LIFE: Molecular and macroecological mechanisms of pigment pathway and fruit color convergence in Solanum

About This Grant

This research examines the genetic changes and environmental conditions responsible for natural variation in an ecologically and economically important trait: fruit color. Ripe fruit color can vary dramatically within and between species, including in fruit crop species such as tomato. The factors thought to influence this color variation are important natural biochemicals and provitamins that have antioxidant and other known health benefits. However, the specific molecular changes that underlie variation in pigmentation and ripe fruit color are rarely known, making it difficult to identify good targets for increasing the health benefits of this variation. This research uses natural variation in fruit color across the plant group Solanum—that includes tomato, eggplant, and potato, and more than 1200 other wild species relatives—to identify the specific changes that underlie dozens of evolutionary origins of ripe fruit color variation. In addition to understanding different origins of the same fruit pigments and the environmental contexts that favor color variation, the research may speed the discovery of potential nature-based solutions for manipulating and enhancing the nutritional content of fruits in an important agricultural group. Products of the research will also be used to generate K-12 STEM outreach materials focused on natural color and vision, using fruit color and animal visual perception as an accessible educational vehicle. The project integrates comparative genomic, transcriptomic, and macroecological data to examine molecular variation in two important plant pigment biosynthetic pathways (carotenoids and anthocyanins), and to associate this variation with independent fruit color transitions and the ecological context of global geographic fruit color variation. First, to identify variation in constraint among members of each pigment biosynthetic pathway, it will quantify patterns of molecular genetic variation across >70 pathway-associated loci in at least 60 Solanum species with whole genome sequence data. Second, to examine whether fruit color convergence repeatedly draws upon the same or similar molecular mechanisms, it will investigate correlated and convergent evolution of fruit color transitions and pigment biosynthesis loci, using >80 independent fruit color transitions among 300+ Solanum species. Third, to identify the joint contribution of ecological and molecular processes to shaping fruit color variation across Solanum, it will identify macroecological features associated with the global distribution of fruit color variation in this group, and with variation in underlying molecular pigmentation mechanisms. This research leverages existing and growing resources, including: a) high quality reference genomes from crop species in Solanum; b) knowledge of fruit color mechanisms from model systems; c) ongoing advances in comparative genomics and phylogenetic comparative methods; d) living and preserved biological collections from hundreds of wild species; and e) organismal and phylogenetic knowledge of a diverse, global, economically important plant genus. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.