Genome-wide mapping of DNase I hypersensitive sites revealed differential chromatin accessibility in rice cultivars
In this study, we employed DNase I hypersensitive assays followed by sequencing to identify the accessible chromatin regions under drought stress in a drought-sensitive and a drought-tolerant rice cultivar. The raw reads from all the samples were processed to remove adaptors and low-quality reads using NGS QC toolkit  with default parameters. The filtered reads of each sample were mapped to the Nipponbare rice reference genome using BWA-MEM at default parameters. The mapped reads from DNase I digested samples were compared against their respective input control for the identification of DHSs by using MACS3 . The DHSs with at least two fold-change were considered as true positives. Further, the consensus DHSs between the biological replicates were identified using a Bioconductor package, Irreproducible Discovery Rate at default parameters and subsequently used for downstream analyses. Next, we identified differential DHSs between the two rice cultivars under control condition and within the rice cultivar under drought stress. The differential DHSs with at least two fold-change were considered to be significant and used for downstream analyses. The annotation to DHSs was assigned using gff file, such as promoter, transcription start site, exon, intron, transcription termination site and intergenic regions.