Gene expression profiling of drought tolerant and sensitive Brassica rapa accessions under control and osmotic stress conditions

In this study genome-wide gene expression profiling was used to analyze mechanisms of drought tolerance in Brassica rapa. Using an Illumina Mi-Seq platform we sequenced RNA from shoot tissues of drought tolerant and drought sensitive B. rapa genotypes in control conditions and after application of osmotic stress. Differentially expressed genes between the different conditions and genotypes were used to identify drought relevant gene networks. Overall design: Two accessions of Brassica rapa with previously-identified contrasting drought responses were exposed to osmotic stress in a hydroponic growth system. Polyethylene glycol (PEG) simulated osmotic stress applied to half of the plants of each accession when plants had 4-5 true leaves while the other half remained with Murashige and Skoog (MS) medium as control for PEG. Total RNA isolated from shoot tissue was used for RNA-sequencing. For each genotype and condition three biological replicates were taken at 4h, 8h and 12h after stress treatment. cDNA libraries were prepared with the TruSeq Stranded Total RNA with Ribo-ZeroTM Plant kit from Illumina. Sequencing was carried out on each library to generate 150 bp PE reads using an Illumina Mi-Seq platform. The transcriptome reads were mapped to the B. rapa cv. Chiifu reference genome v1.5 (Wang et al., 2011) allowing 3 mismatches, then normalised and quantified as FPKM values using the spliced aligner TopHat/Cufflinks (http://ccb.jhu.edu/software/tophat/index.shtml,http://cole-trapnell-lab.github.io/cufflinks/).