Identification of S-genotypes in 17 Chinese cultivars of Japanese plum (Prunus salicina Lindl.) and molecular characterisation of 13 novel S-alleles

Polymerase chain reaction (PCR) was conducted with Prunus S-RNase gene-specific primers on 17 Chinese cultivars of Japanese plum (Prunus salicina Lindl.). These primers were designed from the conserved regions of Prunus S-RNase genes. Each cultivar produced two amplicons, apart from two cultivars that had three amplicons. In all, 36 amplicons were cloned and sequenced. Analysis of these sequences revealed 13 novel S-alleles, the amino acid sequences of which showed 62% (S-15 vs. S-19) to 92% (S-22 vs. S-24) identity. The sequences also demonstrated several typical structural features of Prunus S-RNase genes: three conserved regions (C1, C2 and C3), one hypervariable region (RHV) with one intron, and another intron located at the junction between the signal peptide and the mature protein. Compared to S-2 from apricot, S-26 from Japanese plum had only two nucleotide substitutions in the exon region, which resulted in only one amino acid residue difference in the signal peptide. However, there were large numbers of nucleotide differences in the intron regions. Phylogenetic analysis of the 13 novel S-alleles, and those of other species in the family Rosaceae, resulted in two distinct groups which correlated with their sub-family classification (i.e., the Maloideae and the Prunoideae). These data should be useful in breeding programmes, for choosing suitable pollinators, and may also contribute to studies on S-allele function, the evolution of new allele specificities, and the taxonomy and speciation of Prunus.