Cloning of four new Japanese plum S-alleles and determination of the compatibility between cultivars by PCR analysis

The Japanese plum (Prunus salicina Lindl.) belongs to the Rosaceae, which carries the gametophytic self-incompatibility system. Therefore, commercial plum orchards must contain at least two cultivars, which are able to fertilize each other. However, the S-allele content, which determines the fertilization compatibility, has not yet been identified in most of the Japanese plum varieties. This lack of knowledge may lead to cases of reduced yields due to semi, instead of full, compatibility. In the present study, five S-alleles were cloned from three Japanese plum cultivars. The genes were isolated, from genomic DNA, by applying the PCR (Polymerase Chain Reaction), resulting in fragments containing exons, as well as introns. Four of the five clones turned out to be new alleles: from 'Wickson' S3 and S6, and from 'Royal-Zee', S4 and S5. The fifth allele, S1, which was isolated from 'Red-Beaut', has been cloned previously as a cDNA sequence from 'Sordum' (named Sa, GenBank accession no. AB026981). Sequence analysis revealed an identity of approximately 85% between the exons of the clones, whereas the introns exhibited a much lower identity. The highest degree of identity to a non-Japanese plum gene was displayed by the S2 - RNase of sweet-cherry Prunus avium (74-88% identity). Based on these findings, unique pairs of primers were designed allowing for PCR analysis for each of the cloned alleles. PCR with these primers was carried out to identify the level of compatibility between 'Royal-Zee' and three of its common pollenizers. It revealed that 'Black-Diamond' and 'Angeleno' are semi-compatible, since they shared S4 and S5 with 'Royal-Zee', respectively, whereas 'Black-Gam' was found to be fully compatible.