Allele-specific PCR detection of sweet cherry self-incompatibility (S) alleles S1 to S16 using consensus and allele-specific primers

PCR-based identification of all 13 known self-incompatibility (S) alleles of sweet cherry is reported. Two pairs of consensus primers were designed from our previously published cDNA sequences of S-1 to S-6 S-RNases, the stylar components of self-incompatibility, to reveal length variation of the first and the second introns. With the exception of the first intron of S-13, these also amplified S-7 to S-14 and an allele previously referred to as S-x, which we now label S-16. The genomic PCR products were cloned and sequenced. The partial sequence of S-11 matched that of S-7 and the alleles were shown to have the same functional specificity. Allele-specific primers were designed for S-7 to S-16, so that allele-specific primers are now available for all 13 S alleles of cherry (S-8, S-11 and S-15 are duplicates). These can be used to distinguish between S alleles with introns of similar size and to confirm genotypes determined with consensus primers. The reliability of the PCR with allele-specific primers was improved by the inclusion of an internal control. The use of the consensus and allele-specific primers was demonstrated by resolving conflicting genotypes that have been published recently and by determining genotypes of 18 new cherry cultivars. Two new groups are proposed, Group XXIII (S3S16), comprising 'Rodmersham Seedling' and 'Strawberry Heart', and Group XXIV (S6S12), comprising 'Aida' and 'Flamentiner'. Four new self-compatibility genotypes, S3S3', S-4'S-6, S-4'S-9 and S-4'S-13, were found. The potential use of the consensus primers to reveal incompatibility alleles in other cherry species is also demonstrated.