Comparative transcriptome profiling of rice colonized with beneficial endophyte,Piriformospora indica, under high salinity environment

The salinity stress tolerance in plants has been studied enormously, reflecting its agronomic relevance. Despite the extensive research, limited success has been achieved in relation to the plant tolerance mechanism. The beneficial interaction betweenPiriformospora indicaand rice could essentially improve the performance of the plant during salt stress. In this study, the transcriptomic data betweenP. indicatreated and untreated rice roots were compared under control and salt stress conditions. Overall, 661 salt-responsive differentially expressed genes (DEGs) were detected with 161 up- and 500 down-regulated genes in all comparison groups. Gene ontology analyses indicated the DEGs were mainly enriched in auxin-activated signaling pathway, water channel activity, integral component of plasma membrane, stress responses, and metabolic processes. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the DEGs were primarily related to Zeatin biosynthesis, Fatty acid elongation, Carotenoid biosynthesis, and Biosynthesis of secondary metabolites. Particularly, genes related to cell wall modifying enzymes (e.g. invertase/pectin methylesterase inhibitor protein and arabinogalactans), phytohormones (e.g. Auxin-responsive Aux/IAA gene family, ent-kaurene synthase, and 12-oxophytodienoate reductase) and receptor-like kinases (e.g. AGC kinase and receptor protein kinase) were induced inP. indicacolonized rice under salt stress condition. The differential expression of these genes implies that the coordination between hormonal crosstalk, signaling, and cell wall dynamics contributes to the higher growth and tolerance inP. indica-inoculated rice. Our results offer a valuable resource for future functional studies on salt-responsive genes that should improve the resilience and adaptation of rice against salt stress.