title: Genome-wide identification of turnip mosaic virus-responsive microRNAs in non-heading Chinese cabbage by high-throughput sequencing.
abstract: Turnip mosaic virus (TuMV) is the most prevalent viral pathogen infecting most cruciferous plants. MicroRNAs (miRNAs) are around 22 nucleotides long non-protein-coding RNAs that play key regulatory roles in plants. Recent research findings show that miRNAs are involved in plant-virus interaction. However we know little about plant defense and viral offense system networks throughout microRNA regulation pathway. In this study, two small RNA libraries were constructed based on non-heading Chinese cabbage (Brassica campestris ssp. chinensis L. Makino, NHCC) leaves infected by TuMV and healthy leaves, and sequenced using the Illumina-Solexa high-throughput sequencing technology. A total of 86 conserved miRNAs belonging to 25 known miRNA families and 45 novel ones were identified. Among them, twelve conserved and ten new miRNAs were validated by real-time fluorescence quantitative PCR (qPCR). Differential expression analysis showed that 42 miRNAs were down-regulated and 27 miRNAs were up-regulated in response to TuMV stress. A total of 271 target genes were predicted using a bioinformatics approach, these genes are mainly involved in growth and resistance to various stresses. We further selected 13 miRNAs and their corresponding target genes to explore their expression pattern under TuMV and/or cold (4°C) stresses, and the results indicated that some of the identified miRNAs could link TuMV response with cold response of NHCC. The characterization of these miRNAs could contribute to a better understanding of plant-virus interaction throughout microRNA regulation pathway. This can lead to finding new approach to defend virus infection using miRNA in Chinese cabbage.
authors.affiliation: Horticultural Department, Nanjing Agricultural University, Nanjing 210095, China; State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing 210095, China; Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, Nanjing 210095, China.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Horticultural Department, Nanjing Agricultural University, Nanjing 210095, China; State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing 210095, China; Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, Nanjing 210095, China.
authors.forename: Dahua
authors.initials: D
authors.lastname: Jiang
authors.affiliation: Horticultural Department, Nanjing Agricultural University, Nanjing 210095, China; State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing 210095, China; Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, Nanjing 210095, China.
authors.forename: Changwei
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Horticultural Department, Nanjing Agricultural University, Nanjing 210095, China; State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing 210095, China; Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, Nanjing 210095, China.
authors.forename: Huawei
authors.initials: H
authors.lastname: Tan
authors.affiliation: Horticultural Department, Nanjing Agricultural University, Nanjing 210095, China; State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing 210095, China; Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, Nanjing 210095, China.
authors.forename: Yanxiao
authors.initials: Y
authors.lastname: Li
authors.affiliation: Horticultural Department, Nanjing Agricultural University, Nanjing 210095, China; State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing 210095, China; Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, Nanjing 210095, China.
authors.forename: Shanwu
authors.initials: S
authors.lastname: Lv
authors.affiliation: Horticultural Department, Nanjing Agricultural University, Nanjing 210095, China; State Key Laboratory of Crop Genetics & Germplasm Enhancement, Nanjing 210095, China; Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agriculture, Nanjing 210095, China. Electronic address: hxl@njau.edu.cn.
authors.forename: Xilin
authors.initials: X
authors.lastname: Hou
authors.affiliation: Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China.
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Cui
mesh_terms: D001483:Base Sequence; D001937:Brassica / Q000235:genetics* / Q000821:virology*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D056726:Genetic Association Studies; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010935:Plant Diseases / Q000235:genetics* / Q000821:virology*; D018749:RNA, Plant / Q000737:chemistry / Q000235:genetics*; D017423:Sequence Analysis, RNA; D017806:Tymovirus / Q000276:immunology / Q000502:physiology*
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant
keywords: Cold; MiRNA; Non-heading Chinese cabbage; Turnip mosaic virus