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

J Exp Bot. 2016 Mar;67(6):1993-2005. doi: 10.1093/jxb/erw021. Epub 2016 Feb 5.


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.

Keywords: Copy number variation; flesh texture; melting flesh; peach; polygalacturonase; stone adhesion..

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Copy Number Variations / genetics*
  • Electrophoresis, Agar Gel
  • Fruit / anatomy & histology*
  • Fruit / genetics*
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental
  • Gene Expression Regulation, Plant
  • Genes, Plant
  • Genetic Association Studies
  • Genetic Loci
  • Genome, Plant
  • Models, Genetic
  • Multigene Family*
  • Phylogeny
  • Physical Chromosome Mapping
  • Polygalacturonase / genetics*
  • Prunus persica / anatomy & histology*
  • Prunus persica / genetics*
  • Prunus persica / growth & development
  • Real-Time Polymerase Chain Reaction
  • Reproducibility of Results
  • Sequence Analysis, RNA


  • Polygalacturonase