title: Identification of novel and salt-responsive miRNAs to explore miRNA-mediated regulatory network of salt stress response in radish (Raphanus sativus L.).
abstract: BACKGROUND
  Salt stress is one of the most representative abiotic stresses that severely affect plant growth and development. MicroRNAs (miRNAs) are well known for their significant involvement in plant responses to abiotic stresses. Although miRNAs implicated in salt stress response have been widely reported in numerous plant species, their regulatory roles in the adaptive response to salt stress in radish (Raphanus sativus L.), an important root vegetable crop worldwide, remain largely unknown.
  
  
  RESULTS
  Solexa sequencing of two sRNA libraries from NaCl-free (CK) and NaCl-treated (Na200) radish roots were performed for systematical identification of salt-responsive miRNAs and their expression profiling in radish. Totally, 136 known miRNAs (representing 43 miRNA families) and 68 potential novel miRNAs (belonging to 51 miRNA families) were identified. Of these miRNAs, 49 known and 22 novel miRNAs were differentially expressed under salt stress. Target prediction and annotation indicated that these miRNAs exerted a role by regulating specific stress-responsive genes, such as squamosa promoter binding-like proteins (SPLs), auxin response factors (ARFs), nuclear transcription factor Y (NF-Y) and superoxide dismutase [Cu-Zn] (CSD1). Further functional analysis suggested that these target genes were mainly implicated in signal perception and transduction, regulation of ion homeostasis, basic metabolic processes, secondary stress responses, as well as modulation of attenuated plant growth and development under salt stress. Additionally, the expression patterns of ten miRNAs and five corresponding target genes were validated by reverse-transcription quantitative PCR (RT-qPCR).
  
  
  CONCLUSIONS
  With the sRNA sequencing, salt-responsive miRNAs and their target genes in radish were comprehensively identified. The results provide novel insight into complex miRNA-mediated regulatory network of salt stress response in radish, and facilitate further dissection of molecular mechanism underlying plant adaptive response to salt stress in root vegetable crops.
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P.R. China. 2013204023@njau.edu.cn.|Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, P.R. China. 2013204023@njau.edu.cn.
authors.forename: Xiaochuan
authors.initials: X
authors.lastname: Sun
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P.R. China. nauxuliang@njau.edu.cn.|Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, P.R. China. nauxuliang@njau.edu.cn.
authors.forename: Liang
authors.initials: L
authors.lastname: Xu
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P.R. China. wangyan8217@126.com.
authors.forename: Yan
authors.initials: Y
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P.R. China. yurugang@126.com.
authors.forename: Rugang
authors.initials: R
authors.lastname: Yu
authors.affiliation: Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA. xianwen.zhu@ndsu.edu.
authors.forename: Xianwen
authors.initials: X
authors.lastname: Zhu
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P.R. China. 2013104069@njau.edu.cn.|Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, P.R. China. 2013104069@njau.edu.cn.
authors.forename: Xiaobo
authors.initials: X
authors.lastname: Luo
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P.R. China. jwcgyq@njau.edu.cn.
authors.forename: Yiqin
authors.initials: Y
authors.lastname: Gong
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P.R. China. 2012104070@njau.edu.cn.
authors.forename: Ronghua
authors.initials: R
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P.R. China. cnlimera@gmail.com.
authors.forename: Cecilia
authors.initials: C
authors.lastname: Limera
authors.affiliation: College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, P.R.China. keyunzhang@njau.edu.cn.
authors.forename: Keyun
authors.initials: K
authors.lastname: Zhang
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P.R. China. nauliulw@njau.edu.cn.
authors.forename: Liwang
authors.initials: L
authors.lastname: Liu
mesh_terms: D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D053263:Gene Regulatory Networks; D035683:MicroRNAs / Q000235:genetics*; D058977:Molecular Sequence Annotation; D018517:Plant Roots / Q000235:genetics; D018749:RNA, Plant; D031224:Raphanus / Q000235:genetics* / Q000378:metabolism; D015203:Reproducibility of Results; D055049:Salt Tolerance / Q000235:genetics*; D013312:Stress, Physiological; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant