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

BMC Plant Biology

Research Article

Rohit N Shukla¹  Kiran G Bankar¹  Gopal Joshi²  Arun Jagannath²  Amar Kumar²  Shailendra Goel²  Priyanka Arora²  Manu Agarwal²  Vidhi Malik²  Ankur R Bhardwaj²  Bharti Kukreja²  Surekha Katiyar-Agarwal³  Ritu Pandey³ 

[1] Bionivid Technology [P] Ltd, 560043, Bangalore, India;Department of Botany, University of Delhi Main Campus, 110007, Delhi, India;Department of Plant Molecular Biology, University of Delhi South Campus, 110021, Delhi, India;

关键词: Brassica juncea;    Transcriptome;    High temperature stress;    Drought stress;    Differential gene expression;    Transcription factors;    Kinases;    Gene ontologies and pathways;   

DOI  :  10.1186/s12870-014-0405-1

 received in 2014-09-25, accepted in 2014-12-22,  发布年份 2015

来源: Springer

【 摘 要 】

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 elucidategenome-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.

【 授权许可】

Unknown   
© Bhardwaj et al.; licensee BioMed Central. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.