Identification of two new S-RNases and molecular S-genotyping of twenty loquat cutivars [Eriobotrya japonica (Thunb.) Lindl.]

•Nine S-haplotypes in the 20 loquat cultivars were identified.•Two new S-RNase genes were isolated from loquat.•The new S-RNase genes showed more homologous to the Pyrus S-RNase than they are to intraspecific S-RNases.•Twenty loquat cultivars were classified into12 groups according to S-genotypes.

Loquat (Eriobotrya japonica Lindl.), a member of Rosaceae, exhibits gametophytic self −incompatibility (GSI) that is controlled by the multiallelic S-locus. The S-locus encodes polymorphic S-RNase for the pistil-part S determinant. Identifying the S-genotypes of loquat cultivars is important for the selection of pollen donors for fruit production and breeding of loquat cultivars. In this study, we determined 20 loquat cultivar S-genotypes by PCR-based analysis with the consensus and allele-specific primers. In the 20 loquat cultivars, 9 S-haplotypes were identified including 7 S-RNases (S2, S7, S6, S8, S9, S10, S11) previously reported and two new S-RNase alleles. The partial genomic sequences of the two new S-RNases show high similarity (>95%) with Pyrus S-RNase, inserted by an intron in hypervariable region (RHV) with the length of 151 bp and 806 bp respectively, and encode amino acid sequences having the common structures of S-RNases. The two S-RNase genes were deposited in GenBank with name S12-RNase (accession number: KR149297) and S13-RNase (accession numbers: KR149298). Twenty loquat cultivars were classified into 12 groups according to S-genotypes. Seventeen cultivars have two different S-haplotypes except 'Fengyu', 'Ninghaibai' and 'Bahong' containing one S-haplotype. This research would contribute to a more efficient breeding program and pollinator selection of loquat.