Journal of Plant Molecular Breeding

Investigating members of Arabidopsis WRKYs transcription factors with differential expression under various stresses using bioinformatics approaches

Document Type : Original research paper

Author

Genetics and agricultural biotechnology institute of Tabarestan, Sari agricultural sciences and natural resources university, Iran

Abstract

In the current study, a comprehensive analysis was performed on Arabidopsis WRKY transcription factor (TF) family members that their differential expression (DE) was reported under various stresses in GEO profile database. First, WRKY members with DE were extracted from GEO profile and information of the data set, sequence and their gene structure were obtained. Then, the concept of the intersection of sets was used to select some of WRKY TFs for downstream analysis. DE of candidate members was compared by t-test. The protein– protein interaction network were predicted by STRING web server. A total of 16 WRKY genes were identified in the 11 dataset of GEO profile. Analysis of the gene structure showed that 56% of the studied WRKY genes have 3 exons and all 16 members are distributed across all five chromosomes of Arabidopsis. Also, the results showed that WRKY40, WRKY46, WRKY18, and WRKY33 were most frequently responsive to various stresses. The protein-protein interaction network showed that WRKY40, WRKY46, WRKY18, and WRKY70 have high interactions with four genes: MPK4, ACS6, MKS1, and STZ. Therefore, WRKY40, WRKY46, WRKY18, and WRKY33 can be considered the most important WRKY TFs of Arabidopsis at response to various stresses and may find applications in genetic and metabolic engineering projects.

Keywords

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Journal of Plant Molecular Breeding
Volume 10, Issue 1
June 2022
Pages 48-59
  • Receive Date: 03 April 2023
  • Revise Date: 23 May 2023
  • Accept Date: 01 July 2023
  • First Publish Date: 01 July 2023