title: Transcriptome-wide analysis of chromium-stress responsive microRNAs to explore miRNA-mediated regulatory networks in radish (Raphanus sativus L.).
abstract: MicroRNAs (miRNAs) are small noncoding RNAs that play pivotal roles in plant growth, development and stress response. Chromium (Cr) is one of common environmental contaminants possessing potential health hazards to living organisms. To date, little is known about the regulatory roles of miRNAs in response to Cr stress in radish. To systematically identify Cr-responsive miRNAs and their targets in radish, two sRNA libraries derived from Cr-free (CK) and Cr-treated (Cr200) roots were constructed. With Solexa sequencing, 81 known and 72 novel miRNAs were identified, from which 54 known and 16 novel miRNAs were significantly differentially expressed under Cr stress. Several target genes for Cr-responsive miRNAs encode different transcription factor (TF) families, including SPLs, MYBs, ERFs and bZIPs, might regulate corresponding HM-related transcriptional processes in plants. Notably, a few key responsive enzymes or proteins, including HMA, YSL1 and ABC transporter protein were involved in Cr uptake and homeostasis process. Furthermore, the expression patterns of some Cr-responsive miRNAs and their targets were validated by RT-qPCR. This study represents the first characterization of Cr-responsive miRNAs and their targets in radish. The outcomes of this study could provide novel insights into miRNA-mediated regulatory mechanisms underlying plant response to Cr 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.
authors.forename: Wei
authors.initials: W
authors.lastname: Liu
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, 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, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R.China.
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.
authors.forename: Hong
authors.initials: H
authors.lastname: Shen
authors.affiliation: Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA.
authors.forename: Xianwen
authors.initials: X
authors.lastname: Zhu
authors.affiliation: College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, P.R.China.
authors.forename: Keyun
authors.initials: K
authors.lastname: Zhang
authors.affiliation: School of Earth and Environment, and The UWA's Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia.
authors.forename: Yinglong
authors.initials: Y
authors.lastname: Chen
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R.China.
authors.forename: Rugang
authors.initials: R
authors.lastname: Yu
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R.China.
authors.forename: Cecilia
authors.initials: C
authors.lastname: Limera
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P.R.China.
authors.forename: Liwang
authors.initials: L
authors.lastname: Liu
mesh_terms: D002857:Chromium / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics*; D058977:Molecular Sequence Annotation; D031224:Raphanus / Q000235:genetics* / Q000378:metabolism*; D015203:Reproducibility of Results; D013312:Stress, Physiological / Q000235:genetics*; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D002857:Chromium