Alternative splicing of transcripts under salt stress condition in aromatic rice cultivars

Salt tolerance in plants, particularly in rice, is a complex quantitative trait influenced by multiple genes. Rice, classified as a salt-susceptible cereal, especially at its young stage, faces yield limitations due to salinity stress. Among rice varieties, aromatic indica rice is particularly susceptible to salt stress, leading to reduced yields. To understand the genetic mechanisms underlying salt tolerance, RNA-seq has emerged as a powerful tool due to its high accuracy and sensitivity. RNA-seq enables the comprehensive study of the entire transcriptome, identification of alternative splicing events, novel genes or transcripts, and gene expression at the isoform level. Alternative splicing (AS) of pre-mRNAs in plants is a crucial mechanism regulating gene expression under abiotic stress, enhancing transcriptomic plasticity and proteomic diversity. However, the specific AS patterns and genes involved in salt-stressed aromatic rice cultivars remain unknown. This study aims to compare AS patterns between aromatic non-basmati (Ambemohar-157) and basmati (Basmati-370) rice cultivars under salt stress, revealing divergent AS patterns in biological pathways and identifying potential candidates for enhancing rice tolerance to salinity. This study reveals that aromatic basmati and non-basmati rice cultivars exhibit alternative splicing (AS) under salt stress, impacting key metabolic pathways including DNA repair, lipid metabolism, and carbohydrate metabolism. Despite AS not always altering transcript abundance, it plays a crucial role in enabling plants to withstand salt stress. These findings offer insights into enhancing salt tolerance, improving plant quality, and guiding future research endeavours.