Evolution and Genetics of Floral Color Polymorphisms in Clarkia gracilis ssp. sonomensis and Erythronium umbilicatum

Floral color polymorphisms are pervasive in nature. Understanding the genetic basis of such polymorphisms allows us to address major evolutionary questions including: what types of genetic changes contribute to the evolution of phenotypic diversification? Have they arisen from new or pre-existing genetic material? And are certain types of genetic changes disproportionately involved? This dissertation address these questions by investigating two polymorphisms involving loss of anthocyanin pigmentation in some of the individuals in the populations. In Chapter 1, I characterized the genetic basis of the “white cup” phenotype in Clarkia gracilis ssp. sonomensis, where no anthocyanins are produced in the basal region of the petal. I demonstrated that the cup pigmentation is controlled by an R2R3-MYB transcription factor using transcriptome analysis, gene expression assays and cosegregation examination. I also found that petal pigmentation requires at least four R2R3-MYB genes, each gene exhibiting a spatiotemporal expression pattern that is different from each other, and each color pattern element is controlled by a different R2R3-MYB gene. In Chapter 2, I examined the evolution of petal pigmentation patterning by analyzing the phylogenetic relationship of these petal R2R3-MYB genes from C. g. ssp. sonomensis, its closely related subspecies, C. g. ssp. albicaulis and their progenitor species, C. amoena ssp. huntiana and C. lassenensis. I also compared the expression domains of these R2R3-MYB genes in these four (sub)species. I found that the R2R3-MYB genes that have region-specific expression patterns are derived from duplication events occurred before polyploidization of C. gracilis. These findings suggest that gene duplication of the R2R3-MYB genes plays an important role in the evolution of petal pigmentation patterning in C. gracilis. In Chapter 3, I identified an R2R3-MYB gene involved in producing purple or yellow anthers in Erythronium umbilicatum using transcriptome analysis, gene expression assays and a likelihood-estimation procedure. This R2R3-MYB gene regulates the expression of three anthocyanin enzyme-coding genes coordinately. However, this R2R3-MYB is present in multiple, highly similar copies. Isolating causal genetic changes from these copies has not been successful, as it would require a better knowledge of the Erythronium genome. In sum, this work shows that R2R3-MYB transcription factors are the primary determinants of floral-color polymorphisms and the R2R3-MYB gene family generated by gene duplication facilitates the evolution of novel characters.