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Background  Genome structural variations (SVs) have been associated with key traits in a wide range of agronomically important species; however, SV profiles of peach and their functional impacts remain largely unexplored.    Results  Here, we present an integrated map of 202,273 SVs from 336 peach genomes. A substantial number of SVs have been selected during peach domestication and improvement, which together affect 2268 genes. Genome-wide association studies of 26 agronomic traits using these SVs identify a number of candidate causal variants. A 9-bp insertion in  Prupe.4G186800 , which encodes a NAC transcription factor, is shown to be associated with early fruit maturity, and a 487-bp deletion in the promoter of  PpMYB10.1  is associated with flesh color around the stone. In addition, a 1.67 Mb inversion is highly associated with fruit shape, and a gene adjacent to the inversion breakpoint,  PpOFP1 , regulates flat shape formation.    Conclusions  The integrated peach SV map and the identified candidate genes and variants represent valuable resources for future genomic research and breeding in peach.

An integrated peach genome structural variation map uncovers genes associated with fruit traits