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Transcriptome dynamics of a desert poplar (Populus pruinosa) in response to continuous salinity stress

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Abstract

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Using RNA sequencing analysis, we identified 9,216 regulatory and salt-related genes with differential expression and temporal expression trends which provide a clear picture of transcriptomic dynamics in response to continuous salinity stress in a desert poplar, Populus pruinosa.

Abstract

Populus pruinosa Schrenk is native to the desert region of western China and extraordinarily well adapted to the local salt stress. Thus, it is an ideal model for studying plants’ adaptation to salt stress, but its transcriptomic responses have not been previously characterized. Thus, we analyzed time- courses of these responses via a series of sequencings. In total, we generated 157.4 million 100 bp paired-end clean reads and identified 9,216 differentially expressed genes (DEGs) between salt-stressed calli and controls. Gene ontology classification analysis revealed that salt stress-related categories––including ‘oxidation reduction’, ‘transcription factor activity’, ‘membrane’ and ‘ion channel activity’––were highly enriched among these DEGs. In addition, we grouped the 9,216 DEGs by their expression dynamics into four clusters, and the genes in each cluster showed enrichment for particular functional categories. We also found that most DEGs were activated within 24 h of the stress and their expression stabilized after 48 h. All these findings suggest that gene expression rapidly and coordinately changes during this species’ adaptation to salt stress. In addition, the identified DEGs provide critical genetic resources for further functional analyses and indications of potential transgenic modifications for developing salt-tolerant poplars.

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Abbreviations

DEG:

Differentially expressed gene

FPKM:

Number of fragments per kilobase of exon per million fragments mapped

FDR:

False discovery rate

RNA-Seq:

High throughput sequencing of cDNA libraries

cDNA:

Complementary DNA synthesized from RNA

CDS:

Coding DNA sequences

qRT-PCR:

Quantitative real-time polymerase chain reaction

GO:

Gene ontology

KEGG:

Kyoto encyclopedia of genes and genomes

Nr:

Non-redundant database

COG:

Cluster of orthologous groups databases

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Acknowledgments

Financial support was provided by the National High-Tech Research and Development Program of China (863 Program, No. 2013AA102605), the National Science Foundation of China (30972336, 31270652) and the Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin opening topic fund (BRZD1204). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. State Key Laboratory of Grassland Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou, 730000, Gansu, China

    Jian Zhang, Dechun Jiang, Wenchun Luo, Jing Lu, Tao Ma & Dongshi Wan

  2. Key Laboratory for Bio-resources and Eco-environment, College of Life Sciences, Sichuan University, Chengdu, 610064, Sichuan, China

    Bingbing Liu

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  1. Jian Zhang
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  2. Dechun Jiang
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Correspondence to Dongshi Wan.

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Communicated by Manoj Prasad.

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Zhang, J., Jiang, D., Liu, B. et al. Transcriptome dynamics of a desert poplar (Populus pruinosa) in response to continuous salinity stress. Plant Cell Rep 33, 1565–1579 (2014). https://doi.org/10.1007/s00299-014-1638-z

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