DNA methylation in response to drought stress in chickpea (Cicer arietinum L.)

In this study, we performed whole genome bisulphite sequencing (WGBS) and RNA-Seq of root tissue samples obtained from two "desi" chickpea genotypes contrasting for drought tolerance, namely ICC 4958 (drought tolerant, DT) and ICC 1882 (drought sensitive, DS). For both genotypes, drought stress was imposed by withholding water for 50 days. These set of plants were designated as drought stress treated plants while the control plants were well watered throughout the experimental period. For WGBS, 8 libraries were generated (2 genotypes x 2 treatments x 2 biological replicates) and an average of 100 million paired-end reads were obtained for each sample. The FASTQ files were pre-processed to remove low quality reads and adapter sequences. The reads were mapped onto the reference genome (RefSeq assembly accession: GCF_000331145.1) using Bismark and differentially methylated regions (DMRs) for the three different sequence contexts (CG, CHG and CHH) were identified using Methylkit. For RNA-Seq analysis, 12 libraries (2 genotypes x 2 treatments x 3 biological replicates) were generated with an average of 22 million reads per sample. The reads were mapped onto the reference genome (same as above) using bwa mem algorithm after quality check. Differential gene expression analysis was done using DESeq (version 1)