Abstract: Alternative polyadenylation (APA) generates mRNA isoforms with variable 3′UTR lengths, yet its genetic basis and functional significance at the population level remain unexplored in plants. Here, we present the population-level APA landscape and the APA quantitative trait loci (3′aQTL) map in rice, through profiling of over 200 rice accessions under normal and salt-stress conditions. We identified 19,938 and 22,251 APA events under normal and salt-stress conditions, respectively, and demonstrate that salt stress globally induces 3′UTR shortening via proximal polyA site selection, which can release miRNA-mediated repression on stress-response genes. We further mapped 1,634 and 1,809 cis-3′aQTLs under normal and salt-stress conditions, respectively, which were markedly enriched in 3′UTRs and transcription termination sites, in contrast to expression QTLs that were enriched in promoter regions. This APA genetic framework reveals a post-transcriptional regulatory layer distinct from transcriptional control. Functional validation of two 3′aQTL-associated genes, OsMyb21 and OsRNS3, through CRISPR knockout and 3′UTR deletion confirmed their roles in salt tolerance via APA-mediated regulation. Our findings provide a community resource for understanding post-transcriptional regulation of stress responses and offer genetic targets for breeding salt-tolerant rice varieties.

Key words: 3′ untranslated region (3′UTR), alternative poly-adenylation, pan-genome, rice, salt tolerance