Although peach production worldwide has been increasing for decades, peach production in the United States continues to decline in the face of changing climate, disease pressures, and reduced consumption. Novel and diverse germplasm is required to improve peach breeding efforts with the goal of developing new cultivars better adapted to these challenges. Unfortunately, current peach SNP genotyping platforms are expensive and need to be outsourced to specialized laboratories. The purpose of this project is to use SNPs generated using Capture-Seq technology to evaluate the diversity of potential new sources of breeding material in comparison with germplasm from different regions of the world. In addition, our goal is to create a panel of SNP-based markers that can be used in-house for future studies. Capture-Seq technology yielded 134,424 SNPs when comparing P. persica (221 genotypes) and related Prunus species (29 genotypes). A PCA from these SNPs yielded different clusters representing Asian, Australian, European, and North American germplasm. AMOVA indicated that, among P. persica samples, 21.3% of the genetic variation was between regions with 78.7% of the variation present within regions. STRUCTURE analysis showed differences between regional groups, where the Asian group composition was different to the other regions, North American and European group composition were similar to each other, and the Australian group composition had a large percentage of genotypes sharing a group mostly present in Asia. This study confirms that Australia’s peach populations could be a valuable source of novel germplasm to bolster worldwide peach breeding efforts. Furthermore, a panel of informative SNP markers can be converted into KASP markers, which can be used in-house for numerous applications, including genetic fingerprinting, MAS, GWAS, among others.
