Discovery of a novel CYP76AD1–DODA1 gene cluster associated with betalain pigmentation in quinoa

Abstract

Quinoa (Chenopodium quinoa Willd.) is gaining attention as both a promising food resource and a genetic model for stress-resilient crops; however, its substantial genetic diversity remains largely untapped. In this study, we identified a novel genomic region associated with betalain pigmentation that may contribute to stress tolerance and environmental adaptation in quinoa, using bulked segregant analysis and a fully de novo assembled chromosome-scale genome of quinoa line J131. We identified the first 2 Mb of the chromosome 1B pseudomolecule of J131 as a candidate region associated with pigmentation. Within this region, 35 predicted functional genes were identified, including a tandem gene cluster comprising CqCYP76AD1 and CqDODA1, key genes involved in betalain biosynthesis. A PCR marker adjacent to this cluster completely co-segregated with the pigmentation phenotype in an F₂ population. This gene cluster is embedded within rRNA gene repeats and is absent from three previously published chromosome-scale quinoa genomes—QQ74, J075, and J100. We identified additional homologs of CqCYP76AD1 and CqDODA1 in other genomic regions that may contribute to variation in pigmentation intensity and tissue-specific patterns. Our results underscore the importance of structural variation in lineage-specific trait evolution and demonstrate how high-quality chromosome-scale assemblies enable the detection of hidden genomic features. This is the first study to link visible phenotypic traits in quinoa to differences in genome structure through direct comparison of multiple chromosome-level assemblies. Our findings highlight the potential of graph-based pan-genome approaches for systematically exploring structural diversity and its phenotypic consequences.