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Plant Molecular Biology Reporter

, Volume 33, Issue 4, pp 1013–1029 | Cite as

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

  • Chuanzhi Zhao
  • Han Xia
  • Tingjie Cao
  • Yu Yang
  • Shuzhen Zhao
  • Lei Hou
  • Ye Zhang
  • Changsheng Li
  • Xinyou Zhang
  • Xingjun Wang
Original Paper

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.

Keywords

Peanut miRNA Bacterial wilt High-throughput sequencing Degradome 

Notes

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.

Supplementary material

11105_2014_806_MOESM1_ESM.pdf (1.1 mb)
Fig. S1 Hairpin structures of known miRNAs. (PDF 1103 kb)
11105_2014_806_MOESM2_ESM.pdf (666 kb)
Fig. S2 Hairpin structures of novel miRNAs. (PDF 665 kb)
11105_2014_806_MOESM3_ESM.doc (37 kb)
Table S1 High quality reads generated from four peanut miRNA libraries. (DOC 37 kb)
11105_2014_806_MOESM4_ESM.xls (82 kb)
Table S2 Detail information of known miRNA families of wild and cultivated peanut. (XLS 81 kb)
11105_2014_806_MOESM5_ESM.xls (150 kb)
Table S3 Known miRNA variants identified in wild and cultivated peanut. (XLS 149 kb)
11105_2014_806_MOESM6_ESM.xls (99 kb)
Table S4 The plausible candidates of novel miRNAs identified in wild and cultivated peanut. (XLS 99 kb)
11105_2014_806_MOESM7_ESM.xls (77 kb)
Table S5 Predicted target genes of known and novel miRNAs. (XLS 77 kb)

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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Chuanzhi Zhao
    • 1
  • Han Xia
    • 1
  • Tingjie Cao
    • 2
  • Yu Yang
    • 3
  • Shuzhen Zhao
    • 1
  • Lei Hou
    • 1
  • Ye Zhang
    • 1
  • Changsheng Li
    • 1
  • Xinyou Zhang
    • 2
  • Xingjun Wang
    • 1
  1. 1.Bio-Tech Research CenterShandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinanPeople’s Republic of China
  2. 2.Henan Academy of Agricultural SciencesZhengzhouPeople’s Republic of China
  3. 3.Vegetable Research Institute of Shandong Academy of Agricultural SciencesJinanPeople’s Republic of China

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