A metabolic roadmap of waxy corn flavor

As well as being a popular vegetable crop worldwide, waxy corn represents an important amylopectin source, but little is known about its breeding history and flavor characteristics. In this study, through comparative-omic analyses between 318 diverse waxy corn and 507 representative field corn inbred lines we revealed that many metabolic pathways and genes exhibited selection characteristics during the breeding history of waxy corn, contributing to the divergence between waxy and field corn. We showed that waxy corn is not only altered in its glutinous property but also its sweetness, aroma, and palatability are all significantly affected. A substantial proportion (43%) of flavor-related metabolites have pleiotropic effects, affecting both flavor and yield characteristics, and 27% of these metabolites are related to antagonistic outcomes on yield and flavor. Furthermore, through multiple concrete examples, we demonstrated how yield and quality are coordinately or antagonistically regulated at the genetic level. In particular, some sweet molecules, such as DIMBOA and raffinose, which do not participate in the starch biosynthesis pathway, were identified as potential targets for breeding a new type of "sweet-waxy" corn. Taken together, our findings shed light on the historical selection of waxy corn and demonstrate the genetic and metabolic basis of waxy corn flavor, collectively providing valuable resources and knowledge for future crop breeding for improved nutritional quality.