Copy number variation of a gene cluster encoding endopolygalacturonase mediates flesh texture and stone adhesion in peach

Texture is an important attribute affecting consumer perception of fruit quality. Peach melting flesh and flesh adhesion to stone (endocarp) are simply inherited and controlled by the F-M locus on linkage group (LG) 4. Here, we report that two genes encoding endopolygalacturonase (endoPG) in the F-M locus, designated PpendoPGF and PpendoPGM, are associated with the melting flesh and stone adhesion traits. PpendoPGM controls melting flesh while PpendoPGF has pleiotropic effects on both melting flesh and stone adhesion. The F-M locus has three allelic copy number variants of endoPG, H₁ (PpendoPGF and PpendoPGM), H₂ (PpendoPGM), and H₃ (null). The H₂ haplotype represents the ancestral one while the H₁ and H₃ haplotypes are two variants due to duplication and deletion of PpendoPGM, respectively. Accessions with H₁H₁, H₁H₂, or H₁H₃ genotypes show the freestone or semi-freestone and melting flesh phenotype, while both H₂H₂ and H₂H₃ accessions have the clingstone and melting flesh phenotype. The H₃H₃ accessions have the clingstone and non-melting flesh phenotype. Our study not only demonstrates a driving role of gene copy number variations in flesh texture diversification in fruit trees, but also provides a useful diagnostic tool for early seedling selection in peach breeding programmes.