Detection of S-alleles in a sweet cherry collection from Azerbaijan and Turkey using next generation sequencing

The gametophytic self-incompatibility (GSI) system of sweet cherry (Prunus avium L.) prevents fertilization with own or genetically related pollen. The interaction of style- and pollen-specific gene products from the S-locus determines self-incompatibility. The system consists of an S-allele-specific ribonuclease gene (S-RNase) and an S-haplotype-specific F-box protein gene (SFB). The determination of the S-allele genotype is possible with the help of molecular markers and is important for cherry breeders and producers. Because of domestication and targeted breeding, S-allele diversity in the cultivar spectrum is limited. To expand the scope of breeding material, seeds of different local sweet cherry cultivars and wild cherry genotypes were collected in the center of origin in Turkey and Azerbaijan. Individual plants of the progeny, 163 genotypes originating from Turkey and 97 genotypes from Azerbaijan, were genotyped by fragment length analysis of PCR-products amplified using an S-RNase-specific consensus primer pair. For reference, sweet cherry cultivars with known S-allele genotype were analyzed. In addition, amplicon-deep sequencing of the S-RNase-specific PCR-products of selected genotypes and subsequent BLAST analysis enabled precise determination of the present S-haplotypes. Thirty-one different S-haplotypes could be detected in the collected plant material. For nine of these alleles, no match could be found with previously described S-alleles based on fragment length and sequence analysis.