Biology subjects

Redmond, E. J.

Publications and source records attributed to Redmond, E. J..

8 recordsLinked to original sources

bioRxiv2025

ELF3 controls trait heterogeneity by tuning the rate of maturation in Arabidopsis and barley

Trait heterogeneity in a population increases the likelihood that some individuals will survive an unpredictable environmental stress. Individual plants mature at different rates due to genetics, environmental factors, and random chance. All of this contributes to trait heterogeneity. EARLY FLOWERING3 (ELF3), a core circadian clock component, determines developmental timing, and here we tested the hypothesis that it would shape trait heterogeneity. We developed a model predicting that faster-developing populations exhibit greater heterogeneity during development but reduced heterogeneity at maturity, while slower-growing populations show the opposite pattern. Experiments in Arabidopsis elf3 and barley Hvelf3 mutants supported this prediction. In Arabidopsis, ELF3 controlled hypocotyl elongation variability via maturation rate rather than direct regulation. Bolting time heterogeneity also decreased in faster-growing plants. In barley, Hvelf3 altered growth heterogeneity, but this was initially masked by germination timing differences. Finally, smaller barley plants were found to be more resilient to osmotic stress, suggesting that ELF3-driven trait heterogeneity may contribute to bet hedging. These findings highlight how modifying developmental rates influences population-level trait distributions and stress resilience.

plant biology↗

bioRxiv2025

The genetic basis for synchronized time perception in plant populations

Synchronised developmental timing is important for ensuring crop uniformity and high yields. However, climate change is leading to crops being grown at different latitudes, varying their exposures to photoperiods over seasons and impacting developmental timings. We investigated whether the response of circadian rhythms in seedlings to changes in photoperiod would enable us to predict the timing and synchronization of flowering. Indeed, we show that the same Quantitative Trait Loci (QTLs) are associated to circadian traits in seedlings and developmental traits during bolting, using the first recombinant inbred lines (RILs) between African and European Arabidopsis lineages, spanning diverse latitudes. Two QTLs contain K-Homology Domain RNA binding proteins (KH17, KH29) and are associated with splicing variants in known flowering genes, MADS AFFECTING FLOWERING2 and 3 (MAF2, MAF3), including generating chimeric transcripts, a potential mechanism for accelerated proteome evolution. Natural variants in KH17, including in its prion-like domain, are associated with de-coupling the mean and synchronization of flowering time, enabling greater adaptation of population-level heterogeneity in developmental timings. Our results suggest that circadian traits in seedlings could be used to screen for agriculturally relevant developmental traits in mature plants, enabling efficient breeding of climate-resilient crops.

plant biology↗

bioRxiv2024

Stable and dynamic gene expression patterns over diurnal and developmental timescales in Arabidopsis thaliana

O_LIDevelopmental processes are known to be circadian regulated in plants. For instance, the circadian clock regulates genes involved in the photoperiodic flowering pathway and the initiation of leaf senescence. Furthermore, signals which entrain the circadian clock, such as energy availability, are known to vary in strength over plant development. However, diurnal oscillations of the Arabidopsis transcriptome have typically been measured in seedlings. C_LIO_LIWe collected RNA-seq data from Arabidopsis leaves over developmental and diurnal timescales, concurrently: every 4 hours per day, on 3 separate days after a synchronised vegetative-to-reproductive transition. Gene expression varied more over the developmental timescale than on the diurnal timescale, including genes related to a key energy sensor: the Sucrose non-fermenting-1-related protein kinase (SnRK1) complex. C_LIO_LIMoreover, regulatory targets of core clock genes displayed changes in rhythmicity and amplitude of expression over development. Cell-type-specific expression showed diurnal patterns that varied in amplitude, but not phase, over development. Some previously identified qRT-PCR housekeeping genes display undesirable levels of variation over both timescales. We identify which common qRT-PCR housekeeping genes are most stable across developmental and diurnal timescales. C_LIO_LIIn summary, we establish the patterns of circadian transcriptional regulation over plant development, demonstrating how diurnal patterns of expression change over developmental timescales. C_LI

plant biology↗

bioRxiv2024

Harnessing light heterogeneity to optimise controlled environment agriculture

Yield is impacted by the environmental conditions that plants are exposed to. Controlled environmental agriculture provides growers with an opportunity to fine-tune environmental conditions for optimising yield and crop quality. However, space and time constraints will limit the number of experimental conditions that can be tested, which will in turn limit the resolution to which environmental conditions can be optimised. Here we present an innovative experimental approach that utilises the existing heterogeneity in light quantity and quality across a vertical farm to evaluate hundreds of environmental conditions concurrently. It proposes a three-phase workflow for identifying critical light variables, which can guide targeted improvements in yield and energy use. Using an observational study design, we identify features in light quality that are most predictive of biomass in different microgreens crops (kale, radish and sunflower) that may inform future iterations of lighting technology development for vertical farms. The findings suggest that light quality, rather than just light intensity, plays a crucial role in uniform crop yields and that light sensitivities are variety-specific, highlighting the importance of tailored light recipes for different crops.

plant biology↗

bioRxiv2024

Hypocotyl Development in Arabidopsis and other Brassicaceae Displays Evidence of Photoperiodic Memory

Sensing and responding to photoperiod changes is essential for plants to adapt to seasonal progression. Most of our understanding of how plants sense photoperiodic changes is through studies on flowering time. However, other aspects of plant development are regulated by the photoperiod, including hypocotyl elongation. Unlike flowering, hypocotyl elongation displays a greater plasticity to changes in the photoperiod with increases in daylength causing greater inhibition of growth until a threshold is met. Previous studies have only looked at hypocotyl development in the context of a stationary photoperiod. It is unknown if changes in the photoperiod during development influence hypocotyl elongation. Here, we developed a physiological assay to investigate this question. We have discovered that hypocotyl elongation is influenced by a memory of past photoperiod exposure in Arabidopsis and Brassicaceae cultivars used for microgreen agriculture. Photoperiodic memory persisted for multiple days, although it weakened over time, and the strength of the memory was dependent on the genetic background. We identified that phyB and ELF3, key regulators of hypocotyl development, were required for photoperiodic memory. Finally, we identified that the circadian clock is unlikely to function as a repository for photoperiodic memory as circadian rhythms quickly re-aligned with the new photoperiod. In summary, our work highlights for the first-time evidence of a photoperiodic memory that can control plant development.

plant biology↗

bioRxiv2023

An Arabidopsis leaf expression atlas across diurnal and developmental scales

Mature plant leaves are a composite of distinct cell types, including epidermal, mesophyll and vascular cells. Notably the proportion of these cells, and the relative transcript concentrations within different cell types may change over time. While gene expression data at a single-cell level can provide cell-type specific expression values, it is often too expensive to perform this on high resolution time series. Although bulk RNA-seq can be performed in a high resolution time series, the RNA-seq in whole leaves measures the average gene expression values across all cell types in each sample. In this study, we combined single cell RNA-seq data with time-series data from whole leaves to infer an atlas of cell type-specific gene expression changes over time for Arabidopsis thaliana. We inferred how relative transcript concentrations of cell types vary across diurnal and developmental time scales. Importantly this analysis revealed three sub-groups of mesophyll cells that have distinct temporal profiles of expression. Finally, we develop tissue-specific gene networks that form a new community resource: An Arabidopsis Leaf Time-Dependent Atlas (AraLeTa), which allows users to extract gene networks that are confirmed by transcription factor binding data and specific to certain cell types, at certain times of day and certain developmental stages, which is available at: https://regulatorynet.shinyapps.io/araleta/.

plant biology↗

bioRxiv2023

Single-plant-omics reveals the cascade of transcriptional changes during the vegetative-to-reproductive transition

Plants undergo rapid developmental transitions, as well as gradual developmental processes. Moreover, individual plants within a population will undergo the developmental transitions asynchronously, so it is difficult to assemble a time series to resolve the sequence of transcriptional changes that take place during these rapid transitions. Single-plant-omics has the potential to distinguish between transcriptional events that are associated with these binary and continuous processes. Furthermore, we can utilise single-plant-omics to exploit this developmental asynchrony to order individual plants by their developmental trajectory, revealing a detailed cascade of transcriptional events. Here, we utilise single-plant-transcriptomics to resolve the transcriptional events that coincide with the onset of bolting. We performed RNA-seq on the leaves of individual plants from a large population of wild type Arabidopsis thaliana replicated at one time point during the vegetative-to-reproductive transition. Even though more than half of transcripts were differentially expressed between bolted and unbolted plants, we were able to find a subset of regulators that were more closely associated with gradual developmental traits like leaf size and biomass. Using a novel pseudotime inference algorithm, we determined that some senescence-associated processes, such as the reduction in ribosome biogenesis, are evident in the transcriptome before a bolt is visible. These results show the potential of single-plant-omics to reveal the detailed sequence of events that occur during rapid developmental transitions. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=179 SRC="FIGDIR/small/557157v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@c50448org.highwire.dtl.DTLVardef@9c384aorg.highwire.dtl.DTLVardef@33c336org.highwire.dtl.DTLVardef@55302e_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract: Physiological changes around bolting can be categorised into: binary processes, which appear to have either occurred or not occurred at any given timepoint; or continuous processes, which can be observed quantitatively. For binary processes, expression of strongly correlated genes can appear to follow a step change dynamic over time. However, when considered over a shorter timescale, the dynamics appear much smoother. For continuous processes, the shorter timescale should also capture smooth changes in gene expression. C_FIG

plant biology↗

bioRxiv2023

Complex epistatic interactions between ELF3, PRR9, and PRR7 regulates the circadian clock and plant physiology

Circadian clocks are endogenous timekeeping mechanisms that coordinate internal physiological responses with the external environment. EARLY FLOWERING3 (ELF3), PSEUDO RESPONSE REGULATOR (PRR9), and PRR7 are essential components of the plant circadian clock and facilitate entrainment of the clock to internal and external stimuli. Previous studies have highlighted a critical role for ELF3 in repressing the expression of PRR9 and PRR7. However, the functional significance of activity in regulating circadian clock dynamics and plant development is unknown. To explore this regulatory dynamic further, we firstly employed mathematical modelling to simulate the effect of the prr9/prr7 mutation on the elf3 circadian phenotype. These simulations suggested that simultaneous mutations in prr9/prr7 could rescue the elf3 circadian arrythmia. Following these simulations, we generated all Arabidopsis elf3/prr9/prr7 mutant combinations and investigated their circadian and developmental phenotypes. Although these assays could not replicate the results from the mathematical modelling, our results have revealed a complex epistatic relationship between ELF3 and PRR9/7 in regulating different aspects of plant development. ELF3 was essential for hypocotyl development under ambient and warm temperatures, while PRR9 was critical for root thermomorphogenesis. Finally, mutations in prr9 and prr7 rescued the photoperiod insensitive flowering phenotype of the elf3 mutant. Together, our results highlight the importance of investigating the genetic relationship amongst plant circadian genes.

plant biology↗