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Comparative expression profiling of miRNAs between the cytoplasmic male sterile line MeixiangA and its maintainer line MeixiangB during rice anther development

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Abstract

Main conclusion

miRNAs are involved in the pollen development during the CMS occurrence in rice.

Abstract

miRNAs are 20–24 nt endogenously expressed small RNAs that play key roles in the regulation of many growth and developmental processes in plants. The knowledge on cytoplasmic male sterility (CMS) regulation by miRNAs in rice is rather limited. In this study, Illumina sequencing was employed to examine the expression profiles of rice anther miRNAs from the CMS line MeixiangA (MxA) and its maintainer line MeixiangB (MxB). A total of 518 known miRNAs and 144 novel miRNAs were identified during rice anther development. Based on the number of sequencing reads, a total of 24 miRNAs were discovered to be differentially expressed between MxA and MxB, and the results were partially validated by qRT-PCR. Among these, 16 miRNAs were decreased and 8 miRNAs were increased in MxA compared with MxB. Target prediction showed that they target genes encoding EF-hand family proteins, F-box domain-containing proteins, MYB transcription factors, PPR-containing proteins and transposons. The expression patterns for targets of osa-miR528, osa-miR5793, osa-miR1432, osa-miR159, osa-miR812d, osa-miR2118c, osa-miR172d and osa-miR5498 were selectively examined, and the results showed that there was a negative correlation on the expression patterns between miRNAs and their targets. These targets have previously been reported to be related with pollen development and male sterility, suggesting that miRNAs might act as regulators of CMS occurrence in rice anthers. Furthermore, miRNA editing events were observed. The U → C and U → A editing phenomenon was validated by molecular cloning and sequencing. These findings contribute to our understanding of the roles of miRNAs during anther development and CMS occurrence in rice.

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Abbreviations

CMS:

Cytoplasmic male sterility

TPM:

Transcript per million

DCL1:

Dicer-like 1

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Acknowledgments

This study is supported by “973” Program of China (2013CB126900) and National Nature Science Foundation of China (NSFC 30971740).

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The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. State Key Laboratory of Hybrid Rice, Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, People’s Republic of China

    Junjie Yan, Hongyuan Zhang, Yinzheng Zheng & Yi Ding

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  1. Junjie Yan
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  2. Hongyuan Zhang
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  3. Yinzheng Zheng
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  4. Yi Ding
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Correspondence to Yi Ding.

Electronic supplementary material

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Fig. S1

Size distribution of sRNAs in the libraries of the sterile line MxA and its maintainer line MxB in this study. Supplementary material 1 (TIFF 1931 kb)

Fig. S2

Distributions of the small RNA tags processed from the miRNA precursors. Supplementary material 2 (PDF 155 kb)

Fig. 3

Characteristics of the novel miRNAs. (a) Distribution of the novel small RNA length. (b) Distribution of the first nucleotidesBelow is the link to the electronic supplementary material. Supplementary material 3 (TIFF 428 kb)

Supplementary material 4 (XLS 1781 kb)

Supplemental materials

Table S1 Primers used in this study

Table S2 The filtering for small RNA clean reads in the libraries of MxA and MxB

Table S3 Summary of the known miRNAs identified in the libraries MxA and MxB

Table S4 Summary of the novel miRNAs predicted in the libraries of MxA and MxB

Table S5 Summary of miRNA editing type, position, snp count and editing rate in the sterile line MxA and its maintainer line MxB

Table S6 Comparison of the expression levels for the known miRNAs between the sterile line MxA and its maintainer line MxB

Table S7 Targets predicted for the known miRNAs

Table S8 Targets predicted for the novel miRNAs

Table S9 Predicted targets of the differentially expressed miRNAs

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Yan, J., Zhang, H., Zheng, Y. et al. Comparative expression profiling of miRNAs between the cytoplasmic male sterile line MeixiangA and its maintainer line MeixiangB during rice anther development. Planta 241, 109–123 (2015). https://doi.org/10.1007/s00425-014-2167-2

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