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Transcriptome characterization and sequencing-based identification of drought-responsive genes in potato

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Abstract

Potato (Solanum tubersosum L.) is relatively vulnerable to abiotic stress conditions such as drought, but the tolerance mechanisms to such stress in potato are largely unknown. To gain insight into the transcriptome dynamics that are associated with drought stress, genome-wide gene expression profile was conducted by Solexa sequencing to generate a large dataset and a comprehensive transcriptome profile for potato. Here, we report a reference for the potato transcriptome using leaf tissues under drought-stressed condition from a local potato cultivar ‘Longshu 3’. Analysis of 86,965,482 RNA-Seq reads permitted the detection and quantification of expression levels of 7,284 genes at transcriptional levels, among them, 6,754 genes were enriched in draught-treated leaves while 6,419 in control. We identified 842 drought-responsive up-regulated and 494 down-regulated candidate genes with significantly differentially expression under continued drought stress treatments. Those differently expressed genes were mostly enriched in 89 gene categories and 21 KEGG pathways. Drought-stressed leaves had increased expression of genes involved in stress response compared with control leaves. A subset of differentially expressed genes associated with drought response was examined using quantitative real-time PCR. These results provide a broad spectrum of candidate genes that are essential for understanding the molecular regulation of potato in response to abiotic stresses.

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Abbreviations

DEG:

Differentially expressed genes

ESTs:

Expressed sequence tags

FPKM:

Fragments Per Kilobase of exon model per Million mapped reads

qRT-PCR:

Quantitative real-time PCR

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Acknowledgments

This research program is sponsored by Specialized Research Fund for the Doctoral Program of Higher Education of China (No. 20126202110007), and in part by Gansu Provincial Key Laboratory of Aridland Crop Science of Gansu Agricultural University (No. GSCS-2012-02).

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Authors and Affiliations

  1. Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, 730070, People’s Republic of China

    Ning Zhang, Bailin Liu, Guodong Zhang, Jing Chang, Huaijun Si & Di Wang

  2. College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, People’s Republic of China

    Ning Zhang, Congyu Ma, Guodong Zhang, Jing Chang & Huaijun Si

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  1. Ning Zhang
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Correspondence to Huaijun Si or Di Wang.

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Zhang, N., Liu, B., Ma, C. et al. Transcriptome characterization and sequencing-based identification of drought-responsive genes in potato. Mol Biol Rep 41, 505–517 (2014). https://doi.org/10.1007/s11033-013-2886-7

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