Self-incompatibility of sweet cherry (Prunus avium L.) is controlled by the multiallelic S-locus. While many cultivars and wild accessions have been S-genotyped, only limited data are available on accessions native to the center of origin of this species. Therefore, this study was carried out to determine the S-genotype of 11 landrace cultivars and 17 local genotypes selected from populations growing wild at the Black Sea coast. Eleven sweet cherries (S1–S7, S10, and S12–S14) and some wild cherries (S17–S19, S21/25, and S31) S-RNase alleles were detected. The results indicate that Turkish cultivars represent a broader gene pool as compared with international cultivars. A new (S37) and a doubtful allele (provisionally labelled as S7m) as well as the sour cherry S34-allele were identified in sweet cherry. These data and others (SSR variants within the S13-RNase introns) confirmed that allele pools of sweet and sour cherries in the Black Sea region are overlapping. A new cross-incompatibility group, XLV (S2S18), was also proposed. Allele-specific primers were designed for S17–S19, S21/25, S34, and S37. A phylogenetic analysis of the cherry S31-RNase and its trans-specific sister alleles reliably mirrored the assumed length of the time period after the divergence of species in the subgenera Cerasus and Prunophora. Most variations (insertions/deletions and single-nucleotide polymorphisms) in the S-RNase gene were silent and, hence, have not been exposed to natural selection. The results are discussed from the aspects of S-allele evolution and phylogenetic relationships among cherries and other Prunus species.
