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Transcriptome Profiling of Dehydration Stress in the Chinese Cabbage (Brassica rapa L. ssp. pekinensis) by Tag Sequencing

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Abstract

Chinese cabbage (Brassica rapa L. ssp. pekinensis) is a vegetable crop with high water requirement and is adversely affected by drought during cultivation. A genome-wide transcription analysis in response to drought is essential to provide effective genetic engineering strategies to improve stress tolerance in crop plants. To gain a deeper understanding of the mechanisms of drought tolerance in B. rapa, we conducted the first genome-wide analysis of gene expression during a drought model using tag sequencing with a Solexa Illumina array. Leaf samples at four time points, 0 day, 1 day, 2 days, and 3 days after dehydration treatment, were taken from a B. rapa DH line, T12-19, and the corresponding RNA was used to construct the expression libraries. The total number of tags per library ranged from 5.6 to 7.6 million and, among these, 13,036, 12,472, 12,774, and 12,227 distinct clean tags for the four respective libraries were unambiguously mapped to a publicly available unigene database. The analysis of differentially expressed genes revealed that 1,092 genes were significantly altered in response to water deficit. In this set of genes, we found 37 transcription factors, 28 genes involved in signal transduction, and 61 water- and osmosensing-responsive genes. Overall, the tag sequencing analyses demonstrated a high degree of transcriptional complexity in response to dehydration stress and represents a considerable improvement over microarray data in the large-scale analysis of transcriptional changes.

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Acknowledgements

This work was supported in part by grants from the Program of Beijing Municipal Science and Technology Committee (Z09070500590909, D111100001311002) and the Earmarked Fund for Modern Agro-industry Technology Research System.

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Authors and Affiliations

  1. Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, 100097, China

    Shuancang Yu, Fenglan Zhang, Yangjun Yu, Deshuang Zhang, Xiuyun Zhao & Wenhong Wang

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  1. Shuancang Yu
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  2. Fenglan Zhang
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  3. Yangjun Yu
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  4. Deshuang Zhang
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  5. Xiuyun Zhao
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Correspondence to Fenglan Zhang.

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Supplementary Table 1

Primers used for qRT-PCR (DOC 33 kb)

Supplementary Table 2

Expression abundance of genes identified as significantly affected by water deficit. TPM, transcripts per million clean tags. The threshold used in this study, FDR≤0.001; the maximum value of |log2 (ratio of stress/control)| ≥1; the maximum expression abundance in four time points ≥100 TPM (DOC 1073 kb)

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Yu, S., Zhang, F., Yu, Y. et al. Transcriptome Profiling of Dehydration Stress in the Chinese Cabbage (Brassica rapa L. ssp. pekinensis) by Tag Sequencing. Plant Mol Biol Rep 30, 17–28 (2012). https://doi.org/10.1007/s11105-011-0313-6

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