Network analysis of flowering time genes suggests regulatory changes among SOC1 orthologues in response to cold in Brassica napus

Flowering plants respond to multiple environmental and endogenous cues to determine the timing of their transition from the vegetative to floral state. Most of our knowledge of the gene regulatory network (GRN) controlling the floral transition has been derived from the model plant, Arabidopsis thaliana. This knowledge needs to be translated to crop plants to support the development of varieties that can be grown in different and rapidly changing climate conditions. However, due to increased genome complexity and limited prior knowledge, its translation into crops is not always straightforward. Here, we present a study of the regulatory links among flowering time genes in Brassica napus (oilseed rape), an allotetraploid crop that is a close relative of Arabidopsis. Using a comparative transcriptomics approach, we show that the majority of the orthologous gene pairs have similar expression dynamics over development between Arabidopsis and B. napus. Some genes, however, have experienced regulatory changes, with flowering time genes in B. napus having higher than average differences in their expression profiles from their Arabidopsis orthologues. Despite these differences, the inferred regulatory links among orthologues of known flowering time genes in B. napus exhibit a similar topology to the GRN in Arabidopsis. We present a detailed analysis of orthologues of SUPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) that have similar expression patterns under normal conditions, but different dynamics under cold temperature conditions. These findings suggest possible subfunctionalisation among SOC1 paralogues in response to temperature changes.