skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Genome-wide transcriptomic analysis of a desert willow, Salix psammophila, reveals the function of hub genes SpMDP1 and SpWRKY33 in drought tolerance

Abstract

Background: Drought is a major environmental constraint to plant growth, development and productivity. Compared with most willows that are generally susceptible to drought, the desert willow Salix psammophila has extraordinary adaptation to drought stress. However, its molecular basis of drought tolerance is still largely unknown.Results: During polyethylene glycol 6000 (PEG 6000)-simulated drought stress, we found that the osmotic adjustment substances were accumulated and the antioxidant enzyme activities were enhanced in S. psammophila roots. A total of 8172 differentially expressed genes were identified in roots of S. psammophila through RNA-Sequencing. Based on K-means clustering, their expression patterns were classified into nine clusters, which were enriched in several stress-related processes including transcriptional regulation, response to various stresses, cell death, etc. Moreover, 672 transcription factors from 45 gene families were differentially expressed under drought stress. Furthermore, a weighted gene co-expression network was constructed, and eight genes were identified as hub genes. We demonstrated the function of two hub genes, magnesium-dependent phosphatase 1 (SpMDP1) and SpWRKY33, through overexpression in Arabidopsis thaliana. Overexpression of the two hub genes enhanced the drought tolerance in transgenic plants, suggesting that the identification of candidate drought tolerance genes in this study was highly efficient and credible.Conclusions: Our study analyzedmore » the physiological and molecular responses to drought stress in S. psammophila, and these results contribute to dissect the mechanism of drought tolerance of S. psammophila and facilitate identification of critical genes involved in drought tolerance for willow breeding.« less

Authors:
 [1]; ORCiD logo [2];  [1];  [1];  [1];  [1];  [1];  [1]
  1. Chinese Academy of Forestry, Beijing (China)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Chinese Academy of Forestry, Beijing (China)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1557471
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
BMC Plant Biology
Additional Journal Information:
Journal Volume: 19; Journal Issue: 1; Journal ID: ISSN 1471-2229
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Jia, Huixia, Zhang, Jin, Li, Jianbo, Sun, Pei, Zhang, Yahong, Xin, Xuebing, Lu, Mengzhu, and Hu, Jianjun. Genome-wide transcriptomic analysis of a desert willow, Salix psammophila, reveals the function of hub genes SpMDP1 and SpWRKY33 in drought tolerance. United States: N. p., 2019. Web. doi:10.1186/s12870-019-1900-1.
Jia, Huixia, Zhang, Jin, Li, Jianbo, Sun, Pei, Zhang, Yahong, Xin, Xuebing, Lu, Mengzhu, & Hu, Jianjun. Genome-wide transcriptomic analysis of a desert willow, Salix psammophila, reveals the function of hub genes SpMDP1 and SpWRKY33 in drought tolerance. United States. https://doi.org/10.1186/s12870-019-1900-1
Jia, Huixia, Zhang, Jin, Li, Jianbo, Sun, Pei, Zhang, Yahong, Xin, Xuebing, Lu, Mengzhu, and Hu, Jianjun. Thu . "Genome-wide transcriptomic analysis of a desert willow, Salix psammophila, reveals the function of hub genes SpMDP1 and SpWRKY33 in drought tolerance". United States. https://doi.org/10.1186/s12870-019-1900-1. https://www.osti.gov/servlets/purl/1557471.
@article{osti_1557471,
title = {Genome-wide transcriptomic analysis of a desert willow, Salix psammophila, reveals the function of hub genes SpMDP1 and SpWRKY33 in drought tolerance},
author = {Jia, Huixia and Zhang, Jin and Li, Jianbo and Sun, Pei and Zhang, Yahong and Xin, Xuebing and Lu, Mengzhu and Hu, Jianjun},
abstractNote = {Background: Drought is a major environmental constraint to plant growth, development and productivity. Compared with most willows that are generally susceptible to drought, the desert willow Salix psammophila has extraordinary adaptation to drought stress. However, its molecular basis of drought tolerance is still largely unknown.Results: During polyethylene glycol 6000 (PEG 6000)-simulated drought stress, we found that the osmotic adjustment substances were accumulated and the antioxidant enzyme activities were enhanced in S. psammophila roots. A total of 8172 differentially expressed genes were identified in roots of S. psammophila through RNA-Sequencing. Based on K-means clustering, their expression patterns were classified into nine clusters, which were enriched in several stress-related processes including transcriptional regulation, response to various stresses, cell death, etc. Moreover, 672 transcription factors from 45 gene families were differentially expressed under drought stress. Furthermore, a weighted gene co-expression network was constructed, and eight genes were identified as hub genes. We demonstrated the function of two hub genes, magnesium-dependent phosphatase 1 (SpMDP1) and SpWRKY33, through overexpression in Arabidopsis thaliana. Overexpression of the two hub genes enhanced the drought tolerance in transgenic plants, suggesting that the identification of candidate drought tolerance genes in this study was highly efficient and credible.Conclusions: Our study analyzed the physiological and molecular responses to drought stress in S. psammophila, and these results contribute to dissect the mechanism of drought tolerance of S. psammophila and facilitate identification of critical genes involved in drought tolerance for willow breeding.},
doi = {10.1186/s12870-019-1900-1},
url = {https://www.osti.gov/biblio/1557471}, journal = {BMC Plant Biology},
issn = {1471-2229},
number = 1,
volume = 19,
place = {United States},
year = {2019},
month = {8}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 2 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
journal, May 2010


KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 2000


Magnesium-dependent Phosphatase-1 Is a Protein-Fructosamine-6-phosphatase Potentially Involved in Glycation Repair
journal, May 2006


Differential expression analysis for sequence count data
journal, October 2010


WGCNA: an R package for weighted correlation network analysis
journal, December 2008


Overexpression of OsERF48 causes regulation of OsCML16 , a calmodulin-like protein gene that enhances root growth and drought tolerance
journal, March 2017


Arabidopsis WRKY33 Is a Key Transcriptional Regulator of Hormonal and Metabolic Responses toward Botrytis cinerea Infection
journal, March 2012


Genome-wide transcriptional response of Populus euphratica to long-term drought stress
journal, October 2012


Rapid Estimates of Relative Water Content
journal, February 1974


Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle
journal, January 2007


Superoxide dismutase: Improved assays and an assay applicable to acrylamide gels
journal, November 1971


Proline accumulation in plants: a review
journal, April 2008


Genetic strategies for dissecting complex traits in biomass willows (Salix spp.)
journal, November 2013


Increasing drought under global warming in observations and models
journal, August 2012


A Cotton MYB Transcription Factor, GbMYB5, is Positively Involved in Plant Adaptive Response to Drought Stress
journal, February 2015


The Arabidopsis CLAVATA2 Gene Encodes a Receptor-like Protein Required for the Stability of the CLAVATA1 Receptor-like Kinase
journal, October 1999


Transcriptome dynamics of Arabidopsis during sequential biotic and abiotic stresses
journal, May 2016


Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana
journal, December 1998


Reactive oxygen species homeostasis and signalling during drought and salinity stresses
journal, April 2010


Colorimetric Method for Determination of Sugars and Related Substances
journal, March 1956


Genetic Improvement of Willow for Bioenergy and BiofuelsFree Access
journal, January 2011


Chrysanthemum CmHSFA4 gene positively regulates salt stress tolerance in transgenic chrysanthemum
journal, January 2018


Temperature as a potent driver of regional forest drought stress and tree mortality
journal, September 2012


Towards a better understanding of protein changes in common bean under drought: A case study of N-glycoproteins
journal, September 2017


Functional characterization of Arabidopsis NaCl-inducible WRKY25 and WRKY33 transcription factors in abiotic stresses
journal, October 2008


OsCML4 improves drought tolerance through scavenging of reactive oxygen species in rice
journal, January 2015


Rapid determination of free proline for water-stress studies
journal, August 1973


Arabidopsis Transcriptome Analysis under Drought, Cold, High-Salinity and ABA Treatment Conditions using a Tiling Array
journal, June 2008


Gene networks involved in drought stress response and tolerance
journal, November 2006


Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
journal, August 2005


Time-Series Transcriptomics Reveals That AGAMOUS-LIKE22 Affects Primary Metabolism and Developmental Processes in Drought-Stressed Arabidopsis
journal, February 2016


Drought stress and reactive oxygen species: production, scavenging and signaling
journal, March 2008


Genome-wide transcriptional and physiological responses to drought stress in leaves and roots of two willow genotypes
journal, October 2015


Genome-wide transcriptome analysis of two maize inbred lines under drought stress
journal, December 2009


Water Stress, Growth, and Osmotic Adjustment
journal, February 1976


QTL analyses of drought tolerance and growth for a Salix dasyclados × Salix viminalis hybrid in contrasting water regimes
journal, December 2004


Protein damage, repair and proteolysis
journal, February 2014


Understanding plant responses to drought — from genes to the whole plant
journal, January 2003


Expression of AtWRKY33 Encoding a Pathogen- or PAMP-Responsive WRKY Transcription Factor Is Regulated by a Composite DNA Motif Containing W Box Elements
journal, April 2007


Genome-scale transcriptome analysis of the desert poplar, Populus euphratica
journal, March 2011


Transcriptome analysis revealed the drought-responsive genes in Tibetan hulless barley
journal, May 2016


Catalase, Peroxidase, and Polyphenoloxidase Activities during Rice Leaf Senescence
journal, February 1976


Arabidopsis WRKY33 transcription factor is required for resistance to necrotrophic fungal pathogens
journal, November 2006


TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
journal, January 2013


The Arabidopsis CLAVATA2 Gene Encodes a Receptor-Like Protein Required for the Stability of the CLAVATA1 Receptor-Like Kinase
journal, October 1999


    Works referencing / citing this record:

    Colorimetric Method for Determination of Sugars and Related Substances
    journal, March 1956


    Transcriptome dynamics of Arabidopsis during sequential biotic and abiotic stresses
    journal, May 2016


    Genome-scale transcriptome analysis of the desert poplar, Populus euphratica
    journal, March 2011


    Rapid determination of free proline for water-stress studies
    journal, August 1973


    Gene networks involved in drought stress response and tolerance
    journal, November 2006


    Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research
    journal, August 2005


    Time-Series Transcriptomics Reveals That AGAMOUS-LIKE22 Affects Primary Metabolism and Developmental Processes in Drought-Stressed Arabidopsis
    journal, February 2016


    Magnesium-dependent Phosphatase-1 Is a Protein-Fructosamine-6-phosphatase Potentially Involved in Glycation Repair
    journal, May 2006


    Expression of AtWRKY33 Encoding a Pathogen- or PAMP-Responsive WRKY Transcription Factor Is Regulated by a Composite DNA Motif Containing W Box Elements
    journal, April 2007


    Towards a better understanding of protein changes in common bean under drought: A case study of N-glycoproteins
    journal, September 2017


    Arabidopsis WRKY33 transcription factor is required for resistance to necrotrophic fungal pathogens
    journal, November 2006


    A Cotton MYB Transcription Factor, GbMYB5, is Positively Involved in Plant Adaptive Response to Drought Stress
    journal, February 2015


    Catalase, Peroxidase, and Polyphenoloxidase Activities during Rice Leaf Senescence
    journal, February 1976


    Increasing drought under global warming in observations and models
    journal, August 2012


    Genetic Improvement of Willow for Bioenergy and BiofuelsFree Access
    journal, January 2011


    Chrysanthemum CmHSFA4 gene positively regulates salt stress tolerance in transgenic chrysanthemum
    journal, January 2018


    Genome-wide transcriptional response of Populus euphratica to long-term drought stress
    journal, October 2012


    Transcriptome analysis revealed the drought-responsive genes in Tibetan hulless barley
    journal, May 2016


    Drought stress and reactive oxygen species: production, scavenging and signaling
    journal, March 2008


    Protein damage, repair and proteolysis
    journal, February 2014


    OsCML4 improves drought tolerance through scavenging of reactive oxygen species in rice
    journal, January 2015


    Genome-wide transcriptional and physiological responses to drought stress in leaves and roots of two willow genotypes
    journal, October 2015


    Water Stress, Growth, and Osmotic Adjustment
    journal, February 1976


    Reactive oxygen species homeostasis and signalling during drought and salinity stresses
    journal, April 2010


    Superoxide dismutase: Improved assays and an assay applicable to acrylamide gels
    journal, November 1971


    Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle
    journal, January 2007


    Proline accumulation in plants: a review
    journal, April 2008


    Arabidopsis WRKY33 Is a Key Transcriptional Regulator of Hormonal and Metabolic Responses toward Botrytis cinerea Infection
    journal, March 2012


    QTL analyses of drought tolerance and growth for a Salix dasyclados × Salix viminalis hybrid in contrasting water regimes
    journal, December 2004


    Differential expression analysis for sequence count data
    journal, October 2010


    Genetic strategies for dissecting complex traits in biomass willows (Salix spp.)
    journal, November 2013


    Overexpression of OsERF48 causes regulation of OsCML16 , a calmodulin-like protein gene that enhances root growth and drought tolerance
    journal, March 2017


    WGCNA: an R package for weighted correlation network analysis
    journal, December 2008


    Genome-wide transcriptome analysis of two maize inbred lines under drought stress
    journal, December 2009


    KEGG: Kyoto Encyclopedia of Genes and Genomes
    journal, January 2000


    The Arabidopsis CLAVATA2 Gene Encodes a Receptor-like Protein Required for the Stability of the CLAVATA1 Receptor-like Kinase
    journal, October 1999


    Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    journal, May 2010


    Arabidopsis Transcriptome Analysis under Drought, Cold, High-Salinity and ABA Treatment Conditions using a Tiling Array
    journal, June 2008


    Rapid Estimates of Relative Water Content
    journal, February 1974


    Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana
    journal, December 1998


    Understanding plant responses to drought — from genes to the whole plant
    journal, January 2003


    Functional characterization of Arabidopsis NaCl-inducible WRKY25 and WRKY33 transcription factors in abiotic stresses
    journal, October 2008


    Temperature as a potent driver of regional forest drought stress and tree mortality
    journal, September 2012