Transcriptome-based gene profiling provides novel insights into the characteristics of radish root response to Cr stress with next-generation sequencing

Abstract

Radish (Raphanus sativus L.) is an important worldwide root vegetable crop with high nutrient values and is adversely affected by non-essential heavy metals including chromium (Cr). Little is known about the molecular mechanism underlying Cr stress response in radish. In this study, RNA-Seq technique was employed to identify differentially expressed genes (DEGs) under Cr stress. Based on de novo transcriptome assembly, there were 30,676 unigenes representing 60,881 transcripts isolated from radish root under Cr stress. Differential gene analysis revealed that 2985 uingenes were significantly differentially expressed between Cr-free (CK) and Cr-treated (Cr600) libraries, among which 1424 were up-regulated and 1561 down-regulated. Gene ontology (GO) analysis revealed that these DEGs were mainly involved in primary metabolic process, response to abiotic stimulus, cellular metabolic process and small molecule metabolic process. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis showed that the DEGs were mainly involved in protein processing in endoplasmic reticulum, starch and sucrose metabolism, amino acid metabolism, glutathione metabolism, drug and xenobiotics by cytochrome P450 metabolism. RT-qPCR analysis showed that the expression patterns of 12 randomly selected DEGs were highly accordant with the results from RNA-seq. Furthermore, many candidate genes including signaling protein kinases, transcription factors and metal transporters, chelate compound biosynthesis and antioxidant system, were involved in defense and detoxification mechanisms of Cr stress response regulatory networks. These results would provide novel insight into molecular mechanism underlying plant responsiveness to Cr stress and facilitate further genetic manipulation on Cr uptake and accumulation in radish.

Genome-wide characterization and evolutionary analysis of heat stress transcription factors (HSFs) to reveal their potential role under abiotic stresses in radish (Raphanus sativus L.)

“…In this study, RsHSF genes were significantly differentially expressed in response to [65]. Moreover, four radish HSF genes were up-regulated under Cr stress in radish [66]. Taken together, several RsHSF genes were differentially expressed upon abiotic stresses including heat, salt or heavy metal stress, and these results indicate that they might be involved in the plant response to abiotic stresses.…”

Functional and Integrative Analysis of the Proteomic Profile of Radish Root under Pb Exposure

“…Increasing evidences have revealed that proteomic studies are playing important roles in the post-genomic era for characterizing the molecular mechanisms underlying plant responses to HM stresses (Fukao et al, 2011; Wang et al, 2013, 2014; Sebastiani et al, 2014). Radish is an important root vegetables worldwide, which has been considered as one of the most significant root species for dissecting the molecular regulatory network of HM stress in Brassicaceae crops (Xu et al, 2012; Wang et al, 2014, 2015a; Liu et al, 2015; Xie et al, 2015). In the current study, comparative proteomics analysis by iTRAQ together with other-omics techniques reveals complex regulatory network and provides insights into the response of radish root under Pb exposure.…”

Genome- and Transcriptome-Wide Characterization of bZIP Gene Family Identifies Potential Members Involved in Abiotic Stress Response and Anthocyanin Biosynthesis in Radish (Raphanus sativus L.)

“…The expression patterns from RT-qPCR indicated a general agreement with those from the RNA-seq results (Figure 6b-f, Figure S3). The expression patterns of RsbZIP genes under Cd, Cr, Pb, heat and salt stresses were investigated in radish according to previously root transcriptome data [19][20][21][22][23]. As shown in Figure 6a, a total of 76, 77, 38, 43 and 46 RsbZIP genes were differentially expressed under Cd, Cr, Pb, heat and salt stresses (the absolute value of Fold change > 1, p-value < 0.05), respectively.…”

“…Heatmap of RsbZIP gene expression profile was generated by TBtools software (https://github.com/CJ-Chen/TBtools). Expression patterns of RsbZIP genes under Cd, Cr, Pb, heat and salt stresses were extracted from transcriptome data of radish taproot [19][20][21][22][23].…”

“…Radish (Raphanus sativus L.), belonging to the Brassicaceae family, is a major root vegetable crop with plenty of nutrition, and its taproot is an edible and stable food supplying a great source of phytochemicals such as anthocyanins [16,17]. Owning to the rapidly changeable climate and environment, radish growth and production are often severely limited by various abiotic stresses such as high temperature, salinity or metal pollution [18][19][20][21][22][23]. Although some bZIP TFs have been proven to be associated with different abiotic stress responses in many plant species, little information on the characterization of bZIP family is available in radish.…”