Genome-wide association study unveils ascorbate regulation by PAS/LOV PROTEIN during high light acclimation.

Varying light conditions elicit metabolic responses as part of acclimation with changes in ascorbate levels being an important component. Here, we adopted a genome-wide association-based approach to characterize the response in ascorbate levels on high light (HL) acclimation in a panel of 315 Arabidopsis (Arabidopsis thaliana) accessions. These studies revealed statistically significant SNPs for total and reduced ascorbate under HL conditions at a locus in chromosome 2. Ascorbate levels under HL and the region upstream and within PAS/LOV PROTEIN (PLP) were strongly associated. Intriguingly, subcellular localization analyses revealed that the PLPA and PLPB splice variants co-localized with VITAMIN C DEFECTIVE2 (VTC2) and VTC5 in both the cytosol and nucleus. Yeast 2-hybrid and bimolecular fluorescence complementation analyses revealed that PLPA and PLPB interact with VTC2 and that blue light diminishes this interaction. Furthermore, PLPB knockout mutants were characterized by 1.5- to 1.7-fold elevations in their ascorbate levels, whereas knockout mutants of the cry2 cryptochromes displayed 1.2- to 1.3-fold elevations compared to WT. Our results collectively indicate that PLP plays a critical role in the elevation of ascorbate levels, which is a signature response of HL acclimation. The results strongly suggest that this is achieved via the release of the inhibitory effect of PLP on VTC2 upon blue light illumination, as the VTC2-PLPB interaction is stronger under darkness. The conditional importance of the cryptochrome receptors under different environmental conditions suggests a complex hierarchy underpinning the environmental control of ascorbate levels. However, the data we present here clearly demonstrate that PLP dominates during HL acclimation.

Bringing more players into play: Leveraging stress in genome wide association studies.

In order to meet the demand of the burgeoning human population as well as to adapt crops to the enhanced abiotic and biotic stress caused by the global climatic change, breeders focus on identifying valuable genes to improve both crop stress tolerance and crop quality. Recently, with the development of next-generation sequencing methods, millions of high quality single-nucleotide polymorphisms (SNPs) have been made available and genome-wide association studies (GWAS) are widely used in crop improvement studies to identify the associations between genetic variants of genomes and relevant crop agronomic traits. Here, we review classic cases of use of GWAS to identify genetic variants associated with valuable traits such as geographic adaptation, crop quality and metabolites. We discuss the power of stress GWAS to identify further associations including those with genes that are not, or only lowly, expressed during optimal growth conditions. Finally, we emphasize recent demonstrations of the efficiency and accuracy of time-resolved dynamic stress GWAS and GWAS based on genomic gene expression and structural variations, which can be applied to resolve more comprehensively the genetic regulation mechanisms of complex traits.