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  1. IGB
  2. IGBF-3041

Review splicing literature for salt stress effects

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    • Type: Task
    • Status: Closed (View Workflow)
    • Priority: Blocker
    • Resolution: Done
    • Affects Version/s: None
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      Description

      To understand the significance of our results, we need to learn the current state of knowledge in the field.

      For this task, we assemble and summarize original research articles published in the last two to three years that investigated how salt stress affects splicing patterns in plants.

      Also, when relevant, please make note of software packages used to analyze splicing and detect splicing pattern changes.

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            nfreese Nowlan Freese added a comment -

            Alternative splicing of the OsBWMK1 gene generates three transcript variants showing differential subcellular localizations

            Here, we show that alternative splicing of the OsBWMK1, a member of the rice MAPK family, generates three transcript variants, OsBWMK1L, OsBWMK1M, and OsBWMK1S. The OsBWMK1L transcript variant was highly and constitutively expressed in all rice tissues tested and its expression was not altered by various stress conditions, whereas OsBWMK1M and OsBWMK1S were normally expressed at low levels but were induced by various stresses.

            Show
            nfreese Nowlan Freese added a comment - Alternative splicing of the OsBWMK1 gene generates three transcript variants showing differential subcellular localizations Here, we show that alternative splicing of the OsBWMK1, a member of the rice MAPK family, generates three transcript variants, OsBWMK1L, OsBWMK1M, and OsBWMK1S. The OsBWMK1L transcript variant was highly and constitutively expressed in all rice tissues tested and its expression was not altered by various stress conditions, whereas OsBWMK1M and OsBWMK1S were normally expressed at low levels but were induced by various stresses.
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            nfreese Nowlan Freese added a comment - - edited

            Abiotic Stresses Cause Differential Regulation of Alternative Splice Forms of GATA Transcription Factor in Rice

            In this study, we present an overview of the GATA gene family in rice (OsGATA)

            Transcript abundance analysis in contrasting genotypes of rice-IR64 (salt sensitive) and Pokkali (salt tolerant), for individual GATA members indicated their differential expression in response to various abiotic stresses such as salinity, drought, and exogenous ABA. One of the members of subfamily VII-OsGATA23a, emerged as a multi-stress responsive transcription factor giving elevated expression levels in response to salinity and drought.

            Show
            nfreese Nowlan Freese added a comment - - edited Abiotic Stresses Cause Differential Regulation of Alternative Splice Forms of GATA Transcription Factor in Rice In this study, we present an overview of the GATA gene family in rice (OsGATA) Transcript abundance analysis in contrasting genotypes of rice-IR64 (salt sensitive) and Pokkali (salt tolerant), for individual GATA members indicated their differential expression in response to various abiotic stresses such as salinity, drought, and exogenous ABA. One of the members of subfamily VII-OsGATA23a, emerged as a multi-stress responsive transcription factor giving elevated expression levels in response to salinity and drought.
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            nfreese Nowlan Freese added a comment -

            Salt tolerance involved candidate genes in rice: an integrative meta-analysis approach

            Herein, a genome-wide meta-analysis, using microarray and RNA-seq data was conducted which resulted in the identification of differentially expressed genes (DEGs) under salinity stress at tolerant rice genotypes.

            Briefly, the young seedlings of FL478 (Salt tolerant) and IR29 (Salt sensitive) were treated with 150 mM NaCl and the root samples were collected 24 h after inception of the salt stress.

            A total of 3449 DEGs were detected in 46 meta-QTL positions, among which 1286, 86, 1729 and 348 DEGs were observed in root, shoot, seedling, and leaves tissues, respectively.

            23 potential candidate genes were detected in Saltol and hotspot-regions overlying original QTLs for both yield components and ion homeostasis traits; among which, there were many unreported salinity-responsive genes.

            Show
            nfreese Nowlan Freese added a comment - Salt tolerance involved candidate genes in rice: an integrative meta-analysis approach Herein, a genome-wide meta-analysis, using microarray and RNA-seq data was conducted which resulted in the identification of differentially expressed genes (DEGs) under salinity stress at tolerant rice genotypes. Briefly, the young seedlings of FL478 (Salt tolerant) and IR29 (Salt sensitive) were treated with 150 mM NaCl and the root samples were collected 24 h after inception of the salt stress. A total of 3449 DEGs were detected in 46 meta-QTL positions, among which 1286, 86, 1729 and 348 DEGs were observed in root, shoot, seedling, and leaves tissues, respectively. 23 potential candidate genes were detected in Saltol and hotspot-regions overlying original QTLs for both yield components and ion homeostasis traits; among which, there were many unreported salinity-responsive genes.
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            nfreese Nowlan Freese added a comment -

            I have created an endnote library (IGBF3041.enl) containing the above references and attached it to this ticket.

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            nfreese Nowlan Freese added a comment - I have created an endnote library (IGBF3041.enl) containing the above references and attached it to this ticket.
            Hide
            ann.loraine Ann Loraine added a comment - - edited

            Nowlan Freese notes: A google search for "rice" and "splicing" and "salt" yields only few results.

            Show
            ann.loraine Ann Loraine added a comment - - edited Nowlan Freese notes: A google search for "rice" and "splicing" and "salt" yields only few results.

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              • Assignee:
                nfreese Nowlan Freese
                Reporter:
                ann.loraine Ann Loraine
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