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RNA-Seq Transcriptome Analysis in Date Palm Suggests Multi-Dimensional Responses to Salinity Stress

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Abstract

The ability of date palm tree to survive under adverse abiotic conditions renders it as a valuable genomic resource for identifying tolerance genes. While mechanisms for salt tolerance have been heavily investigated in model as well as in some agronomic crops, no such studies have been undertaken in date palm. The aim of this study is to identify stress tolerance-related genes through transcriptomic analysis to support further functional studies. Young roots of Deglet Beida cultivar have been subjected to salt stress treatment, and used for RNA-Seq expression profiling and transmission electron microscopy (TEM) analysis. A total of 1939 genes are found to be differentially expressed between mock-treated roots and salt-stressed roots using log2FC ≥15≤−15. Many of these regulatory genes belong to DNA/RNA, protein, membrane, and signaling functional categories, suggesting that these genes play functional roles in tolerance to salt stress. Furthermore, RNA-Seq analysis has revealed activation of abscisic acid signaling pathways through SNF1-related protein kinases 2. Additionally, certain key genes involved in sodium uptake and transport are down-regulated, suggesting a potential mechanism for slowing down up-take and transport of salt solutes within plant tissues. TEM analysis has revealed that stressed roots exhibit plasmolysis in cortical cells of the distal region, while epidermal cells do not. Interestingly, root-tip regions of stressed roots do not exhibit plasmolysis, and this is likely due to higher solute contents present in these sink cells. These findings provide new information on multi-dimensional responses of date palm to salinity stress.

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Abbreviations

ABA:

Abscisic acid

DRE:

Dehydration-responsive element

FPKM:

Fragments per kilobase of transcript per million

qRT-PCR:

Quantitative reverse transcriptase PCR

RNA-Seq:

RNA sequencing

ROS:

Reactive oxygen species

SnRK:

SNF1-related protein kinase

LEA:

Late embryogenesis-abundant

SOS2:

Salt overly sensitive2

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Acknowledgments

Authors would like to thank Dr. Robert Krueger (USDA-ARS, National Clonal Germplasm Repository for Citrus and Dates, Riverside CA, USA) for providing date palm seeds. This research was made possible by two grants from the Qatar National Research Fund (QNRF) under National Priorities Research Program (NPRP09-705-4-025 and NPRP-5-1040-4-013). Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the QNRF. We thank Dr. Alvaro Hernandez (Roy J Carver Biotechnology Center/WM Keck Center, University of Illinois at Urbana-Champaign, IL, USA) for construction of libraries and for sequencing.

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Authors and Affiliations

  1. Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, 1201 Gregory Dr., 310 ERML, Urbana, IL, 61801, USA

    Osman Radwan, Jie Arro & Schuyler S. Korban

  2. Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Jie Arro

  3. Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Caroline Keller

  4. Department of Biology, University of Massachusetts Boston, Boston, MA, 02125, USA

    Schuyler S. Korban

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  1. Osman Radwan
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Correspondence to Osman Radwan.

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Communicated by: Ray Ming

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Supplementary Figure 1

Enriched pathways of genes that are highly expressed in response to salt stress. A. Suberin biosynthesis genes showed significant expression level changes, particularly in the phenyalanine biosynthesis step that is showed a >2x fold-change expression in the trans-cinname4.monoexygenase gene. B. Cell wall regeneration pathway, particularly genes involved in the initiating phosphorylation step, showed sustained transcriptional activity at 2 and 4 hpt. Gramene’s Pathway tools on MaizeCyc database was used for this analysis (PPTX 74 kb)

Supplementary Figure 2

GO molecular function terms for up- and down- regulated genes at 2 and 4 hpt under NaCl stress conditions. Hpt: hour post treatment (PPTX 351 kb)

Supplementary Table 1

List of genes used in quantitative RT-PCR (qRT-PCR) for RNA-Seq validation and their respective annotation, primers used and TM °C for each primer. For; forward primer and Rev; reverse primer (XLSX 10 kb)

Supplementary Table 2

Gene enrichment analysis (XLSX 9 kb)

Supplementary Table 3

Differentially expressed genes in response to salt stress treatment at 2 and 4 hpt. Hpt: hour post treatment. Green color refers to down-regulation, while red color refers to up-regulation. (XLSX 241 kb)

Supplementary Table 4

Up- regulated genes at 2 and 4 hpt. Hpt: hour post treatment. Green color refers to down-regulation, while red color refers to up-regulation. (XLSX 12 kb)

Supplementary Table 5

Up-regulated genes at 2 hpt. Green color refers to down-regulation, while red color refers to up-regulation. (XLSX 32 kb)

Supplementary Table 6

Down -regulated genes at 2 and 4 hpt. Hpt: hour post treatment. Green color refers to down-regulation, while red color refers to up-regulation. (XLSX 19 kb)

Supplementary Table 7

Down-regulated genes at 2 hpt. Hpt: hour post treatment. Green color (XLSX 207 kb)

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Radwan, O., Arro, J., Keller, C. et al. RNA-Seq Transcriptome Analysis in Date Palm Suggests Multi-Dimensional Responses to Salinity Stress. Tropical Plant Biol. 8, 74–86 (2015). https://doi.org/10.1007/s12042-015-9155-y

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