Transcriptome-wide characterization of alternative splicing regulation in Najran wheat (Triticum aestivum) under salt stress

Abstract

The process of alternative splicing (AS) has emerged as a crucial mechanism in plant responses to environmental stresses, contributing to the enhancement of the required transcriptome and proteome complexity. Despite the importance of AS, there remains a paucity of studies on the regulatory implications of AS in the responses of wheat to salt stress. In the current study, transcriptome-wide changes in AS profiles were established in roots and shoots of Najran wheat treated with 200 mM NaCl. Salt stress induced AS events increasing the complexity of the transcriptome; out of all expressed genes in all samples, 32,268 genes (22.5% of expressed genes) in the roots and 31,941 genes (23.1% of expressed genes) in the shoots were subjected to AS with 3’ Alternative splice site (A3) being the most frequent AS event and mutually exclusive exon (MX) being the least common event. Moreover, the results revealed that salt stress modulates AS patterns in a tissue-specific way where 82% of AS events were differentially expressed in either root or shoot tissues, participating in organ differentiation. In Total, 423 Differential AS events associated with cytoskeletal-related categories such as microtubule-based processes, actin filament-based movements, and cytoskeletal motor activity were identified in the roots. In contrast, 393 Differential AS events associated with biological categories related to metabolic and signalling processes such as catabolic processes, and response to gibberellin were identified in the shoots. The results presented in this study enhance our understanding of salt tolerance mechanisms in wheat and provide promising insights for future functional investigations and crop improvement efforts.