Light-Dependent Temporal Reprogramming of Alternative Splicing Dynamics Under Salt Stress in Sweet Potato (Ipomoea...

Soil salinity is a major constraint on crop productivity, and plants rely on multilayered regulatory mechanisms to adapt to stress. Alternative splicing (AS) enhances transcriptome plasticity, yet how light modulates AS under salt stress remains unclear. Here, we performed a transcriptome-wide analysis to investigate light-dependent AS dynamics in sweet potato under salt stress. Plant treatments were initiated during daytime (SD) and nighttime (SN) conditions, and samples were collected at five time points (0-8 h). Intron retention (IR) was the predominant AS type (~36-37%), followed by A3SS, A5SS, and exon skipping (SE). Notably, light enhanced both the magnitude and temporal dynamic of AS, with a pronounced early response (0-2 h) under SD, where differential AS (DAS) events were nearly doubled compared with SN. This early AS response was accompanied by an increased prevalence of IR events and upregulation of spliceosome-related genes, suggesting dynamic splicing regulation under light. Enrichment of the mRNA surveillance pathway further indicates that IR-derived transcripts may be subject to RNA quality control. Although enriched pathways were largely conserved between SD and SN, including spliceosome and mRNA surveillance, more DAS genes under SD indicate enhanced responsiveness of conserved regulatory networks. These findings demonstrate that light reshapes the temporal dynamics of AS under salt stress, primarily through IR and its coupling with RNA surveillance, providing new insights into post-transcriptional regulation in crop stress adaptation.