Plant Molecular Biology

, Volume 65, Issue 4, pp 467–485 | Cite as

Genome-wide identification of C2H2 zinc-finger gene family in rice and their phylogeny and expression analysis

  • Pinky Agarwal
  • Rita Arora
  • Swatismita Ray
  • Ashok K. Singh
  • Vijay P. Singh
  • Hiroshi Takatsuji
  • Sanjay Kapoor
  • Akhilesh K. Tyagi


Transcription factors regulate gene expression in response to various external and internal cues by activating or suppressing downstream genes in a pathway. In this study, we provide a complete overview of the genes encoding C2H2 zinc-finger transcription factors in rice, describing the gene structure, gene expression, genome localization, and phylogenetic relationship of each member. The genome of Oryza sativa codes for 189 C2H2 zinc-finger transcription factors, which possess two main types of zinc-fingers (named C and Q). The Q-type zinc fingers contain a conserved motif, QALGGH, and are plant specific, whereas C type zinc fingers are found in other organisms as well. A genome-wide microarray based gene expression analysis involving 14 stages of vegetative and reproductive development along with 3 stress conditions has revealed that C2H2 gene family in indica rice could be involved during all the stages of reproductive development from panicle initiation till seed maturation. A total of 39 genes are up-regulated more than 2-fold, in comparison to vegetative stages, during reproductive development of rice, out of which 18 are specific to panicle development and 12 genes are seed-specific. Twenty-six genes have been found to be up-regulated during three abiotic stresses and of these, 14 genes express specifically during the stress conditions analyzed while 12 are also up-regulated during reproductive development, suggesting that some components of the stress response pathways are also involved in reproduction.


ZOS Zinc finger Rice Microarray Panicle Seed Stress 





ERF-associated amphiphillic repression


Hidden Markov Model


Knowledge-based Oryza Molecular biological Encyclopedia


Massively parallel signature sequencing


National Center for Biotechnology Information




The Institute for Genomic Research




Zinc-finger protein


C2H2 zinc-finger protein TFIIIA type



The research work was supported by the Department of Biotechnology, Government of India. UGC Research Fellowship to P.A. and CSIR Research Fellowship to R.A. and S.R. are acknowledged.

Supplementary material


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Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Pinky Agarwal
    • 1
  • Rita Arora
    • 1
  • Swatismita Ray
    • 1
  • Ashok K. Singh
    • 2
  • Vijay P. Singh
    • 2
  • Hiroshi Takatsuji
    • 3
  • Sanjay Kapoor
    • 1
  • Akhilesh K. Tyagi
    • 1
  1. 1.Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular BiologyUniversity of Delhi South CampusNew DelhiIndia
  2. 2.Division of GeneticsIndian Agricultural Research InstituteNew DelhiIndia
  3. 3.Plant Disease Resistance Research UnitNational Institute of Agrobiological SciencesTsukubaJapan

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