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

A population of wild type plants can contain individuals with drastically different flowering times, due to developmental asynchrony. We performed RNA-seq on individual plants from a large population of wild type (Ws-2) Arabidopsis thaliana, sampling a large number (~70) of replicates at one timepoint during the flowering transition. We have characterised a major transcriptomic switch between plants before and after bolting. Applying methods used in single-cell RNA-seq, we used this data to order the plants by their predicted age – which is referred to as a pseudo-time series. In contrast to a traditional RNA-seq time series, this allows us to view changes in gene expression at a fine temporal scale. Importantly, we can infer the order that transcription factors ‘switch on’ during the vegetative to floral transition. A population of wild type plants were grown under controlled conditions and physiological traits were measured. 75 plants were chosen for sequencing, to represent a diversity of bolting statuses. We then performed RNA-seq and quantified the gene expression of each individual set of plant leaves. In addition, we called variants across the population from the RNA-seq data, to assess the impact of genetic variation on physiology and developmental asynchrony.