Global insights into high temperature and drought stress regulated genes by RNA-Seq in economically important oilseed crop Brassica juncea

Abstract

BackgroundBrassica juncea var. Varuna is an economically important oilseed crop of family Brassicaceae which is vulnerable to abiotic stresses at specific stages in its life cycle. Till date no attempts have been made to elucidate genome-wide changes in its transcriptome against high temperature or drought stress. To gain global insights into genes, transcription factors and kinases regulated by these stresses and to explore information on coding transcripts that are associated with traits of agronomic importance, we utilized a combinatorial approach of next generation sequencing and de-novo assembly to discover B. juncea transcriptome associated with high temperature and drought stresses.ResultsWe constructed and sequenced three transcriptome libraries namely Brassica control (BC), Brassica high temperature stress (BHS) and Brassica drought stress (BDS). More than 180 million purity filtered reads were generated which were processed through quality parameters and high quality reads were assembled de-novo using SOAPdenovo assembler. A total of 77750 unique transcripts were identified out of which 69,245 (89%) were annotated with high confidence. We established a subset of 19110 transcripts, which were differentially regulated by either high temperature and/or drought stress. Furthermore, 886 and 2834 transcripts that code for transcription factors and kinases, respectively, were also identified. Many of these were responsive to high temperature, drought or both stresses. Maximum number of up-regulated transcription factors in high temperature and drought stress belonged to heat shock factors (HSFs) and dehydration responsive element-binding (DREB) families, respectively. We also identified 239 metabolic pathways, which were perturbed during high temperature and drought treatments. Analysis of gene ontologies associated with differentially regulated genes forecasted their involvement in diverse biological processes.ConclusionsOur study provides first comprehensive discovery of B. juncea transcriptome under high temperature and drought stress conditions. Transcriptome resource generated in this study will enhance our understanding on the molecular mechanisms involved in defining the response of B. juncea against two important abiotic stresses. Furthermore this information would benefit designing of efficient crop improvement strategies for tolerance against conditions of high temperature regimes and water scarcity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0405-1) contains supplementary material, which is available to authorized users.

Development of PR genes panel for screening aphid-tolerant cultivars in Brassica juncea

“…All the primers used in the study for the development of PR genes panel were selected from the works of Taj et al (2011), Bhardwaj et al (2015 and Sun et al (2012) (Table 1). Primer sequences of all the genes used in the panel development study are furnished in Table 2.…”

“…Heat map graphically displays the results by hierarchical clustering. Distances Mediates cross talk between JA signaling and auxin biosynthesis to regulate lateral root formation Sun et al (2012) 14 HSFA7A1 Heat shock factor A7A1 Highly expressed during high temperature stress conditions Bhardwaj et al (2015) 15 ACT3 Actin Ubiquitous component of plant cytoskeleton. Involved in cell division, plane localization, cell elongation and cell shape determination Sun et al (2012) between samples and assays are calculated for hierarchical clustering based on the DCT values using pearson's correlation distance.…”

“…The study suggested that the induction of JA biosynthesis required MAPK3 activation and pointed out that interactions of MAPK3 genes with LOX and its proposed role in biosynthesis of JA/JA induced the expression of defense genes in mustard. Bhardwaj et al (2015) carried out a transcriptomic study in Brassica juncea cultivar Varuna to detect genome-wide changes in its transcriptome against high temperature or drought stress. The study revealed that the maximum number of upregulated transcription factors in high temperature and drought stress belonged to heat shock factors (HSFs) and dehydration-responsive element-binding (DREB) families, respectively.…”

Expression of Heat Shock Proteins by Heat Stress in Soybean

“…Because of the low cost and high capacity of data, RNA-sequencing (RNA-seq) has been using to measuring differentially expressed genes (DEGs) in response to stress (Marioni et al 2008;Wang et al 2009;Anders and Huber 2010;Rapaport et al 2013). It was also used to reveal differential expressed transcriptome in rice under cold conditions (Shen et al 2014), HD-Zip transcription factors in soybean under salt stress (Belamkar et al 2014) and regulated genes in Brassica juncea under drought stress and high temperature (Bhardwaj et al 2015).…”

RNA sequencing as a tool for understanding biological complexity of abiotic stress in plants

“…Enquiry into genome-wide differential RNA expression under varying environments may yield intuitions into biological corridors, complexity and molecular mechanisms that police activity of genes involved in adaptation to abiotic stresses (Bhardwaj et al 2015, Van Verk et al 2013, Voytas 2013Dolgin (2015). The technology may be used for detecting cellular pathway alterations and differential gene expression during abiotic stresses.…”