Development of Core KASP Marker Panel for DNA Fingerprinting of Pear (Pyrus spp.) Germplasm Collections

Accurate varietal identification remains a persistent issue in pear germplasm conservation, creating obstacles in breeding parent selection and impeding progress in elite cultivar research and cultivation. This study aims to develop a set of highly polymorphic single-nucleotide polymorphism (SNP) markers for pear variety identification. Based on the design criteria for highly polymorphic KASP primers, 34 primer pairs were synthesized, of which 25 produced reliable genotyping results, showing clear separation among different genotypes with minimal missing data. The 269 pear accessions were successfully genotyped, with observed heterozygosity (Ho) ranging from 0.33 to 0.56, polymorphism information content (PIC) values between 0.336 and 0.375, and minor allele frequency (MAF) ranging from 0.31 to 0.50. A total of 257 distinct genotypes were obtained from 269 pear accessions, among which two groups of known bud mutation were consistent, and ten groups of potential synonym accessions were detected. The cluster analysis based on the 25 KASP markers separated the 269 pear accessions into two clusters, which showed a broad association with taxonomic background and origin. This study shows that this CoreSNP-KASP marker set can be used for preliminary molecular screening of pear accessions and provides useful information to support subsequent breeding programs.