PMID- 22862743 OWN - NLM STAT- MEDLINE DCOM- 20140826 LR - 20220408 IS - 1471-2229 (Electronic) IS - 1471-2229 (Linking) VI - 12 DP - 2012 Aug 3 TI - High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice. PG - 132 LID - 10.1186/1471-2229-12-132 [doi] AB - BACKGROUND: 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. RESULTS: 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). CONCLUSION: 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. FAU - Barrera-Figueroa, Blanca E AU - Barrera-Figueroa BE AD - Department of Botany and Plant Sciences and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA. FAU - Gao, Lei AU - Gao L FAU - Wu, Zhigang AU - Wu Z FAU - Zhou, Xuefeng AU - Zhou X FAU - Zhu, Jianhua AU - Zhu J FAU - Jin, Hailing AU - Jin H FAU - Liu, Renyi AU - Liu R FAU - Zhu, Jian-Kang AU - Zhu JK LA - eng SI - GEO/GSE26357 GR - R01 GM059138/GM/NIGMS NIH HHS/United States GR - R01GM059138/GM/NIGMS NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't PT - Research Support, U.S. Gov't, Non-P.H.S. DEP - 20120803 PL - England TA - BMC Plant Biol JT - BMC plant biology JID - 100967807 RN - 0 (DNA Transposable Elements) RN - 0 (MicroRNAs) RN - 0 (RNA, Plant) RN - 0 (Salts) SB - IM MH - Base Sequence MH - Cold Temperature MH - Computational Biology MH - DNA Transposable Elements/genetics MH - Down-Regulation/genetics MH - Droughts MH - Gene Expression Regulation, Plant/*genetics MH - Gene Knockdown Techniques MH - Gene Library MH - High-Throughput Nucleotide Sequencing MH - Inflorescence/*genetics/physiology MH - MicroRNAs/*genetics/isolation & purification MH - Molecular Sequence Data MH - Oryza/*genetics/physiology MH - RNA Interference MH - RNA, Plant/chemistry/genetics/isolation & purification MH - Repetitive Sequences, Nucleic Acid/genetics MH - Salts MH - Sequence Analysis, RNA MH - Stress, Physiological/*genetics MH - Up-Regulation/genetics PMC - PMC3431262 EDAT- 2012/08/07 06:00 MHDA- 2014/08/27 06:00 PMCR- 2012/08/03 CRDT- 2012/08/07 06:00 PHST- 2012/04/04 00:00 [received] PHST- 2012/07/24 00:00 [accepted] PHST- 2012/08/07 06:00 [entrez] PHST- 2012/08/07 06:00 [pubmed] PHST- 2014/08/27 06:00 [medline] PHST- 2012/08/03 00:00 [pmc-release] AID - 1471-2229-12-132 [pii] AID - 10.1186/1471-2229-12-132 [doi] PST - epublish SO - BMC Plant Biol. 2012 Aug 3;12:132. doi: 10.1186/1471-2229-12-132.