Comparative Population Genomics Reveals the Domestication History of Peach

July 31, 2014
plant genomics peach domestication population sequencing
Comparative Population Genomics Reveals the Domestication History of Peach

Peach (Prunus persica) is one of the most economically and culturally significant fruit crops, with a long history of domestication dating back thousands of years. As a perennial fruit crop, its genetic evolution differs from annual plants, leading to unique selection pressures and domestication patterns. In our latest study, published in Genome Biology, we conducted large-scale resequencing of 84 peach accessions, unveiling critical insights into its genetic diversity, domestication history, and human influences on perennial fruit crops.

Key Findings

  • Whole-Genome Resequencing of Peach Populations:
    • A total of 10 wild and 74 cultivated peach varieties, including 9 ornamental, 23 breeding, and 42 landrace lines, were sequenced.
    • Identified 4.6 million single-nucleotide polymorphisms (SNPs), revealing genetic variations responsible for key traits such as fruit size, flavor, and flower morphology.
  • Single Domestication Event and Population Structure:
    • Phylogenetic analyses showed that modern cultivated peach originated from a single domestication event, diverging from wild peach species.
    • Ornamental and edible peach varieties belong to the same genetic lineage, alongside geographically distinct populations of Prunus ferganensis.
  • Genes Under Selection in Edible and Ornamental Peach:
    • Identified 147 genes under artificial selection related to fruit quality, sugar metabolism, and growth traits in edible peaches.
    • Found 262 genes linked to floral development, pigmentation, and branching patterns, shaping the evolution of ornamental peaches.
  • Impact of Human Cultivation on Peach Evolution:
    • Artificial selection and clonal propagation led to a decline in genetic heterozygosity over time.
    • Comparative analysis of heterozygosity ratios confirmed a sharp reduction in genetic diversity, influenced by selective breeding practices.

Reflections

This project was conducted in collaboration with the Zhengzhou Fruit Research Institute, focusing on population resequencing analysis of peach varieties. Our team was responsible for sequencing and genomic data analysis, enabling a deeper understanding of peach domestication and genetic diversity. The results of this study not only enhance our knowledge of perennial fruit crop evolution but also provide valuable genetic resources for future breeding programs.

The full text of this study can be accessed online at Genome Biology.