Multiomics dissection of the structural and biosynthetic diversity of steroidal glycoalkaloids in wild potatoes

Steroidal glycoalkaloids are defensive and antinutritional metabolites in Solanum plants with extensive structural diversity and bioactivity. However, the chemical profiles and molecular mechanisms underlying the structural diversity of steroidal glycoalkaloids in potato (Solanum section Petota) remain poorly understood. We performed metabolomic analyses on 68 accessions from 46 species, quantifying 64 steroidal glycoalkaloids with three structural types (solanidane, spirosolane 22αN, and spirosolane 22βN). These revealed marked interspecific differences in steroidal glycoalkaloid composition and content, with five distinct steroidal glycoalkaloids clusters corresponding to four sample subgroups. We constructed a de novo pan-transcriptome yielding a high-quality expression dataset encompassing 32,844 genes, including 4,848 assembled genes absent from the reference genome. Integrative metabolome-transcriptome analyses identified 193 candidate genes involved in steroidal glycoalkaloid structural modification. Five 2-oxoglutarate-dependent dioxygenase and GAME25 genes were identified as key regulators driving steroidal glycoalkaloid structural variation. We performed experimental validation to characterize the function of a 2-oxoglutarate-dependent dioxygenase member that specifically catalyzes C-23 hydroxylation of spirosolane 22αN-type steroidal glycoalkaloids, with a preference for glycosylated α-solasonine over solasodine. This study establishes a metabolite-gene atlas elucidating steroidal glycoalkaloid diversity in Solanum sect. Petota, providing valuable resources for leveraging steroidal glycoalkaloid diversity in potato breeding programs.