Regulatory Network of Spinach Under Salt Stress: An Integrated Study of Long Non-coding RNAs and mRNAs

Long non-coding RNAs (lncRNAs) play a crucial role in regulating gene expression, particularly in response to abiotic stresses like salt stress. Despite recent advances, the identification and functional understanding of salt-related lncRNAs in spinach remain limited. Hence, this study aimed to comprehensively identify and characterize salt stress-related lncRNAs in spinach and uncover their molecular mechanisms in stress adaptation. Using transcriptome datasets from two spinach varieties with contrasting salt tolerance, we identified 2,325 lncRNAs, including 385 differentially expressed ones. Among these, several lncRNAs, such as MSTRG.42699.1, MSTRG.27050.1, and MSTRG.28885.1, were linked to critical salt stress-responsive genes like Glutathione peroxidase (GPX), Bidirectional sugar transporter (BST), and Cysteine synthase (CYS), respectively. Functional enrichment analysis further revealed that these lncRNAs were associated with essential metabolic processes and stress response pathways, highlighting their potential roles in salt stress adaptation. Notably, lncRNAs like MSTRG.35604.1 and MSTRG.38429.1 were linked to Abscisic stress-ripening protein 1 (ASR1) and K(+) efflux antiporter 2 (KEA2), underscoring their involvement in stress tolerance mechanisms. The study also uncovered ten distinct co-expression modules of coding genes and lncRNAs through Weighted Gene Co-expression Network Analysis (WGCNA), providing insights into their regulatory networks. This research not only advances our understanding of lncRNAs in spinach but also offers valuable genetic resources for enhancing salt stress tolerance in crops, potentially informing future crop improvement strategies.