Genome-wide transcriptome analysis of roots in two rice varieties in response to alternate wetting and drying irrigation

Tao Song, Debatosh Das, Feng Yang, Moxian Chen, Yuan Tian, Chaolin Cheng, Chao Sun, Weifeng Xu*, Jianhua Zhang*

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

12 Citations (Scopus)


Alternate wetting and drying (AWD) irrigation has been widely used as an efficient rice production method to obtain better yield without continuous flooding (CF) of the paddy field. However, how this practice affects gene expression to regulate rice physiology and morphology is largely unknown. In this study, we used two rice varieties, Nipponbare, a lowland rice cultivar, and Gaoshan 1, an upland cultivar, and found that root dry weight (RDW) and root oxidation activity (ROA) in both cultivars substantially increased in response to AWD. We then analyzed the differences in transcriptome profiles of their roots irrigated in AWD vs. CF conditions. AWD responsive genes are mainly involved in lignin biosynthetic pathway and phytohormone signal transduction pathway and belong mainly to bHLH, bZIP, NAC, WRKY, and HSF transcription factor families. We discussed how these differentially expressed genes may contribute to the morphological adaptations observed in roots exposed to AWD. This analysis also provides useful information to explain the similarities and differences in adaptation to AWD irrigation between the two rice ecotypes.

Original languageEnglish
Pages (from-to)586-601
Number of pages16
JournalCrop Journal
Issue number4
Publication statusPublished - Aug 2020

Scopus Subject Areas

  • Agronomy and Crop Science
  • Plant Science

User-Defined Keywords

  • Lignin
  • Phytohormone
  • Rice root
  • Transcriptome
  • Water-saving irrigation


Dive into the research topics of 'Genome-wide transcriptome analysis of roots in two rice varieties in response to alternate wetting and drying irrigation'. Together they form a unique fingerprint.

Cite this