A leaky pear S-allele was revealed by a new primer set and characterized by bioinformatics analysis

Pear is a commercially important fruit tree widely distributed in China that displays GSI (gametophytic self-incompatibility). It is necessary to determine S-alleles and S-genotypes for clarifying the compatibility between cultivars prior to pear planting and breeding. The S-genotype analysis using conventional method of artificial pollination is time consuming and requires much labor. In addition, the results obtained are often ambiguous due to environmental factors. PCR-based molecular method, however, could rapidly and accurately identified S-alleles and S-genotypes of pear cultivars. In this study, a new S_XH-Rnase was cloned in Xuehua pear that was previously S-genotyped S4S16. Interestingly, the pear S-RNase consensus primers PF1 and PR1 failed to amplify product from the genomic DNA of Xuehua pear although they well matched the cDNA sequence of S_XH-Rnase. To detect S_XH-RNase from genomic DNA, primer pair of SXHSPF and SXHSPR were designed and successfully amplified one S_XH-fragment of 408 bp containing a complete intron of 330 bp. In addition, the new S_XH-Rnase was characterized in detail by bioinformatics analysis. This study is useful for pear planting, breeding and revealing the mechanism of GSI.