Authors
Holušová, K., Žďárská, I., Čmejlová, J., Arabčuková, S., Krška, B., Bartoš, J.
Abstract
Understanding relationships among pear (Pyrus spp.) accessions and ensuring their correct identification is critical for breeding and germplasm management. In this study, we analyzed 445 accessions, primarily Pyrus communis, using three genotyping approaches to assess population structure, determine parentage, and identify cultivars. ddRAD libraries were prepared using the restriction enzymes AvaII and MspI. From more than 7,000 SNPs pruned for linkage disequilibrium, we distinguished species, identified clones, commonly used breeding cultivars and their offspring, and detected misclassified accessions. From the identified SNPs, we developed a panel of over 100 amplicon-based SNP (abSNP) markers. In parallel, we designed a novel set of 17 SSR markers, allowing both marker types to be genotyped in a single PCR reaction and directly compared. The SSR panel proved highly robust, achieving a probability of identity (PID) of 9.1 × 10−25, which allowed for discrimination among individual accessions and facilitated parentage assignment. In contrast, abSNP markers were less reliable for parentage analysis due to amplification bias associated with the highly heterogeneous pear genome. Nevertheless, abSNP markers were highly effective for clone identification, cultivar discrimination, and population-level studies. These results provide a framework for cost-effective genotyping and germplasm management in pear breeding programs.