Modelling of plant circadian clock for characterizing hypocotyl growth under different light quality conditions

To meet the ever-increasing global food demand, the food production rate needs to be increased significantly in the near future. Speed breeding is considered as a promising agricultural technology solution to achieve the zero-hunger vision as specified in the United Nations Sustainable Development Goal 2. In speed breeding, the photoperiod of the artificial light has been manipulated to enhance crop productivity. In particular, regulating the photoperiod of different light qualities rather than solely white light can further improve speed breading. However, identifying the optimal light quality and the associated photoperiod simultaneously remains a challenging open problem due to complex interactions between multiple photoreceptors and proteins controlling plant growth. To tackle this, we develop a first comprehensive model describing the profound effect of multiple light qualities with different photoperiods on plant growth (i.e. hypocotyl growth). The model predicts that hypocotyls elongated more under red light compared to both red and blue light. Drawing similar findings from previous related studies, we propose that this might result from the competitive binding of red and blue light receptors, primarily Phytochrome B (phyB) and Cryptochrome 1 (cry1) for the core photomorphogenic regulator, CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). This prediction is validated through an experimental study on Arabidopsis thaliana. Our work proposes a potential molecular mechanism underlying plant growth under different light qualities and ultimately suggests an optimal breeding protocol that takes into account light quality

Impact of Genetic Variation and Timescale on Diatom Salinity Stress Response

Natural environments are dynamic, and organisms must sense and respond to changing conditions. One common way organisms deal with stressful environments is through gene expression changes, allowing for stress acclimation and resistance which occurs over varying time spans in different species. The recent evolutionary history of populations could greatly influence their ability to respond successfully. An evolutionary history in disturbed or fluctuating conditions could promote increased resistance or a more rapid response to these environmental stressors. To understand the impact of genotypic variation and timescales on response and acclimation to salinity changes, we have been exploiting the abilities of euryhaline diatoms in the order Thalassiosirales. This dissertation explores the mechanisms two species of Thalassiosirales use to mitigate short- and long-term effects of salinity stress. We first clarified the phylogenetic relationships of Cyclotella, one of the largest clades in the order containing numerous marine—freshwater transitions, reclassifying the relatively new genus Spicaticribra as a member of Cyclotella based on phylogenetic analyses of the genes rbcL, psbC, SSU, and LSU. We then determined that variation derived from genotypic differences between strains of Cyclotella cryptica had a greater impact then that imposed by gene expression changes following acclimation to different salinity conditions. When pooled together, the primary transcriptome modifications were related to the regulation of compatible solutes and ion transporters in an effort to maintain the osmotic gradient in suboptimal salinities. Subsequently, we acclimated multiple strains of Skeletonema marinoi, another euryhaline member of Thalassiosirales, to a range of salinities. With sufficient technical replication of these strains, we were able to determine that the variation between strains was due largely to degree of differential expression of genes, rather than strains regulating different genes entirely. Including genetic variation allowed us to identify more genes impacted by salinity changes than any one strain would have revealed and, additionally, we found a small set of 27 shared genes that were differentially expressed in all strains. We argue that this core set may have played an important role in ancestral marine—freshwater transitions for S. marinoi. Similar to C. cryptica, averaged response across all strains relied heavily on long-term maintenance of the cellular osmotic gradient, but there was little other indication of severe stress in the salinity treatments we used. We found considerable disparity in comparing the results of our post-acclimated C. cryptica behavior with previously reported short-term stress behavior in the species. Thus, we conducted a short-term time series experiment looking at C. cryptica’s gene expression response to a rapid exposure to freshwater. Differential gene expression analysis concluded C. cryptica responds to freshwater shock by temporarily halting growth and downregulating genes associated with maintenance of cellular division, such as ribosome biogenesis, transcription, and translation. Genes involved in reactive oxygen species scavenging and regulation of the osmotic gradient (i.e., osmolytes and ion transporters) are upregulated. Although limited, our comparison of results from different timescales found little overlap between the regulated genes during the peak period of stress, initial acclimation, and post-acclimation. This suggests that there is wide variation in the genes responsible for various stages of the stress response. These experiments highlight the power of including genetic variation to uncover mechanisms utilized in environmental stress response, as well as the importance of considering how that response changes from exposure to acclimation in order to develop a complete picture of how organisms cope with stress