Brassicales to Brassica : integrating phylogenomics and population genomics

Abstract

The Brassicales are an economically important order of flowering plants. Many crop species such as kale, broccoli, cabbage, cauliflower, canola oil, capers, and papaya, as well as the model plant organism, Arabidopsis thaliana, all belong to this diverse order. The focus of my dissertation has been to use phylogenomics and population genomics to understand the evolution of the Brassicales, as well as the important crop species Brassica oleracea. Within the Brassicales, the family Brassicaceae is notable for many whole-genome duplication (WGD) events, including one at the base of the family. The sister family to the Brassicaceae, the Cleomaceae, is also known to have a WGD event; however, it has never been placed within the family. Previous studies assessing the relationships between and within these families have either used a few genes or a few taxa. Phylo-transcriptomics, a quickly evolving field that uses RNA-seq data to make phylogenomic inferences from many more nuclear genes than traditional PCR, is a great method to no longer have to choose between too few genes or taxa. For my second chapter, I used phylotranscriptiomics to estimate relationships in the Brassicales and used the resulting phylogeny as a framework for inferring WGD events. These analyses recovered the known At-[beta] and At-[alpha] events, as well as multiple independent WGD events in the Cleomaceae, Capparaceae, and Resedaceae. The horticultural crop Brassica oleracea is a notable member of the Brassicales, playing an important role in global food systems. Brassica oleracea is unique in that it has been domesticated into several morphotypes (cultivars), including broccoli, Brussels sprouts, cabbage, cauliflower, kale, kohlrabi, and several lesser well known morphotypes, such as walking stick kale and marrow cabbage. These crops are widely used as leaf and root vegetables, as well as for animal feed. There are several hypotheses on the origin of these crops. However, after resolving the relationships between wild relatives and domesticated types, I have determined that cultivation likely originated in the Eastern Mediterranean region, with additional domestications occurring around the world. I also identified feral populations that had previously been mistaken as progenitor populations. Using this system of diversity within domesticated B. oleracea, I examined patterns of relationships among morphotypes, including signals of hybridization and introgression. Brassica oleracea vegetable crops are frequently regarded as superfoods (e.g., kale) and are an important diet source for key minerals and elements. Ionomics, the measurement of the total elemental composition of an organism, allows for high throughput characterization of the levels of these elements at the same time, including those important to diet such as iron and zinc. Using association mapping techniques, I have identified genes underlying quantitative phenotypic traits of economic importance such as iron, as well as total element composition. This knowledge can then allow for further decisions of the best accessions to target for human health, as well as provide an excellent resource for future studies wanting to enhance specific elements in different crops. To conclude, I discuss the unique opportunity that feral populations provide for the study of natural selection and how this information can be leveraged for improvement of crops in breeding them to be more locally adapted.