Genetic diversity of peach (Prunus persica (L.)) cultivars in the collection of the Nikitsky botanical garden

The aim of this study was to assess the genetic diversity of peach (Prunus persica (L.)) cultivars in the Nikitsky Botanical Garden collection using ddRAD-seq technology to establish molecular genetic passports and analyze the relationship between genetic structure and phenotypic traits. Leaves from 56 peach cultivars of different origin were used. DNA was isolated using the CTAB buffer method, libraries for sequencing were prepared using MspI and PstI restriction enzymes, and sequencing was performed on an Illumina NovaSeq6000 platform. Data processing included alignment to the P. persica reference genome and SNP filtering using the Stacks2, bowtie2, and R software packages. UPGMA, PCA, and DAPC methods were used to assess genetic relationships. Several thousand SNPs were obtained, allowing us to identify 14 genetic clusters reflecting the high intraspecific diversity of the collection. The genetic structure partially correlated with fruit ripening time, with a pronounced distinction between early- and late-ripening varieties. Forty informative SNP markers, localized primarily on chromosomes 1, 4, and 8, were identified, sufficient to identify all studied genotypes. The ddRAD sequencing method has proven effective for mass genotyping of peach varieties. The obtained results provide the basis for developing a SNP panel suitable for cultivar certification, varietal purity monitoring, and optimization of breeding programs.