Comparative Transcriptome Analysis Reveals Molecular Responses of Salinity Tolerance in Salt-Tolerant Indica Rice Landrace Korgut

The Goan region has the traditional rice cultivar Korgut that have the unique quality to tolerate highly saline waters. The present study explored the comparative transcriptomic profile of Korgut with a sensitive genotype IR64 along with morphophysiological and biochemical behavior under salinity stress. The RNA-seq analysis showed 383 genes were significantly expressed in salt stress. The percentage of downregulated genes was found to be higher (55.4%) than upregulated genes (44.6%). A total of 83 genes with their expression specific to Korgut under salt stress had also been identified. Gene Ontology analysis showed that the upregulated DEGs were enriched with terms, including signaling (GO:0023052), signal transducer activity (GO: 0004871), and catalytic complex (GO: 1,902,494). The downregulated genes under salt treatment showed significant biological processes that comprised of single-organism metabolic process (GO: 0044710), single-organism process (GO: 0044699), and lipid metabolic process (GO: 0006629). KEGG pathway analysis showed the differentially expressed genes were involved in metabolic and biosynthetic processes related to the production of secondary metabolites, DNA replication, repair machinery, and carbohydrate metabolism. We have also identified a MATH domain-containing protein 1-like (LOC107275276) highly expressed under salt stress possibly imparting salt tolerance in Korgut variety and with functions similar to novel OsMBTB32. Many transcription factors such as BHLH089-like (LOC9270770), bHLH137 (LOC4346166), MADS-box 32-like (LOC4324731), L10-interacting MYB domain-containing protein (LOC4345311), and GATA-12 (LOC4326175) were also significantly upregulated in Korgut suggesting their involvement in regulating expression of salt-responsive genes leading to salt tolerance. Further, the upregulation of calmodulin-binding protein 60 B (LOC4351085) under salt stress provides a piece of evidence about its dual role in pathogen response and mitigation of salt stress. Overall, our findings suggest that the salinity stress tolerance of Korgut may be due to the differential expression of a diverse set of genes influencing signal transduction, metabolic pathways, transcription factors, DNA replication and repair mechanisms.