The genetic architecture of the pepper metabolome provides insights into the regulation of capsianoside biosynthesis

Capsicum (pepper) is among the most economically important species worldwide, the fruit accumulates specialized metabolites with essential roles in plant environmental interaction and potential health benefits. However, the underlying genetic basis of their biosynthesis remains largely unknown. In this study, we developed and assessed both wild genetic variance and a bespoke mapping population to determine the genetic architecture of the pepper metabolome. The genetic analysis provided over 30 metabolic quantitative trait loci (mQTL) for over 1100 metabolites. We identified 92 candidate genes involved in various mQTL. Among the identified loci, we described and validated by transient overexpression a domestication gene cluster of eleven UDP-glycosyltransferases involved in monomeric capsianoside biosynthesis. We additionally constructed the biosynthetic reactions and annotated the genes involved in capsianoside biosynthesis in pepper. Given that differential glycosylation of acyclic diterpenoid glycosides contributes to plant resistance and acts as anticancer agents in humans, our data provide new insight, and resources for better understanding the biosynthesis of beneficial natural compounds to improve human health.