{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T13:15:04Z","timestamp":1790082904244,"version":"4.0.1"},"reference-count":49,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T00:00:00Z","timestamp":1790035200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T00:00:00Z","timestamp":1790035200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["JIPB"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Alternative polyadenylation (APA) generates mRNA isoforms with variable 3\u2032UTR lengths, yet its genetic basis and functional significance at the population level remain unexplored in plants. Here, we present the population\u2010level APA landscape and the APA quantitative trait loci (3\u2032aQTL) map in rice, through profiling of over 200 rice accessions under normal and salt\u2010stress conditions. We identified 19,938 and 22,251 APA events under normal and salt\u2010stress conditions, respectively, and demonstrate that salt stress globally induces 3\u2032UTR shortening via proximal polyA site selection, which can release miRNA\u2010mediated repression on stress\u2010response genes. We further mapped 1,634 and 1,809\n                    <jats:italic>cis<\/jats:italic>\n                    \u20103\u2032aQTLs under normal and salt\u2010stress conditions, respectively, which were markedly enriched in 3\u2032UTRs and transcription termination sites, in contrast to expression QTLs that were enriched in promoter regions. This APA genetic framework reveals a post\u2010transcriptional regulatory layer distinct from transcriptional control. Functional validation of two 3\u2032aQTL\u2010associated genes,\n                    <jats:italic>OsMyb21<\/jats:italic>\n                    and\n                    <jats:italic>OsRNS3<\/jats:italic>\n                    , through CRISPR knockout and 3\u2032UTR deletion confirmed their roles in salt tolerance via APA\u2010mediated regulation. Our findings provide a community resource for understanding post\u2010transcriptional regulation of stress responses and offer genetic targets for breeding salt\u2010tolerant rice varieties.\n                  <\/jats:p>","DOI":"10.1111\/jipb.70399","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T12:57:05Z","timestamp":1790081825000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Pan\u2010genomic analysis of alternative polyadenylation reveals a 3\u2032UTR remodeling regulatory layer controlling salt tolerance in rice"],"prefix":"10.1111","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4776-1942","authenticated-orcid":false,"given":"Chuanlin","family":"Shi","sequence":"first","affiliation":[{"name":"Ministry of Education Key Laboratory of Crop Physiology, Ecology and Genetic Breeding Jiangxi Agricultural University Nanchang 330045 China"},{"name":"Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen 518000 China"},{"name":"Yazhouwan Laboratory Sanya 572024 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3226-3505","authenticated-orcid":false,"given":"Wenli","family":"Zou","sequence":"additional","affiliation":[{"name":"School of Life Sciences Jiangxi Science &amp; Technology Normal University Nanchang 330013 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-5336-1946","authenticated-orcid":false,"given":"Yan","family":"Cui","sequence":"additional","affiliation":[{"name":"Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen 518000 China"},{"name":"Yazhouwan Laboratory Sanya 572024 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1286-7766","authenticated-orcid":false,"given":"Zhangqiang","family":"Wang","sequence":"additional","affiliation":[{"name":"Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen 518000 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-2247-5627","authenticated-orcid":false,"given":"Longbo","family":"Yang","sequence":"additional","affiliation":[{"name":"Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen 518000 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-4722-2504","authenticated-orcid":false,"given":"Zhikun","family":"Wu","sequence":"additional","affiliation":[{"name":"Ministry of Education Key Laboratory of Crop Physiology, Ecology and Genetic Breeding Jiangxi Agricultural University Nanchang 330045 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6744-2418","authenticated-orcid":false,"given":"Xianmeng","family":"Wang","sequence":"additional","affiliation":[{"name":"Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen 518000 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9366-6685","authenticated-orcid":false,"given":"Yiwang","family":"Zhu","sequence":"additional","affiliation":[{"name":"Fujian Provincial Key Laboratory of Agricultural Genetic Engineering, Biotechnology Research Institute Fujian Academy of Agricultural Sciences Fuzhou 350003 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-2525-4194","authenticated-orcid":false,"given":"Dandan","family":"Chen","sequence":"additional","affiliation":[{"name":"Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen 518000 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6876-3010","authenticated-orcid":false,"given":"Haohua","family":"He","sequence":"additional","affiliation":[{"name":"Ministry of Education Key Laboratory of Crop Physiology, Ecology and Genetic Breeding Jiangxi Agricultural University Nanchang 330045 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4844-9870","authenticated-orcid":false,"given":"Huiying","family":"He","sequence":"additional","affiliation":[{"name":"Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen 518000 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5640-3421","authenticated-orcid":false,"given":"Hua","family":"Wei","sequence":"additional","affiliation":[{"name":"Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen 518000 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4606-2800","authenticated-orcid":false,"given":"Lianguang","family":"Shang","sequence":"additional","affiliation":[{"name":"Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen 518000 China"},{"name":"Yazhouwan Laboratory Sanya 572024 China"},{"name":"National Center of Technology Innovation for Comprehensive Utilization of Saline\u2010Alkali Land Dongying 257000 China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0349-4937","authenticated-orcid":false,"given":"Qian","family":"Qian","sequence":"additional","affiliation":[{"name":"Yazhouwan Laboratory Sanya 572024 China"},{"name":"State Key Laboratory of Rice Biology, China National Rice Research Institute Hangzhou 310006 China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,22]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"crossref","first-page":"589","DOI":"10.3389\/fpls.2019.00589","article-title":"Root hair single cell type specific profiles of gene expression and alternative polyadenylation under cadmium stress","volume":"10","author":"Cao J.","year":"2019","journal-title":"Front. 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