# Genomic structural variation underlies cell type-specific betacyanin variegation in Chenopodium quinoa

## TL;DR

This study shows how a specific genomic insertion in quinoa leads to red pigment accumulation in certain cells, revealing how structural variations control cell-specific traits.

## Contribution

The study identifies a genomic insertion that restores a key gene's function, linking structural variation to cell-type-specific betacyanin production in quinoa.

## Key findings

- Red epidermal bladder cells in quinoa have ~50-fold higher betacyanin levels than colorless cells.
- A ~4-kb genomic insertion in the P0429 accession restores functionality to the Cqu0091301 gene, driving red pigmentation.
- B-subgenome CYP76ADα genes are dominant in epidermal bladder cells, while A-subgenome homologs are expressed in other tissues.

## Abstract

The allotetraploid crop quinoa (Chenopodium quinoa) accumulates red/violet betacyanins, which function as vital stress-mitigating antioxidants. 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 ~ 50-fold higher than colorless EBCs. Cell-type-specific RNA-sequencing of EBCs identified the cytochrome P450 gene Cqu0091301 (CYP76ADα) 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 ~ 4-kb genomic insertion that restores the full functionality of Cqu0091301, which is otherwise truncated and non-functional in common reference genomes. Genomic analysis reveals that Cqu0091301 is part of a multicopy CYP76ADα–DODA gene cluster. Notably, expression analysis revealed functional divergence between the quinoa subgenomes, with B-subgenome CYP76ADα 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.

The online version contains supplementary material available at 10.1007/s44154-025-00284-z.