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Analysis of Brassica rapa ESTs: gene discovery and expression patterns of AP2/ERF family genes

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Abstract

Chinese cabbage (Brassica rapa subsp. pekinensis) is among the most important vegetables and is widely cultivated in world. Genes in the AP2/ERF family encode transcriptional regulators that serve a variety of functions in the plants. Expressed sequence tags (ESTs) are created by partially sequencing randomly isolated gene transcripts and have proved valuable in molecular biology. Starting from the database with 142 947 ESTs of B. rapa, 62 putative AP2/ERF family genes were identified by in silico cloning using the conserved AP2/ERF domain amino acid sequence of Arabidopsis thaliana as a probe. Based on the number of AP2/ERF domains and functions of the genes, the AP2/ERF transcription factors from B. rapa were classified into four subfamilies (DREB, ERF, AP2 and RAV). Using large-scale available EST information as a source of expression data for digital expression profiling, differentially detected genes were identified among diverse plant tissues. Roots contained the largest number of transcripts of the AP2/ERF family genes, followed by leaves and seeds. Only a few of the 62 AP2/ERF family genes were detected in all tissues: most were detected only in some tissues but not in others. The maximum detected was that of BraERF-B2-5, and it was recorded from seed tissue.

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Acknowledgments

The research was supported by the Project for International Scientific and Technological Cooperation (08540706500); Shanghai Rising-Star Program (08QH14021); Shanghai and National Natural Science Foundation (08ZR1417200, 30670179); Hi-tech Research and Development Program of China (2006AA10Z117, 2008AA10Z401) and National key Project of Transgenic Crops of China (2009ZX08002-011B).

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Authors and Affiliations

  1. Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China

    Jing Zhuang, Ai-Sheng Xiong, Ri-He Peng, Feng Gao, Bo Zhu, Xiao-Yan Fu, Xiao-Feng Jin & Quan-Hong Yao

  2. Nanjing Agricultural University, 210095, Nanjing, China

    Zhen Zhang & Yu-Shan Qiao

  3. Alberta Research Council of Canada, Edmonton Vegreville, AB, T9C 1T4, Canada

    Jing Zhuang & Jian Zhang

  4. Yangzhou University, 88 S. Daxue Road, 225009, Yangzhou, China

    Jian-Min Chen

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  1. Jing Zhuang
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Correspondence to Ai-Sheng Xiong, Yu-Shan Qiao or Quan-Hong Yao.

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Zhuang, J., Xiong, AS., Peng, RH. et al. Analysis of Brassica rapa ESTs: gene discovery and expression patterns of AP2/ERF family genes. Mol Biol Rep 37, 2485–2492 (2010). https://doi.org/10.1007/s11033-009-9763-4

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  • DOI: https://doi.org/10.1007/s11033-009-9763-4

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