GENOMIC STRUCTURAL VARIATION IN SUNFLOWER: DIVERSITY UNDER DOMESTICATION AND IMPORTANCE FOR STRESS TOLERANCE

This project will identify SV in the cultivated and wild H. annuus genome that have been the target of selection, introduced via introgression, or are associated with adaptation to particular environmental conditions. Additionally, SV that contribute to genetic load in sunflower will be identified. Furthermore, this project will test whether SV has changed the correlations between agriculturally important traits, such as seed dimensions. As such, in line with the AFRI priority area: Plant health and production and plant products, the results of this project will provide foundational knowledge to all crop breeding programs and will directly benefit sunflower breeding practices. Through this project, the PD will build skillsets in bioinformatics and genomic analysis, professional development (communications, teaching, project management), and writing (grants, scientific publications) and receive guidance from mentors at academic and governmental agencies.Training and Career Developmentattend and present my research at multiple important conferences, including the Plant and Animal Genome (PAG) and Crop Science Society of America (CSSA) conferences along with the NIFA PD meeting.develop my teaching and mentorship skillsets through pedagogical training in the CIRTL (Center for the Integration of Research, Teaching, and Learning) network.co-teach graduate-level bioinformatics workshops at UBC and CU.professional development workshops on topics including diversity, preparing for the academic job market, and project and team management, that will prepare me for future success running an independent research team.CU Boulder also has a chapter of the association of women in science, which will provide opportunities for me to engage with fellow women in STEM fields.I will disseminate the results of this work to the broader scientific community through publication in peer-reviewed journals and presentations at national and international conferences.Scientific AimsIdentify and characterize SV in domesticated and wild H. annuus.Both the Kane (Primary mentor) and Rieseberg (Collaborating mentor) labs were recently involved in publishing the first pan-genome for sunflower (Hübner et al., 2019), which focused on the gene space only. In this aim, I will identify and characterize inversions, CNV, and PAV in wild, landrace, and modern lines of H. annuus.Identify SV associated with selection, introgression, and the cost of domestication.Domestication involves multiple evolutionary processes that impact the genomic diversity of crop species. Traditionally, domestication genomics examines a few main phenomena: the loss of genetic diversity associated with population bottlenecks during domestication and improvement selective sweeps for traits associated with the domestication syndrome, and historical and modern introgression between crops and their wild relatives, all of which impact the genetic diversity of modern crops. More recently, domestication research has also begun to explore the accumulation of deleterious mutations in domesticated lineages that result from selection and demographic processes; a phenomenon termed the cost of domestication. In this aim, I will identify SV in cultivated H. annuus that have been the targets of selection and/or have been introduced by introgression during the domestication process and estimate the cost of domestication associated with these SV.Connecting SV to agriculturally relevant phenotypes in sunflowerRelatively few studies have directly associated SVs with particular phenotypes using genome wide association (GWA) studies, but those that have demonstrate that SV may have a disproportionately large effect on phenotype compared to SNPs, and can impact agriculturally relevant phenotypes from reproductive morphology to seed color, plant height, and nematode resistance. In this aim, I will identify SV that are linked to important agricultural phenotypes and environmental tolerance in cultivated H. annuus. Data from wild and cultivated (combined landrace and modern) H. annuus is available for a number of agricultural traits, including seed traits, plant architecture, flowering time, vegetative traits, developmental traits, and abiotic and biotic stress tolerance. Additionally, geographic locations and environmental data are available for the collections of wild H. annuus.