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In this study, the technologies of simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers were used to analyze the genetic diversity of 30 sand pear (Pyrus pyrifolia) ‘Nakai’ varieties. Ten pairs of SSR polymorphic primers were selected to amplify P. pyrifolia ‘Nakai’ varieties. A total of 90 alleles were detected. The polymorphism information content index was between 0.5578 and 0.8423, with an average of 0.7585. The selected 10 pairs of AFLP primer combinations were used to amplify the analyzed pear varieties, and 1,046 polymorphic loci were detected. The average amplification results of each primer combination detected 105 bands with an average polymorphism percentage of 86.46%. The combined data of SSR and AFLP analysis showed that the analyzed P. pyrifolia ‘Nakai’ varieties were characterized by extremely rich genetic diversity and were highly representative. According to the results of SSR, AFLP, and SSR+AFLP cluster analysis, the analyzed P. pyrifolia ‘Nakai’ varieties can be categorized into three clusters. The results of genetic structure showed that the hybridization between these P. pyrifolia ‘Nakai’ varieties resulted in the heterozygosity of genotypes. In addition, we found that ‘Nijisseik’, ‘Ejima’, and ‘Fuli’ are good parent resources among the pear varieties through observing the genetic background of the analyzed pear varieties. This study reveals the genetic diversity levels of P. pyrifolia ‘Nakai’ varieties at the molecular level, which was important in molecular identification and protection of pear germplasm resources, as well as pear variety breeding and genetic improvement.

Genetic Diversity and Population Structure Analysis of Sand Pear (Pyrus pyrifolia) ‘Nakai’ Varieties Using SSR and AFLP Markers