Range-wide studies of genetic and transcriptomic diversity in sunflower
McAssey, Edward Vincent
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With the pressures of climate change and human population growth affecting agricultural land use, it is important to consider the use of wild adaptations to maintain and increase where crops can be grown. The study of the genetic basis of local adaptation has accelerated with ease of collecting sequence data from multiple individuals from across the range of a species. Here, I present phenotypic, genotypic, and expression based studies of variation in wild sunflowers across a latitudinal gradient in North America. I found that flowering time and saturated fatty acid percentage of seeds were differentiated across the range, with northern populations both flowering earlier and having less saturated fatty acids in their seeds. In order to understand the genetic basis of these traits I genotyped individuals with two different marker technologies, a SNP chip and Genotyping-by-Sequencing, in order to identify regions of the genome that were exceptionally differentiated when comparing northern and southern populations. An analysis of population genetic variation revealed a number of candidate regions for local adaptation including multiple members of the flowering time pathway. To complement the study of population genetic variation as it relates to local adaptation, I performed RNA-sequencing to identify genes that may be influencing the differences in fatty acid saturation in wild sunflower. When comparing expression levels of developing northern and southern wild sunflower seeds, I found a number of differentially expressed genes, some of which were annotated as part of the fatty acid biosynthesis pathway. Taken together, the genetic differentiation outliers and differentially expressed genes represent excellent candidates for follow up experiments. Importantly, by mapping these variants against the sunflower genome, I was able to further prioritize candidates by assessing whether or not they co-localizing with important QTL. Future work will focus on establishing the extent of linkage disequilibrium in these genomic intervals to clarify the individual role of these putative adaptive variants.