Genetic basis of natural variation in photoprotection in Arabidopsis

Abstract

Light is a necessary factor for most living organism on Earth; however it can also become one of the most important abiotic environmental stresses limiting plant growth. As natural environments are extremely variable, plant has developed several mechanisms to cope with excess light energy such as adjusting leaf angle, chloroplast position, thermal dissipation, and detoxification of the reactive oxygen species resulting from stress. Among those mechanisms, thermal dissipation or Non-Photochemical Quenching (NPQ) seem to be the most rapid photoprotective response in higher plants. To investigate the natural variation of NPQ, different sets of Arabidopsis thaliana (Arabidopsis) including a genetically balanced set of natural accessions, Recombinant Inbred Intercross (RIXs), and photoprotective mutants were studied using simulated natural environments. In natural habitats, natural genetic variation is selected on to result in adaptive allelic variation. The Genome-Wide Association Study (GWAS) has been successful in identifying natural allelic variants underlying natural variation in many traits and in different plant species such as Arabidopsis, rice and maize. In order to expand the current knowledge of the genetic basis of NPQ, which may also be affected by environment, two main approaches were taken in this thesis. Firstly, the natural variation in NPQ under simulated natural environments was explored. Secondly, two mapping approaches, RIXs and GWAS, were applied to reveal candidate genes/loci underlying variation in the NPQ trait. This study investigated the physiological and molecular changes that occur in response to diurnal and seasonal growth conditions which plant experiences in the field. Two dynamic natural environments were simulated: coastal-autumn; which had moderate temperatures and light intensities, and inland-autumn; where plants were exposed to greater temperature variations and higher light intensities. Inland plants presented evidence of rapid NPQ in response to sudden higher light exposure, a decline of steady state NPQ and a decrease in chlorophyll content, indicating long-term acclimation. In contrast, coastal plants had a slower induction of NPQ followed by a slow increase in NPQ over time. This provides a better understanding on how plants have different NPQ kinetics responses under different environments; furthermore the responses are varied between accessions. The findings presented in this thesis demonstrated that natural genetic variation in NPQ phenotype is influenced not only by genetic factor but also environmental effects. TheGWAS and RIX results for the NPQ trait revealed a total of 27 QTL, of which RIX-QTL5-3, QTL5-2, and QTL5-3 overlapped between the two different mapping approaches. One of the most significant findings from this study is the identification of QTL1-4, which was found predominantly in the coastal condition. This QTL was directly over the PSII protein subunit PsbS gene, of which the loss of function mutant, non-photochemical quenching 4 (npq4), has been shown to lack Energy-dependent quenching (qE). The identification of this a priori gene is significant as although it a known NPQ gene it has not been identified in previous NPQ mapping studies. This suggests that the novel use of climate chambers and GWAS in this study allowed the genetic basis of variation in NPQ specific to certain environments and certain plant developmental stages to be identified. Taken together, the findings presented here have provided meaningful insight into the naturally occurring genetic variation in Arabidopsis accessions during stressful condition, providing the opportunity to identify more genes that are involved in the regulation of photoprotection in response to the natural environment.