Panvariome and pangenome of 1,020 global peach accessions shed light on evolution patterns, hidden natural variations, and efficient gene discovery.

Natural variations are the foundation of crop improvement. However, genomic variability remains largely understudied. Here, we present the full-spectrum integrated panvariome and pangenome of 1,020 peach accessions, including 10.5 million single-nucleotide polymorphisms, insertions, deletions, duplications, inversions, translocations, copy-number variations, transposon-insertion polymorphisms, and presence-absence variations, uncovering 70.6% novel variants and 3,289 novel genes. Analysis of the panvariome recapitulated the global evolutionary history of the peach and identified several novel trait-causally rare variants. We found that landraces and improved accessions encode more genes than the wild accessions, implying gene gains during peach domestication and improvement. Analysis of global introgression patterns revealed their value in phenotype prediction and gene mining, and suggested that the most likely wild progenitor of the domesticated peach is Prunus mira and that almond was involved in the origin of Prunus davidiana. Furthermore, we developed a novel panvariome-based one-step solution for association study, GWASPV, which was used to identify several trait-conferring genes and over 2,000 novel associations.. Collectively, our study reveals new insights into peach evolution and genomic variations, providing a novel method for plant gene mining and important targets for peach breeding.