Transcriptomic plasticity through alternative splicing shapes salt stress responses in Korean sorghum

Sorghum ( Sorghum bicolor L.) is a climate-resilient C4 crop that is widely cultivated in arid and saline-prone environments. Soil salinity is a major abiotic stress that adversely affects plant growth and productivity by inducing osmotic, ionic, and oxidative stress. Plants have evolved various molecular mechanisms to mitigate salt stress, including alternative splicing (AS), a post-transcriptional regulatory process that generates diverse transcript isoforms. Among AS event types, intron retention (IR) is the most prevalent in plants under abiotic stress conditions. In this study, we conducted a transcriptome analysis of three sorghum cultivars—Sodamchal, Nampungchal, and Hwanggeumchal—subjected to varying salt stress conditions over different time periods. Our findings revealed that intron retention accounted for more than 70% of AS events across all comparisons. Importantly, several of these intron retention events were associated with salt stress–responsive genes, which support the notion that intron retention may function as a regulatory mechanism contributing to salt stress tolerance. Notably, in Hwanggeumchal and Nampungchal, the trehalose-phosphate phosphatase 6 (TPP6) gene and ATP-binding cassette (ABC) transporter G family member 42 gene exhibited AS-mediated expression changes, suggesting a potential link in salt tolerance. Under normal conditions, IR led to the expression of alternative isoforms that do not increase trehalose levels or ABC transporter function, whereas salt stress promoted normal splicing, which restored the functional biosynthesis pathways of both trehalose and ABC transporter. Given the established roles of trehalose and ABC transporters in stabilizing cellular structures, mitigating osmotic stress, and maintaining ion homeostasis, our results suggest that AS-mediated regulation of these pathways contributes to sorghum’s adaptive response to salinity stress. These findings provide new insights into the molecular basis of sorghum’s salt tolerance and highlight the importance of AS as a regulatory mechanism for improving stress resilience in crops. • Alternative splicing responses to salt stress were profiled in three Korean sorghum cultivars. • Intron retention accounted for over 70% of alternative splicing events under salinity. • Salt-tolerant cultivars showed stress-induced restoration of functional transcript isoforms. • Trehalose and ABC transporter genes were regulated by alternative splicing under salt stress. • Alternative splicing contributes to cultivar-specific salt stress adaptation in sorghum.