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.

Unraveling the Root Proteome Changes and Its Relationship to Molecular Mechanism Underlying Salt Stress Response in Radish (Raphanus sativus L.)

“…In order to investigate whether the protein levels are correlated with the corresponding alterations in mRNA level, we firstly compared the proteomic data with our previous DGE data between CK vs. Na200 (Sun et al, 2016). According to the response of gene expression in protein level and mRNA level, the results could be classified into four groups: (1) both protein species and mRNAs showed a changed abundance (DAPS & DEGs; 102), including the same trends (56) and opposite direction (46); (2) protein species showed altered abundance without a change in mRNA level (DAPS & NDEGs; 308); (3) mRNAs expressed differentially without altered abundance in protein species (NDAPS & DEGs; 261), and (4) both mRNAs and proteins without altered levels (NDAPS & NDEGs; 1121) (Table S8; Figure S1).…”

“… LogFC a Refers to the fold change of differentially expressed miRNAs in radish under 200 mM NaCl for 48 h compared to control (0 mM NaCl, CK), and the formula follows as: Fold change = log 2 (Na200/CK) (Sun et al, 2016) . LogFC b Refers to the fold change of differentially expressed genes under same conditions (Sun et al, 2015) . LogFC c Refers to the fold change of differentially expressed proteins under same conditions in this study .…”

“…The results showed that, under hydroponic culture of two salt-stressed conditions (Na100 and Na 200), some mature leaves of radish individuals were rolling, chlorosis, and the root enlargement and shoot elongation were relatively restrained. The growth conditions and salt treatments of radish plants were performed based on the reported descriptions (Sun et al, 2016). Plants were collected after 48 h with three different treatments including an untreated control (CK) and two salt-stressed conditions (Na100 and Na 200).…”

“…Total RNA extraction and reverse-transcription quantitative PCR (RT-qPCR) analysis were carried out according to our previously described method (Sun et al, 2016). All the primer pairs used for RT-qPCR were designed using the Beacon Designer 7.0 and provided in Table S1.…”

Bacillus licheniformis SA03 Confers Increased Saline–Alkaline Tolerance in Chrysanthemum Plants by Induction of Abscisic Acid Accumulation

“…Then, the quality of integrity of RNA samples were analyzed using Agilent 2100 Bioanalyser (Agilent, United States). Total RNA from three independent plants in each group was used to construct two cDNA libraries in parallel using the Illumina TruSeq TM RNA-seq library prep kit (Illumina, United States) according to the method described by Sun et al (2016). The two cDNA libraries were sequenced using the Hiseq 2500 platform (Illumina, United States).…”