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Difference in miRNA expression profiles between two cotton cultivars with distinct salt sensitivity

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Abstract

MicroRNAs (miRNAs) are a class of endogenous, non-coding small RNAs that play important roles in many developmental processes and stress responses in plants and animals. Cotton (Gossypium hirsutum L.) is considered a relatively salt-tolerant non-halophytic plant species. To study the role of miRNAs in salt adaptation, a salt-tolerant cotton cultivar SN-011 and a salt-sensitive cultivar LM-6 were used to detect differentially expressed miRNAs. Using miRNA microarray analysis and a computational approach, 17 cotton miRNAs belonging to eight families were identified. Although they are conserved, 12 of them showed a genotype-specific expression model in both the cultivars. Under salt stress treatment, miR156a/d/e, miR169, miR535a/b and miR827b were dramatically down-regulated in SN-011, while miR167a, miR397a/b and miR399a were up-regulated. Only miR159 was found to be down-regulated in LM-6 under salt stress. To gain insight into their functional significance, 26 target genes were predicted and their functional similarity was further analyzed. Quantitative real-time PCR showed that the expression of seven target genes showed a significant inverse correlation with corresponding miRNAs. These differentially expressed miRNAs can help in further study into the role of transcriptome homeostasis in the adaptation responses of cotton to salt.

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Abbreviations

miRNA:

microRNA

ARF:

Auxin response factor

MFEI:

Minimal folding free energy index

HAP:

Heme activator protein

PHO2:

Phosphate-responsive mutant 2

SBP:

Squamosa promoter-binding protein

SPL:

SBP-like proteins

GH3:

Grim helix 3

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Acknowledgments

This research was supported by the China Key Development Project for Basic Research (973) (Grant No. 2007CB116208), and the China Major Projects for Transgenic Breeding (Grant No. 2008ZX005-004, 2008ZX08005-002).

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Authors and Affiliations

  1. State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, 271018, Shandong, People’s Republic of China

    Zujun Yin, Yan Li, Yudong Liu, Chunhe Li, Xiulan Han & Fafu Shen

  2. State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455100, Henan, People’s Republic of China

    Zujun Yin & Jiwen Yu

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  1. Zujun Yin
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  2. Yan Li
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  3. Jiwen Yu
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Corresponding author

Correspondence to Fafu Shen.

Additional information

Yan Li and Zujun Yin contributed equally to this work.

Electronic supplementary material

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Supplementary Fig. 1 Flowchart for the prediction of potential miRNAs and target genes in cotton. (TIFF 87 kb)

11033_2011_1292_MOESM2_ESM.tif

Supplementary Fig. 2 Predicted fold-back structures of the cotton miRNA precursors. Sequences of mature miRNAs are underlined. (TIFF 318 kb)

11033_2011_1292_MOESM3_ESM.tif

Supplementary Fig. 3 Northern validation of the microarray result. RNA was isolated from the control and from the salt-treated plants of two cotton cultivars. (S) LM-6, a salt-sensitive cultivar; (T) SN-011, a salt-tolerant cultivar; (CK) untreated plants; (Tr) plants treated with 300 mM NaCl for 24 h. The antisense (AS) and sense (S) oligonucleotides were used as controls. Size markers (21–24 nt RNA fraction) are shown on the left, and the relative amounts of RNA loading is visualized by the degree of ethidium bromide staining of tRNA. (TIFF 210 kb)

Supplementary Table 1 (DOC 85 kb)

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Yin, Z., Li, Y., Yu, J. et al. Difference in miRNA expression profiles between two cotton cultivars with distinct salt sensitivity. Mol Biol Rep 39, 4961–4970 (2012). https://doi.org/10.1007/s11033-011-1292-2

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