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Detection and evolutionary analysis of soybean miRNAs responsive to soybean mosaic virus

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Abstract

MicroRNAs (miRNA) are a class of non-coding RNAs that have important gene regulatory roles in various organisms. However, the miRNAs involved in soybean’s response to soybean mosaic virus (SMV) are unknown. To identify novel miRNAs and biotic-stress regulated small RNAs that are involved in soybean’s response to SMV, two small RNA libraries were constructed from mock-inoculated and SMV-infected soybean leaves and sequenced. This led to the discovery of 179 miRNAs, representing 52 families, among which five miRNAs belonging to three families were novel miRNAs in soybean. A large proportion (71.5 %) of miRNAs arose from segmental duplication, similar to the process that drives the evolution of protein-coding genes. In addition, we predicted 346 potential targets of these identified miRNAs, and verified 12 targets by modified 5′-RACE analysis. Finally, three miRNAs (miR160, miR393 and miR1510) that are involved in plant resistance were observed to respond to SMV infection. The interaction between miRNAs and resistance-related genes provides a novel mechanism for pathogens to evade host recognition.

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Abbreviations

AFB:

Auxin signaling F-box protein

ARF:

Auxin response factor

CC:

Coiled-coil domain

DCL:

Dicer-like

LRR:

Leucine-rich repeat

MFE:

Minimum free energy

miRNA:

MicroRNA

NB:

Nucleotide binding domain

RISC:

RNA induced silencing complex

SMV:

Soybean mosaic virus

ssRNAs:

Single-stranded RNAs

TIR1:

Transport inhibitor response 1

TIR-NBS-LRR:

Toll/interleukin-1 receptor-nucleotide binding site-leucine-rich repeat

TPM:

Transcripts per million

TuMV:

Turnip mosaic virus

WGD:

Whole-genome duplication

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Acknowledgments

We thank Dr. Sihai Yang of Nanjing University for his critical reading of the manuscript. This work was supported in part by the National Basic Research Program of China (973 Program) (2010CB125906, 2009CB118400), the National Natural Science Foundation of China (31000718, 31171573, 31201230), and Jiangsu Provincial Support Program (BE2012328, BK2012768).

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Authors and Affiliations

  1. National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China

    Xianchao Yin, Jiao Wang, Hao Cheng, Xiaolin Wang & Deyue Yu

  2. National Center of Plant Gene Research (Shanghai), Shanghai, 200032, China

    Deyue Yu

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  1. Xianchao Yin
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  2. Jiao Wang
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  4. Xiaolin Wang
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  5. Deyue Yu
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Corresponding author

Correspondence to Deyue Yu.

Additional information

X. Yin and J. Wang contributed equally to this paper.

Electronic supplementary material

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Additional file 1 miRNAs that were identified in our survey (XLS 70 kb)

Additional file 2 The predicted targets of conserved and nonconserved miRNAs in soybean (XLS 62 kb)

425_2012_1835_MOESM3_ESM.doc

Table S1 Statistics of small RNAs sequenced from soybean; Fig. S1 Size distribution of soybean small RNAs in mock (a) and SMV (b) libraries; Fig. S2 Percentages of sequencing results for three miRNA groups based on comparison between sequences of Nannong 1138-2 and those of Williams 82; Fig. S3 Expression analysis of miRNAs by stem-loop qRT-PCR treated by SMV (DOC 213 kb)

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Yin, X., Wang, J., Cheng, H. et al. Detection and evolutionary analysis of soybean miRNAs responsive to soybean mosaic virus. Planta 237, 1213–1225 (2013). https://doi.org/10.1007/s00425-012-1835-3

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