Genetic architecture of key traits for <i>Prunus</i> crop improvement: an overview of 25 years of curated genomic and breeding data

The extensive accumulation of genetic, genomic, expression, and breeding data on <i>Prunus</i> species often results in valuable information being lost or difficult to access for breeding purposes. We report a recent effort to increase curation on <i>Prunus</i> data in the Genome Database for Rosaceae (GDR, rosaceae.org) and a case study that explores 25 years of curated data (from 1998 to 2023) to uncover the genetic architecture of key traits in <i>Prunus</i> species, provide actionable insights for breeding, and encourage the use of shared molecular data across <i>Prunus</i> species. The curated data includes 177 genetic maps, primarily for almond (19), apricot (21), peach (52), and sweet cherry (46). A total of 28 971 trait-associated loci were reported, with 72.4% derived from genome-wide association studies, 18.7% from quantitative trait loci (QTL), and 8.9% from Mendelian trait loci. Notably, 76.4% of these loci are associated with morphological and quality traits, reflecting breeders' focus on consumer preferences. We identified 16 potential QTL hotspots linked to key traits such as morphology, phenology, fruit quality, and disease resistance. Additionally, we identified 17 high-priority syntenic regions among peach, sweet cherry, and almond. The colocalized markers and genes within the QTL hotspots and syntenic regions offer a valuable resource for tool development for <i>Prunus</i> breeding, especially for complex polyploid genomes and lesser studied species with limited genetic and genomic data.