Functional & Integrative Genomics

, Volume 18, Issue 2, pp 155–173 | Cite as

Effect of salt-stress on gene expression in citrus roots revealed by RNA-seq

  • Rangjin XieEmail author
  • Xiaoting Pan
  • Jing Zhang
  • Yanyan Ma
  • Shaolan He
  • Yongqiang Zheng
  • Yingtao Ma
Original Article


Citrus, as one of the most economically important fruits worldwide, is adversely affected by salinity stress. However, its molecular mechanisms underlying salinity tolerance are still not clear. In this study, next-generation RNA-seq technology was applied to analyze the gene expression profiling of citrus roots at 3 time points over a 24-h period of salt treatment. A total of 1831 differentially expressed genes (DEGs) were identified. Among them, 1195 and 1090 DEGs were found at 4 and 24 h, of which 454 were overlapped. Based on functional annotation, the salt overly sensitive (SOS) and reactive oxygen species (ROS) signaling pathways were found to be involved. Meanwhile, we found that hormone metabolism and signaling played important roles in salt stress. In addition, a multitude of transcription factors (TFs) including WRKY, NAC, MYB, AP2/ERF, bZIP, GATA, bHLH, ZFP, SPL, CBF, and CAMTA were identified. The genes related to cell wall loosening and stiffening (xyloglucan endotransglucosylase/hydrolases, peroxidases) were also involved in salt stress. Our data not only provided a genetic resource for discovering salt tolerance-related genes, but also furthered our understanding of the molecular mechanisms underlying salt tolerance in citrus.


Salinity Citrus root RNA-seq Transcription factor Differentially expressed genes 



This study was financed by the Fundamental Research Funds for the Central Universities (XDJK2016B022), National Nature Science Foundation of NSFC (31301743), National Science-technology Support Plan Projects (2014BAD16B02), and Key Scientific Research Project of Henan Higher Education (16A210011).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no competing interests.

Supplementary material

10142_2017_582_MOESM1_ESM.jpg (200 kb)
Fig. S1 Venn diagrams representing the numbers of transcripts and the overlaps of sets obtained across three comparisons S_0h, S_4 h and S_24 h indicate the libraries from the samples at 0 h, 4 h and 24 h under salt treatment, respectively (JPEG 200 kb)
10142_2017_582_MOESM2_ESM.jpg (81 kb)
Fig. S2 Venn diagrams representing the numbers of DEGs and the overlaps of sets obtained across two comparisons S_0h was used as calibrators to normalize the DEGs in other two salt-stressed libraries S_0h, S_4 h and S_24 h indicate the libraries from the samples at 0 h, 4 h and 24 h under salt treatment, respectively (JPEG 80 kb)
10142_2017_582_MOESM3_ESM.docx (29 kb)
Table S1 (DOCX 28 kb)
10142_2017_582_MOESM4_ESM.xlsx (14 kb)
Table S2 (XLSX 14 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2017

Authors and Affiliations

  • Rangjin Xie
    • 1
    Email author
  • Xiaoting Pan
    • 1
  • Jing Zhang
    • 1
  • Yanyan Ma
    • 1
  • Shaolan He
    • 1
  • Yongqiang Zheng
    • 1
  • Yingtao Ma
    • 2
  1. 1.Citrus Research InstituteSouthwest University/Chinese Academy of Agricultural SciencesChongqingChina
  2. 2.Life Science DepartmentLuoyang Normal UniversityLuoyangChina

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