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