Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species

Significance Developmental programs of higher plants show plasticity to environmental signals. In the Brassicaceae, the transcription factor (TF) FLOWERING LOCUS C (FLC) represses reproduction until plants are exposed to winter cold. Here we define the target genes of FLC in two species in different lineages of the Brassicaceae and compare the target sequences across the family. Fewer than 20% of target genes were conserved between the species examined, and genes involved in flowering were overrepresented among these. By contrast, many of the nonconserved target genes were involved in stress responses. We propose that, for TFs like FLC, which control environmental responses of plants, core sets of targets are conserved between species, but the majority change rapidly during evolution.