title: Combined small RNA and degradome sequencing to identify miRNAs and their targets in response to drought in foxtail millet.
abstract: BACKGROUND
  Foxtail millet (Setaria italica) is a diploid C4 panicoid species. Because of its prominent drought resistance, small genome size, self-pollination, and short life cycle, foxtail millet has become an ideal model system for studying drought tolerance of crops. MicroRNAs (miRNAs) are endogenous, small RNAs that play important regulatory roles in the development and stress response in plants.
  
  
  RESULTS
  In this study, we applied Illumina sequencing to systematically investigate the drought-responsive miRNAs derived from S. italica inbred An04-4783 seedlings grown under control and drought conditions. Degradome sequencing was applied to confirm the targets of these miRNAs at a global level. A total of 81 known miRNAs belonging to 28 families were identified, among which 14 miRNAs were upregulated and four were downregulated in response to drought. In addition, 72 potential novel miRNAs were identified, three of which were differentially expressed under drought conditions. Degradome sequencing analysis showed that 56 and 26 genes were identified as targets of known and novel miRNAs, respectively.
  
  
  CONCLUSIONS
  Our analysis revealed post-transcriptional remodeling of cell development, transcription factors, ABA signaling, and cellar homeostasis in S.italica in response to drought. This preliminary characterization provided useful information for further studies on the regulatory networks of drought-responsive miRNAs in foxtail millet.
authors.affiliation: College of Life Science, Hebei Normal University, Shijiazhuang, 050012, People's Republic of China.|Institute of cotton, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 05003, People's Republic of China.
authors.forename: Yongqiang
authors.initials: Y
authors.lastname: Wang
authors.affiliation: College of Life Science, Hebei Normal University, Shijiazhuang, 050012, People's Republic of China.
authors.forename: Lin
authors.initials: L
authors.lastname: Li
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
authors.forename: Sha
authors.initials: S
authors.lastname: Tang
authors.affiliation: Institute of cotton, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 05003, People's Republic of China.
authors.forename: Jianguang
authors.initials: J
authors.lastname: Liu
authors.affiliation: Institute of cotton, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 05003, People's Republic of China.
authors.forename: Hanshuang
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhi
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China. jiaguanqing@caas.cn.
authors.forename: Guanqing
authors.initials: G
authors.lastname: Jia
authors.affiliation: College of Life Science, Hebei Normal University, Shijiazhuang, 050012, People's Republic of China. diaoxianmin@caas.cn.|Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China. diaoxianmin@caas.cn.
authors.forename: Xianmin
authors.initials: X
authors.lastname: Diao
mesh_terms: D018556:Crops, Agricultural / Q000235:genetics; D055864:Droughts; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics*; D009690:Nucleic Acid Conformation; D018749:RNA, Plant / Q000235:genetics; D017423:Sequence Analysis, RNA; D032983:Setaria Plant / Q000235:genetics*; D013312:Stress, Physiological / Q000235:genetics
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant
keywords: Degradome; Drought; Foxtail millet; High-throughput sequencing; miRNA