Uncovering key salt-tolerant regulators through a combined eQTL and GWAS analysis using the super pan-genome in rice

Abstract For sessile plants, gene expression plays a pivotal role in responding to salinity stress by activating or suppressing specific genes. However, our knowledge of genetic variations governing gene expression in response to salt stress remains limited in natural germplasm. Through transcriptome analysis of the Global MiniCore Rice Collection consisting of a panel of 202 accessions, we identified 22 345 and 27 610 eQTLs associated with the expression of 7 787 and 9 361 eGenes under normal and salt stress conditions, respectively, leveraging the super pan-genome map. Notably, combined with GWAS, we swiftly pinpointed the potential candidate gene STG5, a major salt-tolerant locus known as qSTS5. Intriguingly, STG5 is required for maintaining Na+/K+ homeostasis by directly regulating the transcription of multiple members of the OsHKT gene family. Our study sheds light on how genetic variants influence the dynamic changes in gene expression responding to salinity stress and provides valuable resource for the mining of salt-tolerant genes in the future.