Peach (Prunus persica (L.) Batsch) is a member of the genus Prunus within the Rosaceae family and represents one of the most extensively cultivated temperate deciduous fruit crops, ranking after apples and pears in global production. Due to its diploid genome (2n = 16) and relatively small genome size (~230 Mb), peach serves as a model species for fruit tree genome research. In this study, we performed whole-genome sequencing (WGS) on 445 peach genetic resources using the Illumina NovaSeq 6000 platform at a sequencing depth of 15´ coverage. Single nucleotide polymorphisms (SNPs) were identified from the WGS data and used to establish a core collection of peach genetic resources. Additionally, these SNPs will be utilized in a genome-wide association study (GWAS) to investigate key agronomic traits, including fruit shape, pollen fertility, flower morphology, maturity timing and so on. SNP filtration was conducted based on the following criteria: (1) SNPs with a missing rate exceeding 30% were removed, and (2) SNPs with a minor allele frequency (MAF) below 0.05 were excluded. As a result, 944,670 high-confidence SNPs were identified across the peach genetic resources. Based on this dataset, we established a core collection consisting of 150 accessions that retained over 99% of the total genetic diversity observed within the 445 peach genetic resources. Furthermore, we developed a high-resolution melting (HRM) marker derived from WGS-identified SNPs, which enables differentiation between round and flat peach fruit shapes. The SNP regions that can distinguish the fruit shape (round and flat shape) identified in this study were confirmed to be the same regions as the results of previously reported papers. Collectively, we successfully constructed a peach core collection through WGS analysis and developed a HRM marker for fruit shape classification. Also, our results produced in this study should be valuable for peach breeding program, identifying of agriculturally important genes, GWAS analyses, and further genomic studies in peach.
