title: Identification of boron-deficiency-responsive microRNAs in Citrus sinensis roots by Illumina sequencing.
abstract: BACKGROUND
  Boron (B)-deficiency is a widespread problem in many crops, including Citrus. MicroRNAs (miRNAs) play important roles in nutrient deficiencies. However, little is known on B-deficiency-responsive miRNAs in plants. In this study, we first identified miRNAs and their expression pattern in B-deficient Citrus sinensis roots by Illumina sequencing in order to identify miRNAs that might be involved in the tolerance of plants to B-deficiency.
  
  
  RESULTS
  We isolated 52 (40 known and 12 novel) up-regulated and 82 (72 known and 10 novel) down-regulated miRNAs from B-deficient roots, demonstrating remarkable metabolic flexibility of roots, which might contribute to the tolerance of plants to B-deficiency. A model for the possible roles of miRNAs in the tolerance of roots to B-deficiency was proposed. miRNAs might regulate the adaptations of roots to B-deficiency through following several aspects: (a) inactivating reactive oxygen species (ROS) signaling and scavenging through up-regulating miR474 and down-regulating miR782 and miR843; (b) increasing lateral root number by lowering miR5023 expression and maintaining a certain phenotype favorable for B-deficiency-tolerance by increasing miR394 expression; (c) enhancing cell transport by decreasing the transcripts of miR830, miR5266 and miR3465; (d) improving osmoprotection (miR474) and regulating other metabolic reactions (miR5023 and miR821). Other miRNAs such as miR472 and miR2118 in roots increased in response to B-deficiency, thus decreasing the expression of their target genes, which are involved in disease resistance, and hence, the disease resistance of roots.
  
  
  CONCLUSIONS
  Our work demonstrates the possible roles of miRNAs and related mechanisms in the response of plant roots to B-deficiency.
authors.forename: Yi-Bin
authors.initials: YB
authors.lastname: Lu
authors.forename: Lin-Tong
authors.initials: LT
authors.lastname: Yang
authors.forename: Yi-Ping
authors.initials: YP
authors.lastname: Qi
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.forename: Zhong
authors.initials: Z
authors.lastname: Li
authors.forename: Yan-Bin
authors.initials: YB
authors.lastname: Chen
authors.forename: Zeng-Rong
authors.initials: ZR
authors.lastname: Huang
authors.affiliation: College of Resources and Environmental Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China. lisongchen2002@hotmail.com.
authors.forename: Li-Song
authors.initials: LS
authors.lastname: Chen
mesh_terms: D001895:Boron / Q000172:deficiency*; D032084:Citrus sinensis / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D055442:Metabolome / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D058977:Molecular Sequence Annotation; D009243:NAD / Q000378:metabolism; D063245:Plant Development / Q000235:genetics; D018515:Plant Leaves / Q000378:metabolism; D018517:Plant Roots / Q000201:enzymology / Q000235:genetics*; D011392:Proline / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results
chemical_list: D035683:MicroRNAs; D009243:NAD; D011392:Proline; D001895:Boron