New findings in apple S-genotype analysis resolve previous confusion and request the re-numbering of some S-alleles.

Apple trees display gametophytic self-incompatibility which is controlled by a series of polymorphic S-alleles. To resolve the discrepancies in S-allele assignment that appeared in the literature, we have re-examined the identity of S-alleles known from domestic apple cultivars. Upon an alignment of S-allele nucleotide sequences, we designed allele-specific primer pairs to selectively amplify a single S-allele per reaction. Alternatively, highly similar S-alleles that were co-amplified with the same primer pair were discriminated through their distinct restriction digestion pattern. This is an extension of our previously developed allele-specific PCR amplification approach to reveal the S-genotypes in apple cultivars. Amplification parameters were optimised for the unique detection of the 15 apple S-alleles of which the nucleotide sequences are known. Both the old cultivars with a known S-genotype and a number of more common cultivars were assayed with this method. In most cases, our data coincided with those obtained through phenotypic and S-RNase analysis. However, three S-alleles were shown to relate to RNases that were previously proposed as being encoded by distinct S-alleles. For another S-allele the corresponding gene product has not been discriminated. Consequently, we propose the re-numbering of these four S-alleles. Furthermore, two alleles that were previously identified as S(27a) and S(27b) now received a distinct number, despite their identical S-specificity. To ease widespread future analysis of S-genotypes, we identified common cultivars that may function as a witness for bearing a particular S-allele. We discuss the assignment of new S-alleles which should help to avoid further confusion.