled to filter out enriched biological processes among the differentially expressed UniTags. Subsequently, the gathered information was further cross-checked with stress-related pathways. From several filtered pathways, here we focus exemplarily on transcripts associated with the generation and scavenging of reactive oxygen species (ROS), as well as on transcripts involved in Na+ homeostasis. Although both processes are already very well characterized in other plants, the information generated in the present work is of high value. Information on expression profiles and sequence similarity for several hundreds of transcripts of potential interest is now available.

Conclusions: This report demonstrates, that the combination of the high-throughput transcriptome profiling technology SuperSAGE with one of the next-generation sequencing platforms allows deep insights into the first molecular reactions of a plant exposed to salinity. Cross validation with recent reports enriched the information about the salt stress dynamics of more than 9,000 chickpea ESTs, and enlarged their pool of alternative transcripts isoforms. As an example for the high resolution of the employed technology that we coin deepSuperSAGE, we demonstrate that ROS-scavenging and -generating pathways undergo strong global transcriptome changes in chickpea roots and nodules already 2 hours after onset of moderate salt stress (25 mM NaCl). Additionally, a set of more than 15 candidate transcripts are proposed to be potential components of the salt overly sensitive (SOS) pathway in chickpea. Newly identified transcript isoforms are potential targets for breeding novel cultivars with high salinity tolerance. We demonstrate that these targets can be integrated into breeding schemes by micro-arrays and RT-PCR assays downstream of the generation of 26 bp tags by SuperSAGE.

Show MeSH
Related in: MedlinePlus