title: Identification of bolting-related microRNAs and their targets reveals complex miRNA-mediated flowering-time regulatory networks in radish (Raphanus sativus L.).
abstract: MicroRNAs (miRNAs) play vital regulatory roles in plant growth and development. The phase transition from vegetative growth to flowering is crucial in the life cycle of plants. To date, miRNA-mediated flowering regulatory networks remain largely unexplored in radish. In this study, two small RNA libraries from radish leaves at vegetative and reproductive stages were constructed and sequenced by Solexa sequencing. A total of 94 known miRNAs representing 21 conserved and 13 non-conserved miRNA families, and 44 potential novel miRNAs, were identified from the two libraries. In addition, 42 known and 17 novel miRNAs were significantly differentially expressed and identified as bolting-related miRNAs. RT-qPCR analysis revealed that some miRNAs exhibited tissue- or developmental stage-specific expression patterns. Moreover, 154 target transcripts were identified for 50 bolting-related miRNAs, which were predominately involved in plant development, signal transduction and transcriptional regulation. Based on the characterization of bolting-related miRNAs and their target genes, a putative schematic model of miRNA-mediated bolting and flowering regulatory network was proposed. These results could provide insights into bolting and flowering regulatory networks in radish, and facilitate dissecting the molecular mechanisms underlying bolting and flowering time regulation in vegetable crops.
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture of P.R.China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China.
authors.forename: Shanshan
authors.initials: S
authors.lastname: Nie
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture of P.R.China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China.
authors.forename: Liang
authors.initials: L
authors.lastname: Xu
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture of P.R.China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA.
authors.forename: Danqiong
authors.initials: D
authors.lastname: Huang
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture of P.R.China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China.
authors.forename: Everlyne M
authors.initials: EM
authors.lastname: Muleke
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture of P.R.China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China.
authors.forename: Xiaochuan
authors.initials: X
authors.lastname: Sun
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture of P.R.China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China.
authors.forename: Ronghua
authors.initials: R
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture of P.R.China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Xie
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture of P.R.China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China.
authors.forename: Yiqin
authors.initials: Y
authors.lastname: Gong
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture of P.R.China; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R. China.
authors.forename: Liwang
authors.initials: L
authors.lastname: Liu
mesh_terms: D019295:Computational Biology / Q000379:methods; D035264:Flowers / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics*; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D018515:Plant Leaves / Q000235:genetics; D034622:RNA Interference; D012333:RNA, Messenger / Q000235:genetics*; D018749:RNA, Plant; D031224:Raphanus / Q000235:genetics*; D015203:Reproducibility of Results
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D018749:RNA, Plant