Sequence variations underlying contrasting salt responses between two indica rice varieties

ABSTRACT: Pokkali (POK), one of the most salt-resistant rice cultivars, has been widely used to dissect the molecular mechanisms underlying salt resistance and to identify novel genes for breeding salt-tolerant varieties. However, the genotype-specific, sequence-driven differential salt responses between POK and other rice varieties remains largely unexplored. To address this knowledge gap, we performed RNA-seq, genomic resequencing, and genetic validation in POK (salt-tolerant) and 93-11 (salt-sensitive) under salt stress conditions. We found that, compared with 93-11, POK possesses a greater capacity to alleviate salt-induced damage by restricting the accumulation of reactive oxygen species (ROS) and Na+, thereby enhancing salt tolerance. The two varieties displayed distinct sets of differentially expressed genes (DEGs) under salt stress, some of which may play pivotal roles in regulating salt responses and contribute to the divergent salt tolerance between the two varieties. Furthermore, we discovered that sequence variations can alter the expression or protein structure of a subset of genes. These alterations are mediated by sequence polymorphisms within cis-regulatory elements (CREs) and by TF-centered regulatory networks influenced by sequence variations, ultimately resulting in functional divergence in salt responses between the two varieties. Additionally, sequence variations act as key determinants in modulating differential transposable element (TE) activity, thereby influencing the differential expression of associated genes under salt stress. Collectively, our study provides evidence that sequence variations drive differential salt responses between POK and 93-11, and identifies several key genes as promising targets for genomic editing to breed salt-tolerant rice varieties.

ORGANISM(S): Oryza sativa

PROVIDER: GSE346554 | GEO | 2026/09/15

REPOSITORIES: GEO