Single-plant-omics reveals the cascade of transcriptional changes during the vegetative-to-reproductive transition
Year: 2024
Type: article
Abstract: 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 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.
Source: The Plant Cell
Institutions: University of York, University of Glasgow
Language: English
Subfield: Plant Science
Domain: Life Sciences
SDG: Zero hunger
Open Access status: hybrid
Estimated APC paid: $5,255
Awards: BBSRC IAA University of York, The circadian clock in the ageing plant, G4584296072, Cellular and biochemical context of Arabidopsis circadian-clock components, Novel strategies for efficient selection of lines with synchronised development by using properties of the circadian clock, Setting a circadian clock: Structural understanding of the ligand-activation model of the circadian evening complex components ELF4 to ELF3, G5708329931, White Rose Doctoral Training Partnership in Mechanistic Biology and its Strategic Application, Mechanistic Biology and its strategic application, G9000032337, G9000172026
OpenAlex ID: W4401449771