Exploiting natural variation for accelerating discoveries in plant specialized metabolism

Plants have the capacity to produce a staggering array of chemically diverse low molecular weight compounds called specialized metabolites. Though they are non-essential for basic cell activities, these molecules are characterized by their role as integral enhancers of plant fitness, and have distinct biological functions including defense against herbivory, immunity, pollinator attraction, molecular signaling, and abiotic stress tolerance. The chemicals are of particular interest because of their pharmacological, industrial, and agricultural usefulness. The inter- or intraspecies variation in the production of specialized metabolites has been widely observed and found to be largely genetically controlled. The natural genetic variation can be used to help identify biosynthetic and regulatory genes, elucidate mechanistic properties of gene function and gene regulation, and explore evolutionary and ecological questions. Recent advances in sequencing and data mining technologies have facilitated the integration of population genetics tools such as quantitative trait loci (QTL) mapping and genome wide association (GWA) with metabolite and/or gene expression profiling to exploit the natural variation for making new discoveries in the model plant Arabidopsis thaliana, as well as in more agriculturally relevant species. Here we highlight key discoveries that were catalyzed by taking advantage of naturally occurring variation, and comment on technologies and resources employed by this approach, in hopes of providing phytochemists an archetype for harnessing the power of natural variation to accelerate discoveries in plant specialized metabolism.