Genetic basis of metabolic trait variation in the giant duckweed Spirodela polyrhiza (Lemnaceae)

Abstract

Using the giant duckweed Spirodela polyrhiza as a model organism for investigating pleiotropic gene functions in plants, this thesis aims to identify gene candidates controlling herbicide resistance, metabolite contents and sexual reproduction in S. polyrhiza. For this we quantified the intra-specific variation in free metabolite contents, growth and diquat resistance in S. polyrhiza. Candidate genes associated with these traits were identified through genome-wide association studies (GWAS). The first article focuses on quantifying the phenotypic variation in diquat resistance, revealing 8.5-fold differences between the most resistant and most susceptible genotypes. Genotypes showed variation in superoxide dismutase activity, ratios of oxidized to reduced antioxidant contents and uptake kinetics of diquat. On a genetic level, genes involved in biotic stress responses (SpLOX2.1 and SpGBPL2), apoptosis control (SpDLH) and starch metabolism (SpSBE3) were associated with diquat resistance. The second article focuses on identifying candidate genes controlling variation in free metabolite contents and growth in S. polyrhiza. Overall, secondary metabolites showed stronger intra-specific variation than primary metabolites and growth parameters. Often primary metabolites showed strong correlations with plant biomass. A GWAS conducted on free metabolite levels identified candidate genes controlling photosynthesis (SpLHCB5), protein-degradation (SpUBP7), cell-cycle (SpPUB4) and secondary metabolite synthesis (SpMYBC1) to be associated with biomass-correlated traits. The third study investigates the migration history and genetic diversity of S. polyrhiza. Analysis of population structure revealed four genetic populations for this duckweed species, which were largely defined by their geographic locations as American, SE-Asian, Indian and European populations. A genome-wide scan identified 69 genes, whose homologs were mainly linked to sexual reproduction processes to be under selection. Together, this thesis studies gene candidates controlling herbicide resistance, free metabolite contents and sexual reproduction in S. polyrhiza, which can be used for biotechnological optimization of this plant. The results further suggest that pleiotropic genes involved in stress responses confer non-targeted site herbicide resistance.