Dual maternal origin and dispersal history of peach (Prunus persica) from China

Compared to annual crops, the domestication of perennial fruit trees remains poorly understood, and tracing the maternal origins and dispersal history significantly advances our understanding of the domestication process. Peach (Prunus persica) is a vital economic fruit crop with a long and intricate history of human domestication, resulting in diverse varieties and wide dispersal, making it an excellent model for tracing the maternal origin and domestication history. Here, we aim to investigate the peach's maternal origins and elucidate its domestication history in China.

We investigated peach phylogeography by analyzing 714 peach individuals representing diverse germplasm types across its distribution range, using the whole chloroplast genome and nuclear ribosomal DNA sequences to further infer its maternal origin and domestication history.

Genetic structure analyses of both datasets revealed two distinct clades within peach populations (Clade I and Clade II), each associated with similar geographic distributions and containing various germplasm types with diverse fruit phenotypes, suggesting that peach is derived from two distinct maternal ancestors (dual maternal origin). Notably, genetic diversity and private haplotype analysis identified multiple regions with high diversity (the Yellow River, the middle and Yangtze River, and the Pearl River basin) where the oldest fossil records are concentrated, suggesting that peach might exist in multiple domestication regions (diffuse origins). Peach populations experienced two major bottlenecks and sequential founder events during the domestication process, likely shaped by human-driven selection and dispersal: the first occurred around 6,000 years ago, and the second approximately 2,000 years ago.

This study highlights a dual maternal origin and multiple domestication regions of peach within China, resolving a key issue in the history of peach domestication. Our integration of chloroplast and nuclear data, along with other lines of evidence, establishes a clear framework for inferring complex lineages, refining our understanding of the peach demographic history, and offering valuable insights for breeding strategies and conservation efforts.