A high-quality spinach reference genome and co-expression analysis reveal circadian and floral initiation gene networks

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2026
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Abstract
Bolting time is critical for yield stability in spinach, a long-day Amaranthaceae crop whose photoperiod-dependent flowering pathway remains incompletely understood. 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-BBX-associated photoperiodic regulation in spinach. Together, this genome resource and integrative framework provide a basis for prioritizing bolting-associated genes and dissecting circadian-floral regulatory gene networks in spinach.
Reference Key
openalex_W7171542935 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Kaoru Yamano, Sota Yunoki, Kazuki Higuchi, Babil Pachakkil, Keisuke Tanaka, Sachiko Isobe, Kenta Shirasawa, Hideki Hirakawa, Yasuyuki Onodera
Journal Journal of experimental botany
Year 2026
DOI
10.1093/jxb/erag330
URL
https://doi.org/10.1093/jxb/erag330
Keywords Keywords not found

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