Identification of S genotypes in loquat (Eriobotrya japonica Lindl.) based on allele specific PCR

- 9 S-allele specific primer pairs for loquat S-genotyping were designed.
- The specificity of 9 S-allele primer pairs were evaluated.
- Twenty-eight loquat cultivars were S-genotyped for the first time.

Loquat (Eriobotrya japonica Lindl) is an evergreen fruit tree and belongs to Maloideae in the Rosaceae, which carries the RNase-dependent gametophytic self-incompatibility system (GSI). Use of appropriate pollinator trees is essential for increasing fruit production. S-allele specific amplification system is an efficient and rapid method to identify S-genotypes. In this research, according to the sequences of S-RNase alleles, 9 specific primer pairs for amplifying S-RNase alleles (S2, S7, S6, S8, S9, S10, S11,S12 and S13) were designed, which located in the introns or in the areas with high polymorphism. The specificity of the 9 allele specific primer pairs was evaluated by eight loquat cultivars with known S-genotypes. After being verified their effectiveness, they were used to S-genotype 39 loquat cultivars from Longan and loquat nurseries in Fuzhou national fruit germplasm. The results showed that the 39 loquat cultivars were S-genotyped efficiently by allele specific PCR with the 9 primer pairs, in which 28 cultivars were identified for the first time and they were classified into 18 groups according to the genotype. The results also proved that the 9 S-allele specific primer pairs can efficiently identified S-genotype, which will be very useful for choosing pollinators or crossing parents in loquat production and breeding.