Molecular Genetic Diversity and Phylogenetic Investigation of Pyrus communis L. (Rosaceae) Genotypes Using cpDNA Sequences with RAPD and ISSR Analyses

In this study, molecular genetic diversity and phylogenetic investigation of seven Pyrus communis L. genotypes were conducted based on random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) and inter simple sequence repeat PCR (ISSR-PCR) using chloroplast DNA trnL intron and trnL‑F sequences. Pyrus communis genotypes were obtained from Ardahan province, Türkiye. A total of 15 RAPD and 18 ISSR primers were used to determine the molecular genetic diversity of the Pyrus communis genotypes. For trnL intron, trnC, trnD, for trnL‑F, trnE, and trnF primers were used in PCR for amplification. In all, 57 and 91 bands were obtained by RAPD and ISSR analysis, respectively. Polymorphism rates were 78.94% and 85.71%, respectively. For trnL intron analyses, the average nucleotide composition consisted of 39% thymine, 17.5% cytosine, 28.4% adenine, and 15.1% guanine. In trnL‑F assays, the average nucleotide composition consisted of 31.9% thymine, 14.4% cytosine, 37.5% adenine, and 16.1% guanine. The results of the phylogenetic tree constructed with trnL intron and trnL‑F sequences of Alchemilla, Rosa, Sorbus, Malus, Prunus, and Cotoneaster species of the Rosaceae family obtained from NCBI were found to be similar. As a result of the study, polymorphisms were obtained at the rates of 78.94% and 85.71% from RAPD and ISSR analyses, respectively. In conclusion, detailed phylogenetic relationships of pear genotypes using chloroplast trnL intron and trnL‑F sequences with respect to other species from the same family were revealed.