Spicy genes: mapping quantitative genomic regions and candidate genes for capsaicinoid and capsinoid biosynthesis in...

Capsaicinoids, the molecules responsible for pungency in pepper (Capsicum spp.), and their non-pungent analogs, capsinoids, are synthesized through the interaction of two distinct metabolic pathways: the branched chain fatty acid pathway and the phenylpropanoid pathway. These two families of bioactive compounds are unique to the genus Capsicum and, besides their importance for pepper taste, are associated with several beneficial effects, such as weight management, antioxidant activity and prevention of various diseases. Although QTLs associated with capsaicinoid and capsinoid accumulation have been reported in several studies, these findings remain dispersed across different populations, limiting their direct comparison and practical use in breeding. In this study, we aim to collect, compare, integrate, and synthesize the available literature on capsaicinoid and capsinoid QTLs. A total of 155 QTLs associated with these traits were physically mapped onto the reference pepper genome (CM334 -v1.6) and analyzed within a common genomic framework. The physical integration of the selected regions allowed us to identify 23 Quantitative Genomic Regions (QGRs) and prioritize potential candidate genes located within them. This genome-based integration advances beyond previous descriptive summaries, providing a unified physical framework for comparing QTLs across studies and genetic backgrounds. This review provides a comprehensive resource for researchers aiming to understand the genetic mechanisms behind capsaicinoid and capsinoid biosynthesis and for breeders focused on improving the levels of these bioactive compounds in pepper. It enables the identification of key QTL regions through the integration of data from diverse populations, highlights potential donor genotypes reported in the literature for specific traits, and facilitates the discovery of candidate genes for future functional validation and marker-assisted breeding. Overall, this study provides a consolidated genomic framework for understanding the genetic architecture of capsaicinoid and capsinoid biosynthesis and for accelerating the development of pepper cultivars with improved profiles of these bioactive compounds.