Pan-genomic analysis of alternative polyadenylation reveals a 3'UTR remodeling regulatory layer controlling salt tolerance in rice.

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.