Högskolan i Skövde

Plants must continuously adjust to changing environmental light conditions, including exposure to ultraviolet (UV, 280 - 315 nm) radiation and variations in visible light intensity. This study aimed to identify transcriptional patterns and genetic regulators involved in light acclimation, using Arabidopsis thaliana accessions with differing sensitivities to UV radiation. By integrating transcriptomic and genomic datasets, gene expression responses and genetic variation across three accessions (Arabidopsis thaliana, C24, Col-0, and Ga2) subjected to UV radiation were explored under two different intensities of photosynthetically active radiation (PAR) (400 - 700 nm). These treatments allowed comparison of plant responses to high and low UV: PAR ratios and to different PAR light intensities. 

RNA-seq-based differential gene expression analysis revealed accession-specific transcriptional responses, with principal component analysis (PCA) showing clear separation between accessions but limited clustering by treatment. Gene Ontology Enrichment Analysis (GOEA) highlighted condition-specific biological responses, most notably under high UV:PAR ratio in Col-0, where genes associated with RNA biosynthesis, transcriptional regulation, and stress adaptation were significantly enriched. In contrast, only high light intensity induced weaker responses, mainly involving modest activation of ribosome biogenesis and RNA processing pathways. 

To explore the genetic basis of these differences, whole-genome sequencing data from 63 Arabidopsis thaliana C24 accessions were processed to identify high-impact single nucleotide polymorphisms (SNPs) and indels. Over 7,000 high-impact mutations were mapped to 3,213 unique gene regions. Genes carrying high-impact mutations were then intersected with differentially expressed genes across treatment conditions to identify overlapping candidate genes. GO enrichment on these overlapping sets revealed meaningful results only in Arabidopsis thaliana Col-0 under high UV: PAR and high light intensity, and in gene sets shared between Arabidopsis thaliana Col-0 and C24 accessions under UV-related conditions. 

The findings of this work demonstrate accession-specific patterns of gene expression in Arabidopsis thaliana plants exposed to UV radiation. Furthermore, transcriptional responses to UV were modulated by the levels of visible light to which plants were exposed. The identification of condition-specific gene regulation patterns and mutation-linked expression changes provides insight into the molecular basis of UV acclimation in Arabidopsis and suggests candidate genes for future functional validation and crop improvement strategies aimed at enhancing stress resilience.

Popular scientific summary

Plants can't escape harsh conditions but instead, they must adapt to changes in their environment, such as light, temperature, and water. However, climate change and human activity are making climatic conditions more stressful for plants. Climate change may alter light environments by increasing ultraviolet (UV) radiation through stratospheric ozone depletion and by modifying sunlight intensity and duration due to changes in cloud cover and atmospheric composition (Stanhill & Cohen, 2001). Light, in particular, is a key signal for plants, not just as an energy source for photosynthesis, but also as a cue to control growth and development.

Plants sense light through special proteins called photoreceptors. One of these, UVR8, helps plants detect UV-B radiation, which can damage DNA and create harmful molecules called reactive oxygen species (ROS). In response to harmful UV radiation, plants activate protective genes and produce UV-absorbing compounds like flavonoids. Flavonoid concentration, which helps protect plants from UV-B radiation, is influenced also by visible light (PAR) intensity.

This study focused on understanding how plants respond at the molecular level to different combinations of UV and visible light. Although previous scientific research has advanced the understanding of how plants react to UV and PAR separately, it is still don't fully understood how these two environmental factors interact. To explore this, this study used three Arabidopsis thaliana accessions, C24, Col-0, and Ga2 that vary in their UV sensitivity. Plants were grown under specific light treatments, and their gene activity analyzed using RNA sequencing and bioinformatics tools.

The results showed that the different accessions responded in distinct ways to UV and high light conditions. One accession, Arabidopsis thaliana Col-0, showed a more targeted and controlled response to high UV: PAR light, turning on genes involved in RNA processing, DNA repair, and flavonoid production, suggesting it has strong internal mechanisms for UV protection. In contrast, Arabidopsis thaliana C24 activated a broader set of genes, including those related to chromosome organization and lipid metabolism, indicating a more flexible but possibly less focused strategy for dealing with stress.

These findings highlight how natural genetic variation affects plant stress responses. Even when exposed to the same environment, different plant varieties can activate different genetic strategies. Understanding these strategies can help identify key genes that boost stress tolerance. In the future, tools like CRISPR could target these genes to develop crops that are more resistant to UV damage or harsh sunlight. From an agricultural point of view, this research helps identify naturally UV-tolerant traits, like those found in Arabidopsis thaliana Col-0, that could be used in breeding or engineering more strong crops. As climate change leads to more intense sunlight and UV exposure, these insights become increasingly valuable for securing future food production.