Creating an effective DNA identification system for discriminating cherries (Prunus subgenus Cerasus)

BACKGROUND: Cherries, a subgenus of Cerasus within Rosaceae, as fruit trees with high economic value and elegant garden plants, have broad prospects for development and utilization. However, traditional morphology and molecular data have struggled to accurately identify cherry species due to their extensive overlap in the distribution, frequent hybridization, both open and closed flowers, hysteranthy and limited species coverage, hindering the advancement of the cherry industry. In this study, 61 well-documented cherry species were collected and whole chloroplast genome data was used to develop an effective DNA identification system for precise species identification. RESULTS: 36 new cherry chloroplast genomes were added to the public database, resulting in the most comprehensive phylogenetic relationship of cherry species to date. While whole chloroplast genome data achieved an 85.26% species identification success rate, it did not fully resolve all species identification. Relying solely on whole chloroplast genome data is resource-intensive. Therefore, we explored using highly variable regions, species-specific SNPs, and structural variations for accurate species identification. This study revealed that 14 newly developed DNA barcodes could identify 71.88% of cherry samples, while 106 SNPs and Indels allowed for precise identification of 59 out of 61 cherry species. CONCLUSIONS: This study not only clarified the phylogenetic relationships of major cherry species but also developed a precise identification system, providing a robust tool for accurate species identification and laying a solid foundation for breeding and the broader promotion of cherry species. CLINICAL TRIAL NUMBER: Not applicable.