Gene expression profiling during salinity stress response in chickpea (RNA-Seq)

In this study, we performed transcriptomic analysis salinity stress response in salinity sensitive and tolerant genotypes of chickpea using Illumina platform. A total of 87 million reads in RNA-sequencing data were generated in all the samples. Mapping of the reads to the Kabuli genome was performed using tophat (v2.1.1). Differentially expressed genes were identified using cufflilnks-cuffdiff (2.2.1) pipeline. Overall design: Total RNA was extracted and cDNA libraries were prepared from salinity sensitive (ICCV2) and salinity tolerant (JG62) genotypes under salinity stress and control conditions from 17 day old seedlings. RNA-sequencing was performed on Illumina platform to generate 49 bp single-end reads. Pre-processing was performed using NGS QC Toolkit to remove adapters and low-quality reads below 20 Phred score. Filtered high-quality reads were mapped on the Kabuli chickpea genome using TopHat2 (v2.1.1). To analyze gene expression, reference-guided assembly was generated using Cufflinks (v2.2.1) and differential expression of genes was determined by Cuffdiff (v2.2.1).