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 basis of crop improvement. However, genomic variability remains largely understudied. We present the full-spectrum integrated panvariome and pangenome of 1,020 peach accessions, including 10.5 million SNPs, indels, DELs, INSs, DUPs, INVs, TRAs, CNVs, TIPs, and PAVs, uncovering 70.6% novel variants and 3,289 novel genes. Analysis of the panvariome reconstructs the globally evolutionary history of peach and identifies several novel trait-causally rare variants, improving the power of breeding markers. Landraces and improved accessions encode more genes than wild accessions, implying the gene gains during domestication and improvement. Global introgression patterns reveal its new utilizations in phenotype prediction and gene mining and firstly suggest that the most likely wild progenitor of domesticated peach is Prunus mira and almond was involved in the origin of Prunus davidiana. We develop a novel panvariome-based solution for association study, GWASPV, identifying several trait-conferring genes and more than 2,000 novel associations, that achieves rapid and precise identification of trait-conferring genes using only one-step GWAS. Our study provides a novel solution for gene mining, with important implications in accelerating plant breeding.