title: Genome-wide identification of microRNAs associated with taproot development in radish (Raphanus sativus L.).
abstract: MicroRNAs (miRNAs) are small, endogenous, non-coding RNAs that play vital regulatory roles in plant growth and development. To identify the miRNAs associated with taproot development at the whole genome level, we sequenced five RNA libraries constructed from radish taproots at different developmental stages and generated a total of 148M clean reads. Using an integrative bioinformatics analysis, 494 known miRNAs belonging to 434 families and 220 putative novel miRNAs were identified. Combining the differential expression analysis and target prediction, we found that 77 miRNAs were potentially associated with taproot development. Target transcripts generated significant GO terms relating to cell proliferation, root development and hormone-mediated signaling. The KEGG analyses revealed that plant hormone signal transduction, zeatin biosynthesis, biosynthesis of secondary metabolites, cell cycle, MAPK signaling and p53 signaling were closely associated with taproot development. These findings will provide valuable information for further functional verification of miRNAs and their targets in radish taproot development.
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Beijing Research Station of Vegetable Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Beijing 100081, China.
authors.forename: Yuyan
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Beijing Research Station of Vegetable Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Beijing 100081, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Qiu
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Beijing Research Station of Vegetable Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Beijing 100081, China.
authors.forename: Xiaohui
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Beijing Research Station of Vegetable Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Beijing 100081, China.
authors.forename: Xiaohua
authors.initials: X
authors.lastname: Chen
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Beijing Research Station of Vegetable Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Beijing 100081, China.
authors.forename: Di
authors.initials: D
authors.lastname: Shen
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Beijing Research Station of Vegetable Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Beijing 100081, China.
authors.forename: Haiping
authors.initials: H
authors.lastname: Wang
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Beijing Research Station of Vegetable Crop Gene Resource and Germplasm Enhancement, Ministry of Agriculture, Beijing 100081, China. Electronic address: Lixx0612@163.com.
authors.forename: Xixiang
authors.initials: X
authors.lastname: Li
mesh_terms: D001483:Base Sequence; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000096:biosynthesis* / Q000235:genetics; D058977:Molecular Sequence Annotation; D018517:Plant Roots / Q000235:genetics / Q000254:growth & development; D031224:Raphanus / Q000235:genetics* / Q000254:growth & development; D017423:Sequence Analysis, RNA
chemical_list: D035683:MicroRNAs
keywords: MicroRNA; Raphanus sativus L; Taproot development