Epigenetic suppression of Brassica rapa FLC via a COLD MEMORY ELEMENT-like motif during vernalization

Exposure to prolonged cold, such as during winter, enables many winter-annual, biennial, and perennial plants to acquire the ability to transition to flowering, a process known as vernalization. In the Brassicaceae family, including Arabidopsis thaliana, vernalization is essential for floral induction. This process triggers dynamic transcriptomic reprogramming, leading to both phenotypic and physiological changes. To date, molecular studies of vernalization-mediated floral transition have predominantly focused on the model plant Arabidopsis. However, the mechanisms governing this response remain poorly understood in economically important crops such as Chinese cabbage (Brassica rapa ssp. pekinensis). In Arabidopsis, a DNA motif known as the COLD MEMORY ELEMENT (CME) plays a critical role in recruiting the repressive histone modification H3K27me3 to stably silence FLC, a major floral repressor. In this study, we identified CME-like elements within the first intron of Brassica rapa FLC homologs. To investigate the functional significance of this CME-like motif (hereafter referred to as BrCME) in vernalization-induced repression of BrFLC genes, we conducted a series of genetic, molecular, and genomic analyses, including the use of transgenic lines subjected to a vernalization time course. Our findings reveal that sequence alteration of the BrCME motif in the first intron of BrFLC2 significantly impairs PRC2-mediated epigenetic silencing of the gene, resulting in a pronounced delay in flowering in a heterologous Arabidopsis system. These results suggest that BrCME represents a promising target for genetic manipulation aimed at enhancing crop productivity (e.g. extending the vegetative growth period) in Chinese cabbage and related Brassica species.

The online version contains supplementary material available at 10.1007/s11032-025-01615-8.