Functional & Integrative Genomics

, Volume 11, Issue 1, pp 157–178

Modulation of transcription factor and metabolic pathway genes in response to water-deficit stress in rice

  • Swatismita Ray
  • Prasant K. Dansana
  • Jitender Giri
  • Priyanka Deveshwar
  • Rita Arora
  • Pinky Agarwal
  • Jitendra P. Khurana
  • Sanjay Kapoor
  • Akhilesh K. Tyagi
Original Paper

DOI: 10.1007/s10142-010-0187-y

Cite this article as:
Ray, S., Dansana, P.K., Giri, J. et al. Funct Integr Genomics (2011) 11: 157. doi:10.1007/s10142-010-0187-y

Abstract

Water-deficit stress is detrimental for rice growth, development, and yield. Transcriptome analysis of 1-week-old rice (Oryza sativa L. var. IR64) seedling under water-deficit stress condition using Affymetrix 57 K GeneChip® has revealed 1,563 and 1,746 genes to be up- and downregulated, respectively. In an effort to amalgamate data across laboratories, we identified 5,611 differentially expressing genes under varying extrinsic water-deficit stress conditions in six vegetative and one reproductive stage of development in rice. Transcription factors (TFs) involved in ABA-dependent and ABA-independent pathways have been found to be upregulated during water-deficit stress. Members of zinc-finger TFs namely, C2H2, C2C2, C3H, LIM, PHD, WRKY, ZF-HD, and ZIM, along with TF families like GeBP, jumonji, MBF1 and ULT express differentially under water-deficit conditions. NAC (NAM, ATAF and CUC) TF family emerges to be a potential key regulator of multiple abiotic stresses. Among the 12 TF genes that are co-upregulated under water-deficit, salt and cold stress conditions, five belong to the NAC TF family. We identified water-deficit stress-responsive genes encoding key enzymes involved in biosynthesis of osmoprotectants like polyols and sugars; amino acid and quaternary ammonium compounds; cell wall loosening and structural components; cholesterol and very long chain fatty acid; cytokinin and secondary metabolites. Comparison of genes responsive to water-deficit stress conditions with genes preferentially expressed during panicle and seed development revealed a significant overlap of transcriptome alteration and pathways.

Keywords

Oryza sativa L. var. IR64MicroarrayTranscriptome analysisWater-deficit stressMetabolic pathwaysTranscription factors

Supplementary material

10142_2010_187_MOESM1_ESM.pdf (313 kb)
Supplementary Fig. S1(PDF 312 kb)
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Supplementary Fig. S7(PDF 41.2 kb)
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Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Swatismita Ray
    • 1
  • Prasant K. Dansana
    • 1
  • Jitender Giri
    • 1
  • Priyanka Deveshwar
    • 1
  • Rita Arora
    • 1
  • Pinky Agarwal
    • 1
  • Jitendra P. Khurana
    • 1
  • Sanjay Kapoor
    • 1
  • Akhilesh K. Tyagi
    • 1
    • 2
  1. 1.Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia
  2. 2.National Institute of Plant Genome Research, Aruna Asaf Ali MargNew DelhiIndia