title: Response of microRNAs to cold treatment in the young spikes of common wheat.
abstract: MicroRNAs (miRNAs) are a class of small non-coding RNAs that play important roles in biotic and abiotic stresses by regulating their target genes. For common wheat, spring frost damage frequently occurs, especially when low temperature coincides with plants at early floral organ differentiation, which may result in significant yield loss. Up to date, the role of miRNAs in wheat response to frost stress is not well understood.
  
  
  
  We report here the sequencing of small RNA transcriptomes from the young spikes that were treated with cold stress and the comparative analysis with those of the control. A total of 192 conserved miRNAs from 105 families and nine novel miRNAs were identified. Among them, 34 conserved and five novel miRNAs were differentially expressed between the cold-stressed samples and the controls. The expression patterns of 18 miRNAs were further validated by quantitative real time polymerase chain reaction (qRT-PCR). Moreover, nearly half of the miRNAs were cross inducible by biotic and abiotic stresses when compared with previously published work. Target genes were predicted and validated by degradome sequencing. Gene Ontology (GO) enrichment analysis showed that the target genes of differentially expressed miRNAs were enriched for response to the stimulus, regulation of transcription, and ion transport functions. Since many targets of differentially expressed miRNAs were transcription factors that are associated with floral development such as ARF, SPB (Squamosa Promoter Binding like protein), MADS-box (MCM1, AG, DEFA and SRF), MYB, SPX (SYG1, Pho81 and XPR1), TCP (TEOSINTE BRANCHED, Cycloidea and PCF), and PPR (PentatricoPeptide Repeat) genes, cold-altered miRNA expression may cause abnormal reproductive organ development.
  
  
  
  Analysis of small RNA transcriptomes and their target genes provide new insight into miRNA regulation in developing wheat inflorescences under cold stress. MiRNAs provide another layer of gene regulation in cold stress response that can be genetically manipulated to reduce yield loss in wheat.
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.|Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, Jinan, 250100, China.|National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China.
authors.forename: Guoqi
authors.initials: G
authors.lastname: Song
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.|Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, Jinan, 250100, China.|National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China.
authors.forename: Rongzhi
authors.initials: R
authors.lastname: Zhang
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.|Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, Jinan, 250100, China.|National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China.
authors.forename: Shujuan
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.|Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, Jinan, 250100, China.|National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China.
authors.forename: Yulian
authors.initials: Y
authors.lastname: Li
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.|Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, Jinan, 250100, China.|National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Gao
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.|Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, Jinan, 250100, China.|National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China.
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Han
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.|Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, Jinan, 250100, China.|National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China.
authors.forename: Mingli
authors.initials: M
authors.lastname: Chen
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.|Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, Jinan, 250100, China.|National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China.
authors.forename: Jiao
authors.initials: J
authors.lastname: Wang
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.|Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, Jinan, 250100, China.|National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.affiliation: Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China. lgy111@126.com.|Key Laboratory of Wheat Biology & Genetic Improvement on North Yellow & Huai River Valley, Ministry of Agriculture, Jinan, 250100, China. lgy111@126.com.|National Engineering Laboratory for Wheat & Maize, Jinan, 250100, China. lgy111@126.com.
authors.forename: Genying
authors.initials: G
authors.lastname: Li
mesh_terms: D003080:Cold Temperature; D020869:Gene Expression Profiling; D035683:MicroRNAs / Q000235:genetics*; D017423:Sequence Analysis, RNA; D014908:Triticum / Q000235:genetics* / Q000254:growth & development* / Q000502:physiology
chemical_list: D035683:MicroRNAs
keywords: Cold stress; Degradome; Inflorescence development; MicroRNA; Wheat