Genome‐wide discovery of genetic variations between rice cultivars with contrasting drought stress response and their potential functional relevance

Abstract

AbstractDrought stress is a serious threat to rice productivity. Investigating genetic variations between drought‐tolerant (DT) and drought‐sensitive (DS) rice cultivars may decipher the candidate genes/regulatory regions involved in drought stress tolerance/response. In this study, whole‐genome resequencing data of four DS and five DT rice cultivars were analyzed. We identified a total of approximately 4.8 million single nucleotide polymorphisms (SNPs) and 0.54 million insertions/deletions (InDels). The genetic variations (162,638 SNPs and 17,217 InDels) differentiating DS and DT rice cultivars were found to be unevenly distributed throughout the rice genome; however, they were more frequent near the transcription start and stop sites than in the genic regions. The cis‐regulatory motifs representing the binding sites of stress‐related transcription factors (MYB, HB, bZIP, ERF, ARR, and AREB) harboring the SNPs/InDels in the promoter regions of a few differentially expressed genes (DEGs) were identified. Importantly, many of these DEGs were located within the drought‐associated quantitative trait loci. Overall, this study provides a valuable large‐scale genotyping resource and facilitates the discovery of candidate genes associated with drought stress tolerance in rice.