Whole genome duplication, also known as polyploidy, has occurred many times during the evolution of a wide variety of organisms, including most valuable crops, and may be a critical mechanism for the evolutionary origin of novel traits. The genetic mechanisms and evolutionary forces that govern the fate of newly duplicated genes, and how these forces lead to broad-scale genomic changes are unknown. This study will utilize ultra high-throughput DNA sequencing technology to test specific hypotheses regarding evolution in polyploids in the emerging model wildflower genus Mimulus. The genomic and phenotypic evolution that has taken place in naturally-occurring polyploids will be compared to experimentally-generated synthetic polyploids.
This study will provide novel insight into the effects of polyploidy on ecologically-important traits, including traits affecting the survival and reproduction of organisms in relation to their environment. Because many crops are of polyploid origin, a thorough understanding of the immediate and long-term effects of polyploidy may provide promising avenues for crop improvement. The proposed research also will provide many novel avenues for talented undergraduate and high school students to conduct independent, but related research projects in ecology, evolution, genomics, and bioinformatics.
The research funded by grant 0910296 addressed how polyploidization affects genomic and phenotypic evolution in plants. Polyploidy, or whole genome duplication, is a major mechanism for evolutionary change because it is both widespread across taxa and results in a proliferation of genetic material that evolution can act upon. Polyploidy may affect available genetic variation through the introduction of ploidy-induced genomic modifications. The key questions addressed in this research were: (1) how does the genome of polyploids evolve following formation?, and (2) How does genetic and genomic evolution in polyploids affect phenotypic evolution? An herbaceous wildflower, Mimulus sookensis, a tetraploid of hybrid origin between Mimulus guttatus and Mimulus nasutus, was used to address these questions. Genetic marker data and phenotypic data from second generation synthetically-derived hybrid tetraploid Mimulus, as well as whole genome sequence data from naturally-occuring Mimulus sookensis, suggests that polyploidization in Mimulus does not result in rapid genomic evolution or an accumulation of genomic modifications. Consequentially, polyploidy in Mimulus per se does not result in rapid phenotypic evolution. Crossing experiments between wild-collected and synthetically-generated hybrid tetraploids that differ in flower size revealed four regions of the genome that contribute to the flower size in Mimulus sookensis. Some of these regions co-localize with previously identified regions for flower size in diploid Mimulus, while others do not. These results suggest that trait evolution in polyploids may be affected by the unique attributes of polyploids, but that new mutations are always an important source of genetic variation, regardless of ploidy level. Although polyploidy in general is a widely-studied phenomenon, there are still key aspects of polyploidy in relation to evolution and genetics that are quite poorly understood. Many important crops, such as wheat and cotton, are of polyploid origin, and thus understanding how genetic variation is created in polyploid lineages can allow for the improvement of breeding techniques and genetic engineering programs. Our results are contrary to previous findings in other plant species such as Brassica, which suggested that rapid genomic modifications may be accompanied by phenotypic evolution. Our results suggest that although whole genome duplication creates an abundance of genetic material, this genetic material does not always lead to phenotypic novelty or rapid phenotypic evolution, a result that may be crucial for those designing crop breeding programs to take into account. This grant aided the completion of the dissertation of the co-PI, Jennifer Modliszewski. It has resulted in two publications, with three additional publications in preparation, all in peer-reviewed journals. Findings originating from this grant have been presented at the annual meetings for the Society for the Study of Evolution, the American Genetics Association, and the Plant and Animal Genome Conference. In addition, the findings have also been disseminated at seminars given at North Carolina State University, the University of North Carolina at Chapel Hill, the University of Virginia, and one local high school biology class. This research grant has also provided training opportunities for four high-school students. Two high-school sophomores, Alex Lew and Megan Mikhail, were introduced to concepts in genetics, ecology and evolution, and also experienced hands-on training in molecular biology, and bioinformatics. Connie Wang, a participant in the HHMI Pre-College program, conducted an independent research project on allotetraploid Mimulus, in which she learned cultivation techniques, molecular biology laboratory techniques, and importantly, learned how to present and disseminate her research. Connie is now pursuing a bachelor’s degree at the California Institute of Technology. In addition, another HHMI pre-college program student, Crystal Terry, had the opportunity learn cultivation and molecular biology techniques through research related to this grant. Crystal is currently pursuing a bachelor’s degree at Duke University.
