We study the population genetics process of Adaptation in model plants, using state of the art genomic, phenomic, and association genetic techniques. How are populations shaped by their local environment? This may ultimate effect how the environment is shaped by their resident populations (e.g. foundation species and agriculture). High throughput genome sequencing allows us to map the adaptive alleles and fine patterns population structure. We can then determine the dynamics of functional alleles on the landscape. With high resolution phenotyping by imaging in the field and in synthetic populations in climate chambers allows growth (photosynthesis), development (photomorphogenesis), and reproduction (fitness) to be recorded throughout the season. Remote sensing of weather variables tracks local microclimatic environmental change within and among host ecosystems. Idealized microclimates are then recreated in experimental chambers. Finally we hope to paramaterize models of genotype <–> phenotype <–> environment interactions within and among species that lead to ecosystem evolution and ecological sustainability.
Plant Energy Biology
Improving the efficiency of plant solar energy capture, use and yield, is a necessary solution to the increasing demand on finite land, water, and nutrient resources. Increasing environmental challenges adversely affect growth efficiency and further perturb plant energy balance among capture and use, affecting yield. We take a novel approach to improve sustainable yield by optimizing the overall energy efficiency of metabolism, transport, and plant development. We will discover networks of gene variants, signaling pathways and molecular mechanisms that regulate energy efficiency under limiting and fluctuating conditions. This approach will provide a basis for sustainable productivity of crops and future-proof plants in changing climates.
Genetics of local adaptation in plants
Specific interests of the lab include the genetics of adaptation to seasonal light environments. Quantitative and population genetic approaches in Arabidopsis thaliana, Arabidopsis lyrata, Aquilegia (columbines), and switchgrass are used to dissect local and regional phenotypic variation. What genes and what alleles explain differential survival (germination/elongation) and reproduction (flowering time) in the field? Are these new variants or new combinations of existing polymorphisms? Are similar evolutionary steps occurring in related species living in a similar ecological context?
Genetic variation in environmental response
In Arabidopsis, we have revealed extensive genetic variation in world-wide collections for seedling elongation (Nature Genetics 2001) and flowering time (Genetics 2005) under unique light environments and determined quantitative trait loci (QTL) responsible for this variation (Genetics 2002,2004, PLoSONE, 2007). The next questions are what are the genes underlying these QTL and what are the functional allelic differences? How have the patterns of variation at these loci been shaped by natural selection? Can we find evidence for local adaptation and determine the ecological environmental differences driving selection?
Genomic approaches to natural variation
A second focus is on the development of genomics methods to enable comprehensive studies of natural variation. Tools such as genotyping by sequencing are being used for near complete genome studies of polymorphism and haplotype analysis (Morris et al, 2010). These alleles are being associated with Phenotypes through Genome Wide Association Mapping and across the Landscape using spatial and climate models.
From molecular systems to ecosystems: rebuilding biodiversity and biomass
Cellular responses are the integration of genetic and environmental inputs that through development result in altered organismal phenotypes of the adult plant. Whole plant structure and physiology affects the species, community makeup through higher order inter-specific interactions. The resulting landscape effects, in turn have outputs measured as ecosystems services including biomass as bioenergy, habitat for biodiversity, and water, carbon, and nitrogen sequestration, that input again on molecular cellular signaling.