Mining expressed sequence tags of rapeseed (Brassica napus L.) to predict the drought responsive regulatory network

Abstract

It is of great significance to understand the regulatory mechanisms by which plants deal with drought stress. Two EST libraries derived from rapeseed (Brassica napus) leaves in non-stressed and drought stress conditions were analyzed in order to obtain the transcriptomic landscape of drought-exposed B. napus plants, and also to identify and characterize significant drought responsive regulatory genes and microRNAs. The functional ontology analysis revealed a substantial shift in the B. napus transcriptome to govern cellular drought responsiveness via different stress-activated mechanisms. The activity of transcription factor and protein kinase modules generally increased in response to drought stress. The 26 regulatory genes consisting of 17 transcription factor genes, eight protein kinase genes and one protein phosphatase gene were identified showing significant alterations in their expressions in response to drought stress. We also found the six microRNAs which were differentially expressed during drought stress supporting the involvement of a posttranscriptional level of regulation for B. napus drought response. The drought responsive regulatory network shed light on the significance of some regulatory components involved in biosynthesis and signaling of various plant hormones (abscisic acid, auxin and brassinosteroids), ubiquitin proteasome system, and signaling through Reactive Oxygen Species (ROS). Our findings suggested a complex and multi-level regulatory system modulating response to drought stress in B. napus.

Molecular and systems approaches towards drought‐tolerant canola crops

“…The only study in canola to date identified five drought‐induced microRNAs and one drought‐repressed microRNA, with six transcription factors and a kinase as predicted targets (Shamloo‐Dashtpagerdi et al ., ). These predicted targets are involved in ABA biosynthesis, BR and auxin signaling, and transcription (Shamloo‐Dashtpagerdi et al ., ). Results from this study, together with conserved drought‐responsive microRNAs discovered in other species, form an initial inventory of microRNA candidates that could potentially be manipulated to improve drought tolerance in canola.…”

“…A recent study investigated drought‐responsive genes in B. juncea seedlings and observed that 132 transcription factors (40 induced and 92 repressed) and 452 kinases (42 induced and 410 repressed) were regulated by drought (Bhardwaj et al ., ). A similar observation was reported in an analysis of ESTs of B. napus under drought treatment (Shamloo‐Dashtpagerdi et al ., ). This study found that 17 transcription factors, eight protein kinases, and one protein phosphatase were drought‐regulated, including homologs of Arabidopsis protein phosphatase 2C ABI1 and the ABA biosynthesis gene ABA1 .…”

“…Small RNAs, especially microRNAs, have been identified in canola crops through sequence-based predictions and deep sequencing (Buhtz et al, 2008;Zhao et al, 2012;Shen et al, 2015). Some of the known canola microRNAs are developmentrelated and stress-responsive (Pant et al, 2009;K€ orbes et al, 2012;Zhou et al, 2012;Huang et al, 2013;Shamloo-Dashtpagerdi et al, 2015). However, at present there are relatively few canola microRNAs in the registry database (http://www.mirbase.org).…”

“…MicroRNAs particularly responsive to drought stress have been studied in several species, including rice (Jeong & Green, 2013), Arabidopsis (Liu et al, 2008), and Medicago truncatula (Wang et al, 2011d). The only study in canola to date identified five drought-induced microRNAs and one drought-repressed microRNA, with six transcription factors and a kinase as predicted targets (Shamloo-Dashtpagerdi et al, 2015). These predicted targets are involved in ABA biosynthesis, BR and auxin signaling, and transcription (Shamloo-Dashtpagerdi et al, 2015).…”

Untitled

“…This issue rises from the fact that stress response in plants is an extremely complicated process (Pessarakli 2011). Multiplicity of the gene families and the complex interactions between TFs and cis-elements on the promoters of target genes as well as cross-talk between TFs in response to stress indicate the complexity of signaling networks involved in plant stress responses (Seki et al 2003;Shamloo-Dashtpagerdi et al 2015;Tuberosa and Salvi 2006). Therefore, assigning the relations among TFs in response to drought stress will uncover the actual function of them facilitating improvement of drought tolerant crops.…”