{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T17:56:40Z","timestamp":1790618200059,"version":"4.1.0"},"reference-count":74,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["advanced.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Advanced Genetics"],"published-print":{"date-parts":[[2026,9]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>Plant pan\u2010genomics is entering a new phase beyond genome variation discovery, requiring a shift from cataloguing genomic diversity toward understanding how variation generates biological function and breeding value. Here, we propose that the future of plant pan\u2010genomics will be shaped by three conceptual transitions. First, structural variation (SV), presence\u2013absence variation (PAV), and haplotype diversity should be interpreted not merely as genomic differences, but as regulatory components that influence gene networks, chromatin organization, and complex traits. Second, the expansion from species\u2010level pan\u2010genomes to genus\u2010level super pan\u2010genomes provides an evolutionary framework for uncovering adaptive genetic modules preserved in wild relatives and overlooked during domestication. Third, integrating pan\u2010genomes with pan\u2010omics, three\u2010dimensional genome analyses, and artificial intelligence will enable the transformation of genomic variation into predictive models for crop improvement. We further propose that the ultimate value of pan\u2010genomes lies not in generating increasingly complete genome collections, but in establishing a mechanistic bridge between genome diversity, biological function, and breeding decisions. This transition will move crop improvement from empirical selection toward rational genome design, where evolutionary diversity can be systematically interpreted, predicted, and engineered.<\/jats:p>","DOI":"10.1002\/ggn2.70044","type":"journal-article","created":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T04:31:11Z","timestamp":1788323471000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The Rise of Plant Pan\u2010Genomes: From Genome Variation to Predictive Breeding"],"prefix":"10.1002","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-6164-4132","authenticated-orcid":false,"given":"Dan","family":"Peng","sequence":"first","affiliation":[{"name":"State Key Laboratory of Tropical Crop Breeding Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture Key Laboratory of Synthetic Biology Ministry of Agriculture and Rural Affairs Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences  Shenzhen China"},{"name":"School of Ecology Hainan University  Haikou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4599-5809","authenticated-orcid":false,"given":"Xuezhu","family":"Liao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Tropical Crop Breeding Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture Key Laboratory of Synthetic Biology Ministry of Agriculture and Rural Affairs Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences  Shenzhen China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liang","family":"Tang","sequence":"additional","affiliation":[{"name":"School of Ecology Hainan University  Haikou China"},{"name":"International Joint Center For Terrestrial Biodiversity Around South China Sea of Hainan Province School of Ecology Hainan University  Haikou 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