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Genome-wide survey and characterization of the WRKY gene family in Populus trichocarpa

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Abstract

WRKY transcription factors participate in diverse physiological and developmental processes in plants. They have highly conserved WRKYGQK amino acid sequences in their N-termini, followed by the novel zinc-finger-like motifs, Cys2His2 or Cys2HisCys. To date, numerous WRKY genes have been identified and characterized in a number of herbaceous species. Survey and characterization of WRKY genes in a ligneous species would facilitate a better understanding of the evolutionary processes and functions of this gene family. In this study, 104 poplar WRKY genes (PtWRKY) were identified in the latest poplar genome sequence. According to their structural features, the predicted members were divided into the previously defined groups I–III, as described in rice. In addition, chromosomal localization of the genes demonstrated that there might be WRKY gene hot spots in 2.3 Mb regions on chromosome 14. Furthermore, approximately 83% (86 out of 104) WRKY genes participated in gene duplication events, including 69% (29 out of 42) gene pairs which exhibited segmental duplication. Using semi-quantitative RT-PCR, the expression patterns of subgroup III genes were investigated under different stresses [cold, drought, salinity and salicylic acid (SA)]. The data revealed that these genes presented different expression levels in response to various stress conditions. Expression analysis exhibited PtWRKY76 gene induced markedly in 0.1 mM SA or 25% PEG-6000 treatment. The results presented here provide a fundamental clue for cloning specific function genes in further studies and applications.

Key message This study identified 104 poplar WRKY genes and demonstrated WRKY gene hot spots on chromosome 14. Furthermore, semi-quantitative RT-PCR showed variable stress responses in subgroup III.

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Acknowledgments

This work was supported by the Anhui Major Science and Technology Projects (No.08010302073) and National Science Technology Support Program (No.2009BADA6B06-1). We thank the members of the Laboratory of Modern Biotechnology and especially thank Daqiang Wu, Guo Wei and Yang Zhao for their skillful technical assistance in this study.

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Authors and Affiliations

  1. Lab of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China

    Hongsheng He, Yuanhua Shao & Yan Xiang

  2. Key Lab of Biomass Improvement and Conversion, Anhui Agriculture University, Hefei, 230036, China

    Hongsheng He, Qing Dong, Haiyang Jiang, Suwen Zhu, Beijiu Cheng & Yan Xiang

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  1. Hongsheng He
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  2. Qing Dong
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  3. Yuanhua Shao
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  4. Haiyang Jiang
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  5. Suwen Zhu
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  6. Beijiu Cheng
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  7. Yan Xiang
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Correspondence to Yan Xiang.

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Communicated by Q. Zhao.

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Fig. S1Phylogram based on Arabidopsis and poplar WRKY domains. The alignment of amino acid sequences was produced using the MEGA v4.0 program with the neighbor-joining (NJ) method. AtWRKY domain sequences were obtained from Wu et al. (2005).

Fig. S2Phylogenetic tree of triploid white poplar (( P. tomentosa x P. bolleana ) x P. tomentosa ), selected Arabidopsis and rice WRKY domains. The unrooted tree was constructed using MEGA 4.0 with the Neighbor-Joining (NJ) method. Clades of the WRKY domain are labeled according to the classifications of OsWRKY and AtWRKY domains by Wu et al. (2005). WRKY protein sequences of triploid white poplar were obtained from NCBI. Bootstrap values (≥500) based on 1,000 replications are exhibited beside the nodes.

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He, H., Dong, Q., Shao, Y. et al. Genome-wide survey and characterization of the WRKY gene family in Populus trichocarpa . Plant Cell Rep 31, 1199–1217 (2012). https://doi.org/10.1007/s00299-012-1241-0

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