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Comprehensive Analysis of Dicer-Like, Argonaute, and RNA-dependent RNA Polymerase Gene Families in Grapevine (Vitis Vinifera)

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Abstract

Regulation of gene expression is associated with RNA interference (RNAi) at the posttranscriptional level and chromatin modification in transcriptional silencing during plant development. Dicer-like (DCL) and Argonaute (AGO) proteins, along with RNA-dependent RNA polymerase (RDR), play integral roles in these processes. Many members of the DCL, AGO, and RDR gene families have been characterized in Arabidopsis, rice, maize, and tomato. However, little is known about these genes in grapevine. Here, we implemented a comprehensive bioinformatics analysis of the DCL, AGO, and RDR gene families in grapevine. In this study, a total of four VvDCL, thirteen VvAGO, and five VvRDR genes were identified in grapevine. These genes were categorized into four groups for each family based on phylogenetic analysis. Twenty-two genes were distributed across 11 chromosomes. We detected five segmental or tandem duplication events, which suggested their conserved functions during evolution. In each subfamily, protein motif composition was relatively conserved. The digital EST expression analyses provided a first glimpse of the expression patterns of DCL, AGO, and RDR gene in grapevine. It is worth mentioning that one gene, VvAGO10a, only expressed in the stem, which suggested that VvAGO10a may function in the regulation of siRNAs in the grapevine stem. Gene expression patterns during berry development and under different abiotic stresses were investigated utilizing microarray data. Thus, these detailed investigations provide a foundation for transcriptional silencing-associated gene families in grapevine for future functional genomics studies.

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Acknowledgments

This work was supported by the National Natural Science Foundation (31370561), Specialized Research Fund for the Doctoral Program of Higher Education (20133418110005), Anhui Provincial Natural Science Foundation (1308085MC36), and Anhui Agricultural University disciplinary construction Foundation (XKTS2013001). We thank to the members of the Laboratory of Modern Biotechnology and especially thank Guo Wei and YuanHua Shao for their assistance in this study.

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Authors and Affiliations

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

    Hualin Zhao, Kang Zhao, Jie Wang, Xue Chen, Zhu Chen & Yan Xiang

  2. Key Laboratory of Crop Biology of Anhui Agriculture University, Hefei, 230036, China

    Ronghao Cai & Yan Xiang

Authors
  1. Hualin Zhao
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  2. Kang Zhao
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  3. Jie Wang
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  4. Xue Chen
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  5. Zhu Chen
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  6. Ronghao Cai
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  7. Yan Xiang
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Correspondence to Yan Xiang.

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Zhao, H., Zhao, K., Wang, J. et al. Comprehensive Analysis of Dicer-Like, Argonaute, and RNA-dependent RNA Polymerase Gene Families in Grapevine (Vitis Vinifera). J Plant Growth Regul 34, 108–121 (2015). https://doi.org/10.1007/s00344-014-9448-7

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  • DOI: https://doi.org/10.1007/s00344-014-9448-7

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