A genomic and functional framework for the rapid domestication of the wild plant Chenopodium album

Abstract Global reliance on a small number of genetically uniform crops makes our food system increasingly vulnerable to pests, diseases, and climate change, highlighting the need to develop resilient local species as crops. Chenopodium album , a stress-tolerant, protein-rich wild plant whose seeds were part of prehistoric Northern European diets and whose leaves are still foraged worldwide, remains undomesticated despite its agrifood potential. We established a Danish collection of 143 accessions and combined seed metabolomics, ploidy assessment and genomics to uncover the molecular basis of key nutritional and anti-nutritional traits. Seed profiling revealed substantial variation in protein content (14-22%), comparable to or higher than major crops, and 16 distinct triterpenoid saponins, which are widespread bitter and anti-nutritional compounds. Seed production of field-grown lines reached up to 1.5 t/ha in trials conducted in Denmark, demonstrating promising yield potential. A high-quality tetraploid genome of a low-saponin line was assembled and contrasted with resequencing of a diploid high-saponin line in order to uncover the genetic basis of saponin variation in C. album . Comparative genomic, phylogenetic, and transcriptomic analyses identified structural variants and candidate genes associated with saponin biosynthesis, and functional validation confirmed the coordinated activity of a β-amyrin synthase, three CYP716 cytochromes P450, and a glucuronosyltransferase that reconstitute the core C. album saponin pathway. Together, these results define the genomic and biochemical foundation of C. album , establishing a platform for its rapid domestication as a locally adapted, high-protein seed crop and a model for translating wild plant diversity into future food security.