Characterising novel S-RNase and SFB alleles in Prunus virginiana

Self-incompatibility (SI) in the genus Prunus is controlled by alleles of two genes at the S-locus, S-RNase and SFB. Both genes exhibit high levels of polymorphism and sequence diversity, characteristic of plant self-incompatibility systems. In this study, eight S-RNase alleles and five SFB alleles were isolated from five accessions of P virginiana using PCR. These alleles were novel and have been submitted to GeneBank with the following Accession Numbers: S-1-RNase - S-8-RNase (JF907557 - JF907564), SFB1 (JF907565), SFB2 (JF907566), and SFB4 (JF907567). The Accession Numbers of SFB7 and SFB8 are the same as S-7-RNase and S-8-RNase, respectively. These S-RNase and SFB alleles shared the typical structural features of the equivalent alleles in other Prunus species. The identities of the deduced amino acid sequences range from 70.5 - 80.9% among the S-RNase alleles, and from 66.5 - 82.9% among the SFB alleles. The S-RNase and SFB genes were transcribed in opposite directions. The distances between pairs of alleles in these S-haplotypes varied from 325 - 1,789 bp. Sequence comparisons showed that the identities of the deduced amino acid sequences were 99.4% between Pvir-S-3 and Pweb-S-10, 99.0% between Pvir-S-3 and Pd-S6(4), 97.1% between Pvir-S-7 and Pps-S-5, 98.2% between Pvir-S-4 and Pa-S-6, 98.2% between Pvir-S-6 and Pspe-S-3, 98.4% between Pvir-SFB4 and Pa-SFB6, and 97.4% between Pvir-SFB7 and Pps-SFB5. Moreover, the identity between the intergenic sequences of the S-7-haplotype of P virginian and the S-5-haplotype of P. pseudocerasus was 99.7%, with only one nucleotide difference (C -> T). These results show that these two S-haplotypes were the closest related lineages and further support the view that alleles at these two S-loci evolved before the divergence of Prunus species.