Altered interactions between cis-regulatory elements cause divergent expression patterns that partially resolve the redundancy between BLADE-ON-PETIOLE genes in Capsella rubella

Duplicated genes are thought to follow one of three evolutionary trajectories that resolve their redundancy: neofunctionalization, subfunctionalization or pseudogenization. Differences in expression patterns have been documented for many duplicated gene pairs and interpreted as evidence of subfunctionalization and a resolution of redundancy. However, little is known about the functional impact of such differences and about their molecular basis. Here we investigate the genetic and molecular basis for the partial resolution of redundancy between the two BLADE-ON-PETIOLE genes BOP1 and BOP2 in Capsella rubella compared to Arabidopsis thaliana. While both genes remain almost fully redundant in A. thaliana, BOP1 in C. rubella can no longer ensure wild-type floral organ numbers and suppress bract formation, due to an altered expression pattern in the region of the cryptic bract primordium. We use two complementary approaches, transgenic rescue of A. thaliana atbop1 atbop2 double mutants and deletions in the endogenous AtBOP1 promoter, to demonstrate that several BOP1 promoter regions containing conserved non-coding sequences interact in a non-additive manner to control BOP1 expression in the bract primordium, and that changes in these interactions underlie the evolutionary divergence between C. rubella and A. thaliana BOP1 expression and activity. Similarly, we find that altered interactions between cis-regulatory regions underlie the divergence in functional promoter architecture regarding the control of floral-organ abscission by BOP1. These findings highlight the complexity of promoter architecture in plants and suggest that changes in the interactions between cis-regulatory elements are key drivers for evolutionary divergence in gene expression and the resolution of redundancy.