Ecological and functional genomics of plant adaptation

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One of biology's major goals is to describe understand adaptive evolution on multiple levels of organization: from the genes and mutations involved, to their effects on phenotypes and degree of pleiotropy, to how those traits function in a realistic ecological context. One area to address this challenge is in the life history and developmental transition from vegetative growth to flowering, which is often under geographically variable selection due to climatic variation and seasonality. We have investigated this in the annual plant, Arabidopsis thaliana, which in addition to being the pre-eminent model system for plant biology, genomics, and genetics, is also in the same family as the important crop, Canola. The genetic and genomic resources for Arabidopsis are being increasingly leveraged for studies in the ecology, evolution, and genetics of adaptation. Arabidopsis thaliana invaded North America, and appears to show evidence of rapid, adaptive evolution. Recent work in our group has identified 53 novel candidate genes underlying flowering time differentiation in the introduced range. We followed this up with knockout studies, which revealed a handful of promising genes for further genetic investigation. We are now creating CRISPR-mediated transgenic lines, in which we are substituting naturally occurring late flowering variants into an early flowering background, and vice-versa. These transgenic lines require ecological verification. We will examine their effects on focal phenotypes, correlated phenotypes, and fitness. Collectively, this will be comprehensive investigation of the effect size, allele frequency, and ecological consequences of variation at these genes. My specific aims are to: 1) Verify the phenotypic effects of these transgenic lines, in a battery of chamber experiments, with commonly used growth conditions, 2) Perform field experiments to validate their effects in ecologically realistic settings, how they are under natural selection, and quantitatively compare them to levels of naturally occurring variation and selection, 3) Use population resequencing to obtain unbiased estimates of allele frequencies for these naturally occurring variants affecting flowering time, and 4) mathematically combine these estimates to evaluate their contribution to genetic variance, covariance, and how changes in allele frequency might affect future evolutionary responses. The proposed work will support training several HQP in the rapidly expanding areas of ecological and evolutionary genomics, and advance our knowledge of flowering time, plant reproduction, and the genetics of invasive species because it evaluates the roles of molecular genetic and environmental variation in shaping complex traits. The results are likely to be of great importance in understanding adaptive responses of species to biological invasion and climate change.