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We generated a chromosome-scale reference genome for an early-bolting spinach line (944.6 Mb; 97.9% BUSCO completeness) and used it to integrate QTL mapping, sequence variation, and transcriptome-based co-expression analysis. Remapping bolting-time QTLs on this improved reference retained qBt2.1, qBt3.1, and qBt3.2, while refining their physical intervals and candidate gene content. Candidate loci included SoCOL14\/SoFL1 at qBt2.1, SoFT3 at qBt3.1, and SoLNK1\/SoAGL21 at qBt3.2. Co-expression analysis identified ten modules, including a circadian-associated module M9 containing SoLNK1\/2, SoGI, SoCOL5, SoPRR7, and SoBBX19, and a floral-initiation module M10 enriched for shoot-apex regulators. A predicted loss-of-function allele of SoLNK1 in the late-bolting line further supports its prioritization as a candidate regulator. Phylogenetic and network evidence suggest Amaranthaceae-specific remodelling of PRR\u2013BBX-associated photoperiodic regulation in spinach. Together, this genome resource and integrative framework provide a basis for prioritizing bolting-associated genes and dissecting circadian\u2013floral regulatory gene networks in spinach.<\/jats:p>","DOI":"10.1093\/jxb\/erag330","type":"journal-article","created":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T23:06:23Z","timestamp":1785279983000},"page":"6393-6407","source":"Crossref","is-referenced-by-count":0,"title":["A high-quality spinach reference genome and co-expression analysis reveal circadian and floral initiation gene networks"],"prefix":"10.1093","volume":"77","author":[{"given":"Kaoru","family":"Yamano","sequence":"first","affiliation":[{"name":"Graduate School of Agriculture, Hokkaido University , N-9, W-9, Sapporo 060-8589 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sota","family":"Yunoki","sequence":"additional","affiliation":[{"name":"Graduate School of Agriculture, Hokkaido University , N-9, W-9, Sapporo 060-8589 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazuki","family":"Higuchi","sequence":"additional","affiliation":[{"name":"School of Agriculture, Hokkaido University , N-9, W-9, Sapporo 060-8589 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1110-3107","authenticated-orcid":false,"given":"Babil","family":"Pachakkil","sequence":"additional","affiliation":[{"name":"Department of International Agricultural Development, Faculty of International Agriculture and Food Studies, Tokyo University of Agriculture , 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0658-7781","authenticated-orcid":false,"given":"Keisuke","family":"Tanaka","sequence":"additional","affiliation":[{"name":"NODAI Genome Research Center, Tokyo University of Agriculture , 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502 ,","place":["Japan"]},{"name":"Department of Informatics, Tokyo University of Information Sciences , 4-1 Onaridai, Wakaba-ku, Chiba 265-8501 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9555-5054","authenticated-orcid":false,"given":"Sachiko","family":"Isobe","sequence":"additional","affiliation":[{"name":"Graduate School of Agricultural and Life Sciences, The University of Tokyo , 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 ,","place":["Japan"]},{"name":"Department of Frontier Research and Development, Kazusa DNA Research Institute , 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7880-6221","authenticated-orcid":false,"given":"Kenta","family":"Shirasawa","sequence":"additional","affiliation":[{"name":"Department of Frontier Research and Development, Kazusa DNA Research Institute , 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7128-7390","authenticated-orcid":false,"given":"Hideki","family":"Hirakawa","sequence":"additional","affiliation":[{"name":"Department of Bioscience and Biotechnology, Kyushu University , 744 Motooka, Nishi-ku, Fukuoka 819-0395 ,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2932-8491","authenticated-orcid":false,"given":"Yasuyuki","family":"Onodera","sequence":"additional","affiliation":[{"name":"The Research Faculty of Agriculture, Hokkaido University , N-9, W-9, Sapporo 060-8589 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