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Small RNA and Degradome Deep Sequencing Reveals Peanut MicroRNA Roles in Response to Pathogen Infection

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Abstract

Bacterial wilt (BW) disease is a widespread disease in peanut (Arachis hypogaea L.), reducing peanut production because of high susceptibility of most cultivated species. However, Arachis glabrata, a perennial wild relative, has high resistance to soil-borne diseases. MicroRNAs (miRNAs) have been characterized as important factors in plant growth, development, and biotic/abiotic stress responses. However, their roles in response to pathogen are still unknown in peanut. Here, we constructed four miRNA libraries from A. hypogaea and A. glabrata and identified 155 known miRNAs, 31 novel miRNAs, and 173 plausible candidates of novel miRNAs. After infected with BW, the expression of many known miRNA was induced or inhibited in both cultivated and wild-type peanuts. Many miRNAs displayed differential expression patterns in these two species, and the expression of some miRNAs was confirmed by quantitative real-time PCR (qRT-PCR) analysis. A total of 309 targets were predicted, among which 74 of them were confirmed by degradome sequencing. More than 10 % of the targets were defense response genes, such as hypersensitive-induced response protein, leucine-rich repeat (LRR) receptor-like serine/threonine-protein kinase, GRAS, aquaporin, lipid transfer protein, ARF, MYB transcription factors, and MLP-like protein. Our results indicate that diverse set of miRNAs of cultivated and wild peanut species is responsive to BW infection and suggests a possible role in peanut disease resistance.

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Acknowledgments

This work is supported by the National Natural Science Foundation of China (31101427), grants from the Initial Special Research for 973 Program of China (2012CB126313), Ministry of Science and Technology of China (2013AA102602, 2011BAD35B04, 2012BAD33B07), Shandong Province Taishan Scholar Foundation (tshw20100416), Shandong Province Germplasm Innovation and Utilization Project and grants from Shandong Province (ZR2010CZ002, ZR2010CQ008, 201103023), Young Talents Training Program of Shandong Academy of Agricultural Sciences.

Conflict of Interests

The authors declare that they have no competing interests.

Authors’ contributions

XW and XZ designed the study. CZ, HX, TC, YY, SZ, LH, YZ, and CL carried out most of the experiments and data analysis and wrote the material and method part of the manuscript. XW and XZ wrote the manuscript, made the figures, and finalized the tables.

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Authors and Affiliations

  1. Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People’s Republic of China

    Chuanzhi Zhao, Han Xia, Shuzhen Zhao, Lei Hou, Ye Zhang, Changsheng Li & Xingjun Wang

  2. Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People’s Republic of China

    Tingjie Cao & Xinyou Zhang

  3. Vegetable Research Institute of Shandong Academy of Agricultural Sciences, Jinan, 250100, People’s Republic of China

    Yu Yang

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  1. Chuanzhi Zhao
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  2. Han Xia
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  3. Tingjie Cao
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  4. Yu Yang
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  5. Shuzhen Zhao
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  6. Lei Hou
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  7. Ye Zhang
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  8. Changsheng Li
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  9. Xinyou Zhang
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  10. Xingjun Wang
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Corresponding authors

Correspondence to Xinyou Zhang or Xingjun Wang.

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Chuanzhi Zhao and Han Xia contributed equally to this paper.

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Fig. S1

Hairpin structures of known miRNAs. (PDF 1103 kb)

Fig. S2

Hairpin structures of novel miRNAs. (PDF 665 kb)

Table S1

High quality reads generated from four peanut miRNA libraries. (DOC 37 kb)

Table S2

Detail information of known miRNA families of wild and cultivated peanut. (XLS 81 kb)

Table S3

Known miRNA variants identified in wild and cultivated peanut. (XLS 149 kb)

Table S4

The plausible candidates of novel miRNAs identified in wild and cultivated peanut. (XLS 99 kb)

Table S5

Predicted target genes of known and novel miRNAs. (XLS 77 kb)

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Zhao, C., Xia, H., Cao, T. et al. Small RNA and Degradome Deep Sequencing Reveals Peanut MicroRNA Roles in Response to Pathogen Infection. Plant Mol Biol Rep 33, 1013–1029 (2015). https://doi.org/10.1007/s11105-014-0806-1

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