Gene expression profiling of drought-sensitive (ICC1882) and tolerant (ICC4958) chickpea genotypes

We generated the global transcriptome profile of the two chickpea genotypes under control and drought conditions. Approximately 12 million high-quality reads were obtained for each cultivar and different conditions using the Illumina platform. Reference-based assembly was generated for each cultivar and condition. Differentially expressed genes were identified between drought and control conditions for each cultivar. Overall design: We collected 27-day-old seedlings of the drought sensitive (ICC1882) and tolerant (ICC4958) chickpea genotypes under drought and control conditions. The RNA-seq libraries were prepared for sequencing using standard Illumina protocols and sequencing was performed on the Illumina HiSeq platform by a commercial sequencing service provider. The raw reads were filtered using NGSQC Toolkit (v2.3.3) at default parameters. Kabuli chickpea genome (v1.0) was indexed using bowtie (v2.3.3.1) and filtered reads were mapped against the chickpea genome using TopHat2 pipeline (v2.1.1) at default parameters. Reference-based transcriptome assembly was performed using cufflinks (v2.2.1), followed by cuffmerge. The FPKM for each transcript was calculated using cufflinks by fragments per kilobase of transcript per million mapped fragments. Differential gene expression (log2 fold change ± 1 and FDR = 0.05) analysis was performed using cufdiff (2.2.1).