Understanding carotenoid biosynthetic pathway control points using metabolomic analysis and natural genetic variation

Advances in analytical methodologies, including those coupled with mass spectrometry (gas chromatography and liquid chromatography; GC-MS and LC-MS) have facilitated profiling of carotenoids in complex plant extracts. The combination of metabolomic data together with diverse germplasm resources provides a means to discover the underlying genetic factors responsible for modulating the carotenoid biosynthetic pathway. Here we summarize metabolomics methodologies for large-scale metabolite analysis and provide guidelines for genetic analysis to leverage natural variation for identification of genes encoding biosynthetic pathway enzymes based on linkage mapping and/or genome-wide association studies (GWAS). We also demonstrate the workflow for identifying genes in carotenoid biosynthesis based on natural variation using case studies in several species.