SG: RUI: Paralogous paths to gaining anthocyanin pigmentation in Chilean monkeyflowers

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The goal of this research is to understand whether the repeated evolution of a trait of an organism is more likely to occur through the same genetic change or through different genetic changes. A major challenge in biology is to understand how specific genes and genetic mutations affect the ability of organisms to function in their environments. In some groups of plants, a red pigmentation called "anthocyanin" has repeatedly evolved, probably because of the benefits that those pigments provide to plants. In flowers, brightly-colored red pigments help attract pollinators such as hummingbirds. The pigments also serve as antioxidants which help protect plants from stress-induced cell damage. This research will identify the types of genes and mutations used in three repeated gains of red anthocyanin pigmentation in a group of monkeyflowers (Mimulus). It will address the question of how flexible evolution (or artificial selection, in the case of crop breeding) might be. Are there multiple interchangeable, equally good ways of achieving a certain trait, or does each different route to the gain of anthocyanin pigmentation come with its own unique set of costs and benefits? The project will provide advanced genetic and molecular training for teams of undergraduate researchers. In addition, one internship will be provided each year to a promising student from the local alternative high school for youth who struggle in traditional schools.A primary goal of this project is to identify the specific genes and types of mutations responsible for the gain of petal anthocyanin in each of three species, M. cupreus, M. l. variegatus, and M. naiandinus. Aim 1 will test whether evolution is repeated through activation of a specific gene of the R2R3 MYB gene family, or alternatively, whether different MYB genes are functionally equivalent and interchangeable with respect to the evolutionary gain of Petal Lobe Anthocyanin (PLA). The researchers will use transgenic transformation, followed by phenotype and fitness assays, to determine (i) whether the same gene is responsible for the repeated PLA gain in M. cupreus versus M. naiandinus, and (ii) whether the two distinct causal genes in M. cupreus and M.I. variegatus are functionally equivalent and interchangeable. Aim 2 will test whether the broader genomic regions (pla1 and pla2) are functionally equivalent. The researchers will use introgression to move the +PLA alleles (along with the associated genomic regions) into different -PLA backgrounds. The hybrids will be screened by phenotype and fitness assays to determine if the pla1 and pla2 regions are either equivalent or functionally distinct. Aim 3 will test whether PLA evolution consists of a single molecular mechanism or type of mutation. Chimeric transgenes, which combine +PLA coding sequence with -PLA regulatory sequence and vice versa, will be used to determine whether the causal mutation is coding or cis-regulatory for three evolutionary timepoints: within-population, within-species, and between species. Fine structure mapping will be used to identify the mutational changes at the nucleotide level.