Exploring transcription factors reveals crucial members and regulatory networks involved in different abiotic stresses in Brassica napus L.

Abstract

BackgroundBrassica napus (B. napus) encompasses diverse transcription factors (TFs), but thorough identification and characterization of TF families, as well as their transcriptional responsiveness to multifarious stresses are still not clear.ResultsTotally 2167 TFs belonging to five families were genome-widely identified in B. napus, including 518 BnAP2/EREBPs, 252 BnbZIPs, 721 BnMYBs, 398 BnNACs and 278 BnWRKYs, which contained some novel members in comparison with existing results. Sub-genome distributions of BnAP2/EREBPs and BnMYBs indicated that the two families might have suffered from duplication and divergence during evolution. Synteny analysis revealed strong co-linearity between B. napus and its two ancestors, although chromosomal rearrangements have occurred and 85 TFs were lost. About 7.6% and 9.4% TFs of the five families in B. napus were novel genes and conserved genes, which both showed preference on the C sub-genome. RNA-Seq revealed that more than 80% TFs were abiotic stress inducible and 315 crucial differentially expressed genes (DEGs) were screened out. Network analysis revealed that the 315 DEGs are highly co-expressed. The homologous gene network in A. thaliana revealed that a considerable amount of TFs could trigger the differential expression of targeted genes, resulting in a complex clustered network with clusters of genes responsible for targeted stress responsiveness.ConclusionsWe identified and characterized five TF families in B. napus. Some crucial members and regulatory networks involved in different abiotic stresses have been explored. The investigations deepen our understanding of TFs for stress tolerance in B. napus.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1417-z) contains supplementary material, which is available to authorized users.

Comparative Transcriptome Analysis of Two Aegilops tauschii with Contrasting Drought Tolerance by RNA-Seq

“…Wild relatives may provide new gene resources for improving drought tolerance of crops. RNA-seq is a useful approach for the identification of DEGs in a regulatory network at the transcriptome level, which provides insights into the molecular mechanisms in response to abiotic stresses [32]. Through the transcriptomic analysis of the maize seedling leaves under salinity, drought, heat, and cold stresses, the responses were found to be mediated by pathways involving hormone metabolism and signaling, transcription factors (TFs), very-long-chain fatty acid biosynthesis and lipid signaling [33].…”

Transcriptional analyses reveal the molecular mechanism governing shade tolerance in the invasive plant Solidago canadensis

“…To adapt to adverse environmental conditions, many plants have developed different mechanisms in response to abiotic stresses. Most transcription factors (TFs) can act as regulatory proteins that play an important role in these mechanisms (Wang, Yang, et al, 2018). For example, the TIFY family is a novel plant‐specific gene family that participates in the regulation of various plant‐specific biologic processes (Sun et al, 2017).…”

Transcriptome analysis reveals key genes involved in the regulation of nicotine biosynthesis at early time points after topping in tobacco (Nicotiana tabacum L.)

“…We selected one of seven genes in the bHLH family (Nitab4.5_0000093g0110) for study using RNAi, finding the resultant plant showed an altered nicotine level (unpublished data), and implying an important regulatory role in nicotine biosynthesis. Other newly identified AP2/ EREBP, bHLH, WRKY, ARF, MYB, and NAC TF genes might also be involved in nicotine biosynthesis, since all of these TF families have been described as functioning in the regulation of plant secondary metabolism [45][46][47]. These are therefore good targets for further experiments.…”