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Systematic discovery and characterization of stress-related microRNA genes in Oryza sativa

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Abstract

Abiotic stresses including drought, salinity, extreme temperatures, chemical toxicity and oxidative are the natural status of the environment to exert serious threats to agriculture. Abiotic stress-related microRNAs (ASmiRNAs) are a group of microRNAs (miRNAs) regulating stress responses in plants. However, the systematic investigation of ASmiRNAs is limited in Rice (O. sativa), a typical abiotic stress-resistant crop species. In the present work, we systematically investigated ASmiRNAs in silico. First, we identified 177 putative ASmiRNAs in O.sativa. Second, we found most ASmiRNAs were driven by TATA-promoter and most stress-related miRNA promoter regions contained the stress-related elements. Third, we found many ASmiRNAs families were species/family specific and a set of miRNAs might derive from genomic repeat-sequences in O. sativa. Finally, we found the ASmiRNAs in O. sativa target 289 genes with 1050 predicted target sites in which 98% sites have cleavage activity and 2% sites have translation inhibition activity. In conclusion, our findings provide an insight into both the function and evolution of ASmiRNAs and improve our understanding on the mechanism of abiotic stress resistance in O. sativa.

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Abbreviations

miRNA:

microRNA

pri-miRNA:

primary miRNA

pre-miRNA:

precursor miRNA

ASmiRNA:

abiotic stress-related microRNA

osa:

Oryza sativa

GO:

gene ontology

TSS:

transcription start site

TFs:

transcription factors

mRNA:

message RNA

C:

cellular component

P:

biological process

F:

molecular function

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Acknowledgements

This work was supported in part by grants from the National Natural Science Foundation of China (No. 30971830 and 30970348), the National Transgenic Plant R&D Project of China (No. 2009ZX08009-063B), the Major Program of Natural Science Research of Jiangsu Higher Education Institutions (No. 12KJA180005), the Youth Foundation of Nanjing Normal University Taizhou College (No. Q201206), and a grant from Priority Academic Program Development of Jiangsu Higher Education Institutions.

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Authors and Affiliations

  1. Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China

    Kai Bin Xie, Xue Zhou, Tian Hai Zhang & Guo Xiang Chen

  2. Taizhou College, Nanjing Normal University, Taizhou, 225300, China

    Xue Zhou

  3. Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences (JAAS), Nanjing, 210014, China

    Bao Long Zhang

  4. The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Institute of Life Science, Southeast University, Nanjing, 210009, China

    Li Ming Chen

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  1. Kai Bin Xie
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Correspondence to Xue Zhou or Guo Xiang Chen.

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Xie, K.B., Zhou, X., Zhang, T.H. et al. Systematic discovery and characterization of stress-related microRNA genes in Oryza sativa. Biologia 70, 75–84 (2015). https://doi.org/10.1515/biolog-2015-0001

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