Assessment of genetic structure among different pear species (Pyrus spp.) using apple-derived SSR and evidence of duplications in the pear genome

Simple sequence repeat (SSRs) markers derived from Malus were used to assess their transferability in the analysis of the genetic diversity and relationship of some Pyrus species. All studied microsatellite loci produced fragments and were polymorphic among the studied samples. Fifty-one allelic variants were detected at eight SSR loci, ranging from five (MS14h03, CH02b10 and CH03g06) to nine (CH02h11a), with a mean of 6.37 alleles per locus. A relatively high level of diversity was recorded among the studied accessions. The average of Shannon's index (I) was 1.04. The Dice genetic similarity coefficient ranged greatly and ‘Khoj 1’ (a member of P. communis) and ‘Shinko’ (a cultivar belonging to P. pyrifolia) had the lowest (0.21) values, while ‘Chojuro’ and ‘Nijisseiki’, two cultivars belonging to P. pyrifolia, had the highest genetic similarity (0.97) among the studied samples. Bayesian cluster analysis and principal coordinates analysis plot separated the P. pyrifolia samples from other species, and formed three distinct groups, indicating high genetic differences between P. pyrifolia and other studied pear species. Several private alleles were observed in some of the studied species that would be of great importance for species identification. Furthermore, in 23 samples, more than two alleles were observed in the CH04e03 locus, indicating presence of locus duplication in these samples. Our observations suggest that, for this locus, at least two homologous chromosomes or genomic regions may be presented in the genome of some pear samples