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We investigated the genetic basis of red\/green variegation observed in the aerial organs of the P0429 accession. We demonstrated that this color mosaic is primarily localized to epidermal bladder cells (EBCs), with red EBCs accumulating betacyanin levels\u2009~\u200950-fold higher than colorless EBCs. Cell-type-specific RNA-sequencing of EBCs identified the cytochrome P450 gene\n                    <jats:italic>Cqu0091301<\/jats:italic>\n                    (\n                    <jats:italic>CYP76AD\u03b1<\/jats:italic>\n                    ) as the dominant and rate-limiting factor, exhibiting strong upregulation in red EBCs. This high pigmentation requires a specific structural variation in the P0429 accession: a\u2009~\u20094-kb genomic insertion that restores the full functionality of\n                    <jats:italic>Cqu0091301<\/jats:italic>\n                    , which is otherwise truncated and non-functional in common reference genomes. Genomic analysis reveals that\n                    <jats:italic>Cqu0091301<\/jats:italic>\n                    is part of a multicopy\n                    <jats:italic>CYP76AD\u03b1<\/jats:italic>\n                    \u2013\n                    <jats:italic>DODA<\/jats:italic>\n                    gene cluster. Notably, expression analysis revealed functional divergence between the quinoa subgenomes, with B-subgenome\n                    <jats:italic>CYP76AD\u03b1<\/jats:italic>\n                    genes highly dominant in EBCs, while A-subgenome homologs were preferentially expressed in other tissues. Our results establish a clear link between structural genomic variation and cell-type-specific betalain biosynthesis, providing molecular insight into pigment regulation and subgenome specialization in allotetraploid quinoa.\n                  <\/jats:p>","DOI":"10.1007\/s44154-025-00284-z","type":"journal-article","created":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T05:52:44Z","timestamp":1770789164000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic structural variation underlies cell type-specific betacyanin variegation in Chenopodium quinoa"],"prefix":"10.1007","volume":"6","author":[{"given":"Zheting","family":"Zhang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuwei","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiangwei","family":"Hu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tiansheng","family":"Yu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yaozu","family":"Feng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jungao","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ting","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guojun","family":"Feng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1541-3890","authenticated-orcid":false,"given":"Heng","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2026,2,11]]},"reference":[{"key":"284_CR1","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1016\/j.tplants.2014.01.013","volume":"19","author":"S Boycheva","year":"2014","unstructured":"Boycheva S, Daviet L, Wolfender JL, Fitzpatrick TB (2014) The rise of operon-like gene clusters in plants. 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