Intellectual Merit. A central finding of modern plant biology is that plant lineages often originate from and diversify following hybridization between species and subsequent doubling of the hybrid genome. This biological reunion among two different genomes sets in motion a wide spectrum of genetic and genomic phenomena with that occur through unknown mechanisms and have largely unknown functional and evolutionary consequences. To advance understanding of the dynamics and outcomes of genome doubling, this project will study the consequences of genome merger and doubling on pathways and networks. Using the cotton genus (Gossypium) as a well-developed model for studies of whole-genome doubling, this study will focus on two different pathways and networks. For the anthocyanin biosynthetic pathway, multiple relationships among mutational processes, changes in gene expression, and metabolite accumulation will be clarified. Using a second, more complex network involving flowering time, experiments will address responses of a network to the intense directional selection practiced by early cotton domesticators as the wild species was transformed by humans from a wild, photoperiod-sensitive, perennial plant into a day-length neutral, annualized row crop. Remarkably, this process was replicated for two different species, providing a unique opportunity to test the repeatability of the response to selective breeding. The research entails three complementary experimental approaches. First, using novel technologies, all genes for the key proteins involved in the core anthocyanin biosynthetic pathway and the approximately 70 proteins involved in the flowering time network will be isolated and sequenced from the progenitor genomes, as well as from domesticated and wild forms of two different cultivated species of cotton. Second, changes in gene expression will be detailed for each evolutionary stage in the process, including hybridization, genome doubling, and human selection during crop improvement. Third, the consequences of genome doubling on metabolite accumulation will be studied for the anthocyanin pathway. Synthesis of these three data sources will reveal the interrelationships among mutations, gene expression, and metabolite accumulation, during the evolutionary processes of species divergence, inter-genomic hybridization, and genome doubling. Collectively, these studies will provide a novel perspective on an important process in plant biology, with broad conceptual generality and applicability.
Broader Impacts: Multiple activities are planned that target inclusion and training of students from underrepresented groups and provide research experiences for students and K-12 educators. The project has a special focus on a seven-week summer research experience for teachers program, which provides 7th -12th grade biology teachers with an opportunity to enhance their understanding of scientific inquiry while introducing them to cutting-edge science. Teachers will learn theory and methods in workshops and conduct independent projects associated with larger on-going projects. They will receive hands-on training in modern laboratory techniques, including those associated with gene sequence and gene expression analysis, metabolite accumulation, and bioinformatics. Also, teachers will meet weekly under the guidance of selected experienced master teachers to discuss transfer of their research experiences into the 7th -12th grade science classroom. To provide teachers with a deeper understanding and appreciation evolutionary biology, Wendel will lead a teacher training study group each summer, with the explicit focus of incorporating molecular genetics perspectives into the teaching of evolutionary biology. At the end of each summer session, teachers will prepare a plan for implementing research-based education modules in the classroom.