Plant Growth Regulation

, Volume 87, Issue 1, pp 139–148 | Cite as

Comparative analysis of microRNAs and their targets in the roots of two cultivars with contrasting salt tolerance in rice (Oryza sativa L.)

  • Xi Huang
  • Jiejie Feng
  • Rui Wang
  • Hongsheng Zhang
  • Ji HuangEmail author
Original paper


MicroRNAs (miRNAs) are small, non-coding RNAs that play essential roles in plant growth, development, and stress responses. Rice cultivars IR26 (sub. xian) and Jiucaiqing (sub. geng) exhibit significant salt tolerance differences during their growth. This study performed a genome-wide discovery of salt responsive miRNAs in rice roots, and in particular, the differentially expressed miRNAs between two cultivars. Specifically- and commonly-regulated miRNAs involved in salt stress between two cultivars were identified. The genes targeted by these miRNAs were involved in multiple biological processes including transcriptional regulation and response to stimulus. This preliminary characterization provides a framework for future analysis of miRNAs and their roles in rice salt stress response and describes the possible mechanisms for miRNA mediated salt tolerance by comparative analysis of miRNAs and their targets in salt-resistant and -sensitive cultivars.


Oryza sativa Salt MicroRNA High-throughput sequencing Root 



This work was supported by the National Science Foundation of China (Grant No. 31571627), the Fundamental Research Funds for the Central Universities (Grant No. KYZ201804) and the Jiangsu Collaborative Innovation Center for Modern Crop Production (Grant No. JCICMCP).

Author Contributions

XH performed the most of experiments and analysis and drafted the manuscript. JF and RW participated in data analysis. JH and HZ projected design and supervision.

Supplementary material

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Supplementary material 4—Fig. S1 Length distribution of mappable reads in different samples (JPG 257 KB)
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Supplementary material 5—Fig. S2 Length distribution of counts of sRNAs in different samples (JPG 183 KB)
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Supplementary material 6—Fig. S3 Length distribution of counts of unique sRNAs in different samples (JPG 169 KB)
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Supplementary material 10—Fig. S4 miRNAs predicted by degradome sequencing in two cultivars (JPG 69 KB)
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Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  • Xi Huang
    • 1
  • Jiejie Feng
    • 1
  • Rui Wang
    • 1
  • Hongsheng Zhang
    • 1
  • Ji Huang
    • 1
    Email author
  1. 1.State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina

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