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. 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).