{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T04:55:19Z","timestamp":1790571319380,"version":"4.1.0"},"reference-count":59,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T00:00:00Z","timestamp":1788739200000},"content-version":"vor","delay-in-days":6,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/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"}],"funder":[{"DOI":"10.13039\/501100017590","name":"Hubei University of Science and Technology","doi-asserted-by":"publisher","award":["No.BK202503"],"award-info":[{"award-number":["No.BK202503"]}],"id":[{"id":"10.13039\/501100017590","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["No.32401647"],"award-info":[{"award-number":["No.32401647"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["acsess.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["The Plant Genome"],"published-print":{"date-parts":[[2026,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Sweet osmanthus (\n                    <jats:italic>Osmanthus fragrans<\/jats:italic>\n                    ), a traditional ornamental plant in China, exhibits substantial variation in autumn flowering time, which significantly affects landscape application and cultivation efficiency. Here, we performed a genome\u2010wide association study on 127 resequenced accessions classified into early, intermediate, and late flowering types, using a set of 2,325,410 single\u2010nucleotide polymorphisms (SNPs) and 246,824 structural variants (SVs). By integrating SNP\/insertion and deletion (Indel) and SV data with weighted gene co\u2010expression network analysis, machine learning, and genomic prediction, we dissected the genetic architecture of flowering time. We identified 24 associated SNP\/Indels and six SVs, mapping to 30 candidate genes, including known flowering regulators\n                    <jats:italic>FLK<\/jats:italic>\n                    ,\n                    <jats:italic>LOS1<\/jats:italic>\n                    ,\n                    <jats:italic>Y14<\/jats:italic>\n                    ,\n                    <jats:italic>MIF2<\/jats:italic>\n                    , and\n                    <jats:italic>GID1B<\/jats:italic>\n                    . These genes showed tissue\u2010specific expression, with some responding to low temperature. The two hub genes,\n                    <jats:italic>GUX1<\/jats:italic>\n                    and\n                    <jats:italic>LYG027904<\/jats:italic>\n                    , were located within modules of the co\u2010expression network associated with low\u2010temperature treatment. Haplotype analysis revealed a specific three\u2010SNP haplotype associated with late flowering and linked to\n                    <jats:italic>LOS1<\/jats:italic>\n                    , and epistatic interactions among combined genotypes contributed to phenotypic variation. Notably, integrating SVs with SNP\/Indels improved genomic prediction accuracy; the gradient boosting decision tree model outperformed other machine learning algorithms, achieving a mean accuracy of 0.859 and an AUC\u00a0&gt;\u00a00.8 (where AUC is area under receiver operating characteristic curve) for all flowering types. These findings provide insights into the genetic mechanisms underlying flowering time variation in\n                    <jats:italic>O. fragrans<\/jats:italic>\n                    , offer candidate genes and haplotypes for molecular breeding, and highlight the value of integrating SVs with machine learning for genomic prediction in woody ornamentals.\n                  <\/jats:p>","DOI":"10.1002\/tpg2.70301","type":"journal-article","created":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T04:37:24Z","timestamp":1788842244000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Dissecting genetic architecture and improving machine learning\u2011based genomic prediction of flowering time in\n                    <i>Osmanthus fragrans<\/i>\n                    by integrating structural variants"],"prefix":"10.1002","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9165-6125","authenticated-orcid":false,"given":"Hui","family":"Xia","sequence":"first","affiliation":[{"name":"Key Laboratory of National Forestry and Grassland Administration on <i>Osmanthus fragrans<\/i> Hubei University of Science and Technology  Xianning China"},{"name":"State Key Laboratory of Woody Oil Resources Utilization, College of Forestry Central South University of Forestry and Technology  Changsha China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongguo","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory of National Forestry and Grassland Administration on <i>Osmanthus fragrans<\/i> Hubei University of Science and Technology  Xianning China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanhang","family":"Wu","sequence":"additional","affiliation":[{"name":"Key Laboratory of National Forestry and Grassland Administration on <i>Osmanthus fragrans<\/i> Hubei University of Science and Technology  Xianning China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ting","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of National Forestry and Grassland Administration on <i>Osmanthus fragrans<\/i> Hubei University of Science and Technology  Xianning China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guifu","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of National Forestry and Grassland Administration on <i>Osmanthus fragrans<\/i> Hubei University of Science and Technology  Xianning China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingiing","family":"Zou","sequence":"additional","affiliation":[{"name":"Key Laboratory of National Forestry and Grassland Administration on <i>Osmanthus fragrans<\/i> Hubei University of Science and Technology  Xianning China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yingting","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of National Forestry and Grassland Administration on <i>Osmanthus fragrans<\/i> Hubei University of Science and Technology  Xianning China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,7]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1002\/tpg2.20012"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1080\/15592324.2018.1473687"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13007\u2010025\u201001418\u20100"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1023\/A:1010933404324"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jplph.2017.03.018"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1007\/978\u20101\u20100716\u20100199\u20100_3"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41438\u2010021\u201000531\u20100"},{"key":"e_1_2_10_9_1","doi-asserted-by":"crossref","unstructured":"Chen T. &Guestrin C.(2016).XGBoost: A scalable tree boosting system. 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