The genetic basis of a novel self-recognition system in Phlox drummondii (Polemoniaceae)

Genetic mechanisms to recognize and reject self-pollen (termed “self-incompatibility”) have evolved independently many times throughout flowering plant evolution. Of the four known mechanisms, each achieves self-incompatibility through distinct molecular pathways with a unique genetic basis, and most self-recognition systems remain uncharacterized. We combine classical genetic crosses with genomic tools to identify the genetic basis of a novel self-recognition mechanism in the wildflower, *Phlox drummondii*. We find no expression of known self-recognition genes (so called “S-loci”) in pistil transcriptomes, consistent with a currently uncharacterized self-recognition mechanism having evolved in the lineage containing *Phlox*. We use a bulk segregant analysis to map self-recognition to a single genomic region in two independent populations. Analyses of expression and polymorphism for genes within this region narrow our search to a single gene candidate. Allelic variation at this gene predicts cross-compatibility in a full diallel cross, providing further confirmation of its role in self-recognition. Our work identifies the genetic basis of a novel self-recognition system in flowering plants, adding to our understanding of the diverse mechanisms through which flowering plants achieve this evolutionarily significant phenotype.