Low temperature-induced profiling of transcription and alternative splicing during seed germination in rice

Low-temperature germination (LTG) is a critical agronomic trait for direct-seeded rice as it ensures uniform seedling establishment. Alternative splicing (AS), a key post-transcriptional mechanism, plays a crucial role in plant responses to abiotic stresses; however, the specific AS events and mechanisms involved in LTG remain poorly understood.

In this study, we conducted RNA-Seq to profile the cold stress response in germinating seeds, and identified 12,558 differentially expressed genes (DEGs) in ZH11 seeds after 24 h of low‑temperature treatment during germination. GO annotation showed enrichment in genes associated with circadian rhythm, MAPK and plant hormone signaling, and metabolic processes including nitrogen metabolism. We also detected 12,494 cold-induced differential alternative splicing (DAS) events across 4,812 genes, primarily exon skipping (SE) and intron retention (RI). Cold-induced DAS genes were associated with lipid metabolism and terpenoid biosynthesis implying functions in metabolic adjustment and stress adaptation under cold stress. Furthermore, we identified several potential key regulators of LTG: genes OsCKLP2 and OsSTPK encoding protein kinase, OsPP2C11 encoding protein phosphatase, and transcription factors OsbHLH034, OsKNA2 and OsEREBP26.

This study indicates that alternative splicing is involved in rice germination under cold stress. The findings not only advance the theoretical understanding of AS in LTG but also provide valuable genetic resources for breeding cold-tolerant rice.