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High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice

Blanca E Barrera-Figueroa12, Lei Gao1, Zhigang Wu1, Xuefeng Zhou3, Jianhua Zhu4, Hailing Jin5, Renyi Liu1* and Jian-Kang Zhu6

Author Affiliations

1 Department of Botany and Plant Sciences and Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA

2 Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec, Oaxaca, 38601, Mexico

3 Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA

4 Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA

5 Department of Plant Pathology and Microbiology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA

6 Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA

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BMC Plant Biology 2012, 12:132  doi:10.1186/1471-2229-12-132

Published: 3 August 2012



MicroRNAs (miRNAs) are small RNA molecules that play important regulatory roles in plant development and stress responses. Identification of stress-regulated miRNAs is crucial for understanding how plants respond to environmental stimuli. Abiotic stresses are one of the major factors that limit crop growth and yield. Whereas abiotic stress-regulated miRNAs have been identified in vegetative tissues in several plants, they are not well studied in reproductive tissues such as inflorescences.


We used Illumina deep sequencing technology to sequence four small RNA libraries that were constructed from the inflorescences of rice plants that were grown under control condition and drought, cold, or salt stress. We identified 227 miRNAs that belong to 127 families, including 70 miRNAs that are not present in the miRBase. We validated 62 miRNAs (including 10 novel miRNAs) using published small RNA expression data in DCL1, DCL3, and RDR2 RNAi lines and confirmed 210 targets from 86 miRNAs using published degradome data. By comparing the expression levels of miRNAs, we identified 18, 15, and 10 miRNAs that were regulated by drought, cold and salt stress conditions, respectively. In addition, we identified 80 candidate miRNAs that originated from transposable elements or repeats, especially miniature inverted-repeat elements (MITEs).


We discovered novel miRNAs and stress-regulated miRNAs that may play critical roles in stress response in rice inflorescences. Transposable elements or repeats, especially MITEs, are rich sources for miRNA origination.