title: De novo sequencing of root transcriptome reveals complex cadmium-responsive regulatory networks in radish (Raphanus sativus L.).
abstract: Cadmium (Cd) is a nonessential metallic trace element that poses potential chronic toxicity to living organisms. To date, little is known about the Cd-responsive regulatory network in root vegetable crops including radish. In this study, 31,015 unigenes representing 66,552 assembled unique transcripts were isolated from radish root under Cd stress based on de novo transcriptome assembly. In all, 1496 differentially expressed genes (DEGs) consisted of 3579 transcripts were identified from Cd-free (CK) and Cd-treated (Cd200) libraries. Gene Ontology and pathway enrichment analysis indicated that the up- and down-regulated DEGs were predominately involved in glucosinolate biosynthesis as well as cysteine and methionine-related pathways, respectively. RT-qPCR showed that the expression profiles of DEGs were in consistent with results from RNA-Seq analysis. Several candidate genes encoding phytochelatin synthase (PCS), metallothioneins (MTs), glutathione (GSH), zinc iron permease (ZIPs) and ABC transporter were responsible for Cd uptake, accumulation, translocation and detoxification in radish. The schematic model of DEGs and microRNAs-involved in Cd-responsive regulatory network was proposed. This study represents a first comprehensive transcriptome-based characterization of Cd-responsive DEGs in radish. These results could provide fundamental insight into complex Cd-responsive regulatory networks and facilitate further genetic manipulation of Cd accumulation in root vegetable crops.
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR 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, PR 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, PR China.
authors.forename: Wei
authors.initials: W
authors.lastname: Liu
authors.affiliation: College of Life Science, Nanjing Agricultural University, Nanjing 210095, PR China.
authors.forename: Jin
authors.initials: J
authors.lastname: Wang
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 Science, Nanjing Agricultural University, Nanjing 210095, PR China.
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, PR 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, PR China.
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, PR China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Xie
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China.
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, PR China. Electronic address: nauliulw@njau.edu.cn.
authors.forename: Liwang
authors.initials: L
authors.lastname: Liu
mesh_terms: D002104:Cadmium / Q000378:metabolism*; D004785:Environmental Pollutants / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D018517:Plant Roots / Q000378:metabolism; D031224:Raphanus / Q000235:genetics / Q000502:physiology*; D060888:Real-Time Polymerase Chain Reaction; D013312:Stress, Physiological; D059467:Transcriptome
chemical_list: D004785:Environmental Pollutants; D002104:Cadmium
keywords: Cadmium (Cd) stress; Differentially expressed gene (DEG); Gene expression profile; Raphanus sativus; Transcriptome; microRNAs