Intron retention as a hub for splicing regulation in plant environmental adaptation and developmental programming.

Abstract

Alternative splicing (AS) greatly expands transcriptome and proteome diversity in eukaryotes. Intron retention (IR) is the predominant AS type in plants, with critical roles in environmental adaptation and developmental control. Long viewed as splicing noise, IR is now established as a precisely regulated mechanism that modulates RNA stability, translation, subcellular localization, and protein function. Here, we review recent advances in plant IR research, covering technical progress in accurate IR identification using long-read and single-cell sequencing, cis- and trans-regulatory mechanisms, epigenetic coupling with transcription, and signal integration pathways. We highlight key functions of IR in flowering time regulation and stress responses, including the IR-nonsense-mediated mRNA decay (NMD) axis, functional protein isoforms, and nuclear transcript reservoirs for rapid stress memory. Finally, we discuss unresolved questions and future directions toward single-cell spatiotemporal dynamics, phase separation, and synthetic IR modules for crop improvement. This review provides an integrated framework for understanding IR as a central regulatory hub in plant post-transcriptional control.