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Molecular Genetics and Genomics

, Volume 289, Issue 6, pp 1289–1306 | Cite as

Transcriptome-wide analysis of WRKY transcription factors in wheat and their leaf rust responsive expression profiling

  • Lopamudra Satapathy
  • Dharmendra Singh
  • Prashant Ranjan
  • Dhananjay Kumar
  • Manish Kumar
  • Kumble Vinod Prabhu
  • Kunal Mukhopadhyay
Original Paper

Abstract

WRKY, a plant-specific transcription factor family, has important roles in pathogen defense, abiotic cues and phytohormone signaling, yet little is known about their roles and molecular mechanism of function in response to rust diseases in wheat. We identified 100 TaWRKY sequences using wheat Expressed Sequence Tag database of which 22 WRKY sequences were novel. Identified proteins were characterized based on their zinc finger motifs and phylogenetic analysis clustered them into six clades consisting of class IIc and class III WRKY proteins. Functional annotation revealed major functions in metabolic and cellular processes in control plants; whereas response to stimuli, signaling and defense in pathogen inoculated plants, their major molecular function being binding to DNA. Tag-based expression analysis of the identified genes revealed differential expression between mock and Puccinia triticina inoculated wheat near isogenic lines. Gene expression was also performed with six rust-related microarray experiments at Gene Expression Omnibus database. TaWRKY10, 15, 17 and 56 were common in both tag-based and microarray-based differential expression analysis and could be representing rust specific WRKY genes. The obtained results will bestow insight into the functional characterization of WRKY transcription factors responsive to leaf rust pathogenesis that can be used as candidate genes in molecular breeding programs to improve biotic stress tolerance in wheat.

Keywords

WRKY transcription factors Wheat Leaf rust Gene ontology Differential expression 

Abbreviations

ESTs

Expressed sequence tags

GEO

Gene expression omnibus

GRAVY

Grand average of hydropathicity

IWGSC

International wheat genome sequencing consortium

MEGA

Molecular evolutionary genetic analysis

NCBI

National Centre for Biotechnology Information

NLS

Nuclear localization signals

SAGE

Serial analysis of gene expression

SOLiD

Sequencing by oligonucleotide ligation and detection

SRA

Sequence read archive

R-genes

Resistant genes

TF

Transcription factor

Notes

Acknowledgments

This work was supported by Department of Biotechnology, Government of India (Grant No. BT/PR6037/AGR/02/308/05), BTISNet SubDIC (BT/BI/04/065/04), Department of Agriculture, Government of Jharkhand (5/B.K.V/Misc/12/2001) and CoE-TEQIP-II (Grant No. NPIU/TEQIP II/FIN/31/158). L. S. is grateful to Department of Science and Technology-INSPIRE (Fellowship/2011/318) and D. K. to Council of Scientific and Industrial Research [9/554 (0026) 2010-EMR-I] for Ph. D. fellowships.

Conflict of interest

Authors declare no conflicts of interest.

Supplementary material

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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Lopamudra Satapathy
    • 1
  • Dharmendra Singh
    • 1
  • Prashant Ranjan
    • 1
  • Dhananjay Kumar
    • 1
  • Manish Kumar
    • 1
  • Kumble Vinod Prabhu
    • 2
  • Kunal Mukhopadhyay
    • 1
  1. 1.Department of Bio-EngineeringBirla Institute of Technology, MesraRanchiIndia
  2. 2.Department of GeneticsIndian Agriculture Research InstituteNew DelhiIndia

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