title: Bioinformatic identification and experimental validation of miRNAs from foxtail millet (Setaria italica).
abstract: MiRNAs are a novel group of non-coding small RNAs that negatively regulate gene expression. Many miRNAs have been identified and investigated extensively in plant species with sequenced genomes. However, few miRNAs have been identified in foxtail millet (Setaria italica), which is an ancient cereal crop of great importance for dry land agriculture. In this study, 271 foxtail millet miRNAs belonging to 44 families were identified using a bioinformatics approach. Twenty-three pairs of sense/antisense miRNAs belonging to 13 families, and 18 miRNA clusters containing members of 8 families were discovered in foxtail millet. We identified 432 potential targets for 38 miRNA families, most of which were predicted to be involved in plant development, signal transduction, metabolic pathways, disease resistance, and environmental stress responses. Gene ontology (GO) analysis revealed that 101, 56, and 23 target genes were involved in molecular functions, biological processes, and cellular components, respectively. We investigated the expression patterns of 43 selected miRNAs using qRT-PCR analysis. All of the miRNAs were expressed ubiquitously with many exhibiting different expression levels in different tissues. We validated five predicted targets of four miRNAs using the RNA ligase mediated rapid amplification of cDNA end (5'-RLM-RACE) method.
authors.affiliation: Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China. Electronic address: hanjun4226@163.com.
authors.forename: Jun
authors.initials: J
authors.lastname: Han
authors.affiliation: Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Xie
authors.affiliation: Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
authors.forename: Qingpeng
authors.initials: Q
authors.lastname: Sun
authors.affiliation: Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi 046011, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
authors.forename: Min
authors.initials: M
authors.lastname: Lu
authors.affiliation: Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China.
authors.forename: Weixiang
authors.initials: W
authors.lastname: Wang
authors.affiliation: Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi 046011, China.
authors.forename: Erhu
authors.initials: E
authors.lastname: Guo
authors.affiliation: Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China. Electronic address: baczhkxy@gmail.com.
authors.forename: Jinbao
authors.initials: J
authors.lastname: Pan
mesh_terms: D019295:Computational Biology; D060467:Disease Resistance / Q000502:physiology; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D035683:MicroRNAs / Q000096:biosynthesis / Q000235:genetics; D018749:RNA, Plant / Q000096:biosynthesis / Q000235:genetics; D032983:Setaria Plant / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction / Q000502:physiology
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant
keywords: Bioinformatic identification; Foxtail millet; MicroRNA; Targets; qRT-PCR