Biosynthesis of Steroidal Alkaloids Are Coordinately Regulated and Differ Among Tomatoes in the Red-Fruited Clade

Background/rationale: We quantitatively profiled and genotyped two tomato populations representing diversity in the red-fruited clade to address the lack of knowledge regarding the chemical diversity, concentration, and genetic architecture controlling tomato steroidal alkaloids. Methods: We grew 107 genetically diverse fresh market, processing, land-race, and wild tomatoes in multiple environments. Nine steroidal alkaloids were quantified using ultra-high performance liquid chromatography tandem mass spectrometry. The diversity panel and a biparental population segregating for high alpha-tomatine, were genotyped to identify and validate quantitative trait loci (QTL) associated with steroidal alkaloids. Results: Land-races and wild material exhibited higher alkaloid concentrations and more chemical diversity. Average total content of steroidal alkaloids, often dominated by lycoperoside F/G/esculeoside A, ranged from 1.9 to 23.3 mg/100 g fresh weight across accessions. Land-race and wild cherry accessions distinctly clustered based on elevated early or late steroidal alkaloid concentrations. Significant correlations were observed among early and late steroidal alkaloids in a species-dependent manner. A QTL controlling multiple, early steroidal alkaloid pathway intermediates on chromosome 3 was identified by genome wide association (GWAS) and validated in a backcross population. Conclusions: Tomato steroidal alkaloids are diverse in the red-fruited tomato clade and their biosynthesis is regulated in a coordinated manner.