title: Transcriptome-based gene expression profiling identifies differentially expressed genes critical for salt stress response in radish (Raphanus sativus L.).
abstract: Transcriptome-based gene expression analysis identifies many critical salt-responsive genes in radish and facilitates further dissecting the molecular mechanism underlying salt stress response. Salt stress severely impacts plant growth and development. Radish, a moderately salt-sensitive vegetable crop, has been studied for decades towards the physiological and biochemical performances under salt stress. However, no systematic study on isolation and identification of genes involved in salt stress response has been performed in radish, and the molecular mechanism governing this process is still indistinct. Here, the RNA-Seq technique was applied to analyze the transcriptomic changes on radish roots treated with salt (200 mM NaCl) for 48 h in comparison with those cultured in normal condition. Totally 8709 differentially expressed genes (DEGs) including 3931 up- and 4778 down-regulated genes were identified. Functional annotation analysis indicated that many genes could be involved in several aspects of salt stress response including stress sensing and signal transduction, osmoregulation, ion homeostasis and ROS scavenging. The association analysis of salt-responsive genes and miRNAs exhibited that 36 miRNA-mRNA pairs had negative correlationship in expression trends. Reverse-transcription quantitative PCR (RT-qPCR) analysis revealed that the expression profiles of DEGs were in line with results from the RNA-Seq analysis. Furthermore, the putative model of DEGs and miRNA-mediated gene regulation was proposed to elucidate how radish sensed and responded to salt stress. This study represents the first comprehensive transcriptome-based gene expression profiling under salt stress in radish. The outcomes of this study could facilitate further dissecting the molecular mechanism underlying salt stress response and provide a valuable platform for further genetic improvement of salt tolerance in radish breeding programs.
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.|Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, People's Republic of China.
authors.forename: Xiaochuan
authors.initials: X
authors.lastname: Sun
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.|Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, People's Republic of 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, People's Republic of China.|Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, People's Republic of 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, People's Republic of China.
authors.forename: Xiaobo
authors.initials: X
authors.lastname: Luo
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: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
authors.forename: Karanja Benard
authors.initials: KB
authors.lastname: Kinuthia
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.|Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, People's Republic of China.
authors.forename: Shanshan
authors.initials: S
authors.lastname: Nie
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
authors.forename: Haiyang
authors.initials: H
authors.lastname: Feng
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
authors.forename: Chao
authors.initials: C
authors.lastname: Li
authors.affiliation: National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China. nauliulw@njau.edu.cn.|Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing, 210014, People's Republic of China. nauliulw@njau.edu.cn.
authors.forename: Liwang
authors.initials: L
authors.lastname: Liu
mesh_terms: D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D031224:Raphanus / Q000187:drug effects / Q000235:genetics*; D012965:Sodium Chloride / Q000494:pharmacology; D013312:Stress, Physiological / Q000235:genetics*; D059467:Transcriptome
chemical_list: D012965:Sodium Chloride
keywords: Differentially expressed gene (DEG); RNA-Seq; Raphanus sativus L.; Salt stress