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Association genetics and local adaptation of Populus trichocarpa Torr. & Gray Hari Bahadur Chhetri A major goal in plant science is overcoming the recalcitrance of plant biomass to cellulose extraction, to enable efficient production of cellulosic biofuel. We have started to understand the genetic basis of some important traits such as cell wall chemistry, but we do not know anything about the key structural and functional traits such as wood anatomy that greatly affect plant biomass recalcitrance. Furthermore, biofuel feedstocks have to be adapted to varied environmental conditions to ensure high productivity in plantations, but little is known about the molecular mechanisms underlying local adaptation. With the advancement in sequencing and genotyping technologies, association genetics has emerged as a powerful approach for unraveling complex traits in plants, thereby linking the natural variation present in the phenotype with the underlying genotype. Furthermore, the integration of phenotypic, genomic and environmental data has great premise for understanding plant adaptation in the face of climate change. Because of its rapid growth, hybrid vigor, broad geographic distribution, transformation potential, and the availability of tremendous genetic resources and wide phenotypic variation, Populus is a highly desirable genus for biofuel production and other wood products. My dissertation research uses an association genetics approach focused on important anatomical, morphological and physiological traits to address three key questions: (1) What genetic mechanisms underlie variation in morphological and physiological traits in P. trichocarpa? (2) What are the factors affecting local adaptation in P. trichocarpa and what is the relative contribution of climate and geography variables to population structure? (3) What genes or genomic regions are associated with variation in important functional and structural traits that can be targeted to enhance productivity and reduce recalcitrance of woody bioenergy feedstocks? My research will enhance understanding of the biology of Populus trichocarpa by determining the genetic basis of key agronomic traits such as vessel size and density, leaf area, and stomatal density that affect overall performance under field conditions using genome-wide association study (GWAS). Understanding the genetic basis of these traits is key for developing Populus as a biomass feedstock for biofuel production. Furthermore, morphological and structural traits are often tightly correlated with physiological performance. Therefore, another aspect of this study is to unravel the genetic basis of key physiological traits such as leaf chlorophyll content, carbon isotope composition and leaf water potential, and their correlation with morphological traits. This will aid in better understanding of stress tolerance and the overall biology of this species. Furthermore, by performing these studies in plantations that are clonally replicated in three environments, I evaluated the robustness of the associations. Using genotype environment association (GEA) and redundancy analysis (RDA) I identified loci conferring local adaptation in P. trichocarpa. Moreover, with RDA analysis I determined the relative contribution of climate and geography in neutral population structure. Similarly, I determined the relative contribution of genomic, climate and geography data in explaining phenotypic variation. A long-term goal of the project is to develop a selection model based on comprehensive genetic and phenotypic information so that the genome enabled breeding value can be estimated. This will enhance the efficiency of Populus breeding programs by shortening the breeding cycle and improving the accuracy of selection. This will aid in developing genetically improved trees with high biomass production and reduced recalcitrance to cellulose extraction, thereby furthering the development of the lignocellulosic biofuels industry.

Association Genetics and Local Adaptation of Populus trichocarpa Torr. & Gray