A Genome-Wide Association Study of Non-Photochemical Quenching in response to local seasonal climates in Arabidopsis thaliana

Abstract

Field-grown plants have variable exposure to sunlight as a result of shifting cloud-cover, seasonal changes, canopy shading, and other environmental factors. As a result, they need to have developed a method for dissipating excess energy obtained from periodic excessive sunlight exposure. Non-photochemical quenching (NPQ) dissipates excess energy as heat, however the physical and molecular genetic mechanics of NPQ variation are not understood. In this study, we investigated the genetic loci involved in NPQ by first growing different Arabidopsis thaliana accessions in local and seasonal climate conditions, then measured their NPQ kinetics through development by chlorophyll fluorescence. We used genome-wide association studies (GWAS) to identify 15 significant quantitative trait loci (QTL) for a range of photosynthetic traits, including a QTL co-located with known NPQ gene PSBS (AT1G44575). We found there were large alternative regulatory segments between the PSBS promoter regions of the functional haplotypes and a significant difference in PsbS protein concentration. These findings parallel studies in rice showing recurrent regulatory evolution of this gene. The variation in the PSBS promoter and the changes underlying other QTLs could give insight to allow manipulations of NPQ in crops to improve their photosynthetic efficiency and yield. B.P. & J.B. conceived the project; B.P., J.B., P.W. and T.R. designed the research plan and analysis; P.W. supervised the experiments; T.R. performed most of the experiments and analysis; P.G., T.S., A.A. & E.A. designed and undertook experimental design, experiments and analysis for Figure 4; R.C. did the GWAS analysis; P.W., T.R. & A.A. wrote the article with contributions of all the authors. O_FIG O_LINKSMALLFIG WIDTH=158 HEIGHT=200 SRC="FIGDIR/small/539379v1_fig4.gif" ALT="Figure 4"> View larger version (57K): org.highwire.dtl.DTLVardef@12ba2f9org.highwire.dtl.DTLVardef@1d88c15org.highwire.dtl.DTLVardef@1d4f21eorg.highwire.dtl.DTLVardef@16396aa_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 4:C_FLOATNO (A-D) Coverage tracks of the PSBS genomic regions from five low NPQ (A and B) and five high NPQ (C and D) Arabidopsis accessions aligned with the TAIR 10 Col-0 reference genome (low NPQ accession; A and C) and KBS-Mac-74 genome (high NPQ accession; B and D). Values along x-axes indicate the base pair distance relative to the PSBS transcription start site. Genes along the track are coloured green and the intergenic region is coloured pink. (E) Graphical view of the alignment of the TAIR 10 Col-0 and the KBS-Mac-74 PSBS genomic regions. Axis values refer to base pair positions within the respective tracks. (F) Comparison of the average relative PsbS protein abundance between low and high NPQ accessions. Error bars represent standard deviations. N=30; *** P < 0.001 with paired Students T test. C_FIG