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Genome-Wide Identification of Embryogenesis-Associated microRNAs in Radish (Raphanus sativus L.) by High-Throughput Sequencing

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Abstract

microRNAs (miRNAs), endogenous non-coding RNAs of approximately 21–24 nucleotides, are important regulators of transcriptional and post-transcriptional gene expression. These regulators play a key role during plant growth and development, including embryogenesis, which is crucial to the life cycle of most plant species. However, although embryogenesis-associated miRNAs have been isolated in a few species, the diversity of these regulatory miRNAs remains largely unexplored, especially in radish. In this study, two small RNA libraries were constructed from radish ovules before and after fertilization. Both libraries were sequenced by next generation sequencing (NGS) technology. This analysis identified 144 conserved and 34 non-conserved miRNAs (representing 43 known miRNA families) and 38 novel miRNAs (representing 28 miRNA families). Comparative analysis revealed that 29 known and 10 novel miRNA families were differentially expressed during embryogenesis. QRT-PCR analysis confirmed miRNA expression patterns and revealed tissue-specific and/or developmental stage-dependent expression for some miRNAs. Moreover, potential target predictions indicated that most of these targets were transcription factors involved in regulating plant growth, development and metabolism. Notably, target transcripts such as squamosa promoter-binding protein, auxin response factor and agamous-like MADS-box protein participated in radish embryogenesis.

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Acknowledgements

This work was supported in part by grants from the Program for the National Natural Science Foundation of China (31171956, 31372064), the Key Technologies R & D Program of Jiangsu Province, China (BE2010328,BE2013429), the PAPD and JASTIF [CX(12)2006]. We thank Dr. Oliver R. E. from North Dakota State University, ND, USA for her critical review and helpful comments during the preparation of this manuscript.

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  1. National Key Laboratory of Crop Genetics and Germplasm Enhancement; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture of P.R. China; College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China

    Lulu Zhai, Liang Xu, Yan Wang, Rugang Yu, Cecilia Limera, Yiqin Gong & Liwang Liu

  2. Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA

    Danqiong Huang

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  1. Lulu Zhai
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  2. Liang Xu
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Correspondence to Liwang Liu.

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Zhai, L., Xu, L., Wang, Y. et al. Genome-Wide Identification of Embryogenesis-Associated microRNAs in Radish (Raphanus sativus L.) by High-Throughput Sequencing. Plant Mol Biol Rep 32, 900–915 (2014). https://doi.org/10.1007/s11105-014-0700-x

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