Self-incompatibility (SI) is one of the most important genetic systems maintaining genetic diversity in flowering plants. The gametophytic self-incompatibility (GSI) system of the Solanaceae, Rosaceae, and Plantaginaceae are called the S-RNase-based GSI system. In this GSI system, the self and cross incompatibility reaction specificities of pistil and pollen are determined by ribonuclease (RNase) and F-box protein, respectively. Although the three plant families use the same molecule as the pistil S and pollen S determinants, molecular and genetic analyses of Prunus SC S haplotypes and polyploid sour cherry reveal the possible existence of a distinct self and cross recognition mechanism in the S-RNase-based GSI system of Prunus. In Prunus, the specificity determinants of pistil and pollen are called S-RNase and S haplotype-specific F-box protein (SFB), respectively. We previously proposed a working hypothesis in which Prunus SFB is supposed to have a distinct function from the pollen S determinant F-box proteins (SLF) of Solanaceae and Plantaginaceae. Here, we performed a detailed phylogenetic analysis of Prunus SFB and its orthologs in the Prunus genome and other angiosperm genomes. Our results indicated that Prunus SFB was generated from recent Prunus-specific gene duplications. Prunus F-box protein genes that are located flanking regions the S locus (SLFLs) are classified to the same clade as the pollen S F-box protein genes of Solanaceae, Plantaginaceae, and the subtribe Pyrinae (Rosaceae), indicating that duplication and sub-functionalization of the original pollen S genes generated SFB. We discuss the possible mechanisms of (in)compatibility reaction in Prunus.
