Why we did this work

Peach (Prunus persica) is one of the most widely cultivated and economically important fruit crops globally. As a model system for genomic research in Rosaceae fruit trees, it combines a manageable genome size (<300 Mb) with highly diverse phenotypes (e.g., fruit shape, flesh color, stone adhesion), providing abundant germplasm resources for precision breeding. Yet, peach breeding remains challenged by a narrow genetic background, a small yet highly heterozygous genome, complex trait dissection and characterization, and the need to balance fruit quality with yield, extended shelf-life, and adaptability to diverse growing regions.In the era of genomics-assisted breeding (GAB), tools like high-density SNP arrays have become essential for enabling precise and efficient improvement—particularly in perennial horticultural crops. High-density SNP platforms have supported genome-wide studies; however, their practical application in molecular design breeding—especially the integration of marker-assisted and haplotype-based selection—remains limited. Our work advances this field by developing a customized SNP array that enhances both genetic dissection of traits and breeding efficiency in peach.

Peach (Prunus persica) has been extensively studied, with multiple SNP arrays including 9K and 18K chips—already contributing significantly to genome mapping and discovery of genes regulating specific traits. However, the increasing complexity of breeding objectives—encompassing both fruit quality traits (e.g., sweetness, acidity, flavor) and adaptation traits (e.g., flowering time)—calls for a more versatile, inclusive, and breeder-oriented genotyping platform.

Building upon the success of these existing arrays, which have greatly advanced peach genetics, we recognized the need for a tool that combines higher marker density, broader germplasm representation, and dual utility in both genomic research and practical breeding. This motivated the development of the PeachSNP170K array, designed to support polygenic discovery for target traits, genetic dissection, and marker-assisted selection within an integrated breeding framework.

While population-based GWAS has provided valuable insights into the genetic basis of complex traits—including in our previous studies—its application in breeding is often limited by confounding effects from inherent population structure interference. To bridge this gap, it is essential to complement GWAS with strategies such as kinship analysis, pedigree reconstruction, and identity-by-descent (IBD) mapping. These approaches enable the construction of breeding relationship networks and the tracking of favorable alleles across generations.

By integrating marker-assisted selection (MAS) with IBD-based selection, such frameworks can significantly improve the efficiency, accuracy, and speed of breeding in clonally propagated perennial fruit crops like peach—supporting background selection, parental design, and early-stage progeny screening.

What we did and what we found

We developed a high-resolution SNP chip—PeachSNP170K—by selecting high-quality SNPs from globally representative peach genomes. This chip balances genome-wide coverage with trait-relevant markers and offers robust performance across both Eastern and Western germplasm. We then genotyped 489 peach accessions using PeachSNP170K, and combined this with multi-year phenotypic data for traits including fruit organic acid content and flowering time. Importantly, we constructed kinship networks using these SNP data, enabling the tracing of breeding lineages and shared ancestry blocks—thereby laying a foundation for IBD-based breeding designs.

• Kinship-informed breeding design: By reconstructing relatedness at high resolution, we identified elite germplasm clusters and traced hidden shared ancestry, providing new opportunities for background and foreground selection.
• Citrate content: We identified haplotypes in PpNHX1gene that is significantly correlated with citrate level, and explainedacidity divergence across peach genotypes, thus helping breeders in balancing flavor profiles.
• Early flowering: We found that alow-frequency haplotypethat associated with early flowering and is enriched in Southern germplasm, suggesting that the haplotype-specific latitudinal adaptation via selection drives for phenotypic differentiation.

PeachSNP170K, combined with trait mapping and trait-associated haplotype, opens up a practical path for molecular design breeding in peach—where MAS, pedigree-informed selection, and genomic prediction can be tightly integrated.

Our existing groundwork for PeachSNP170K

This research extends our team’s earlier efforts, including:
- The release of high-quality peach genomes (e.g., Longhua Shui Mi and Rui You Pan 1);
- The genetic dissection of peach fruit flavor-related traits, such as PpERDL16 and PpALMT1-mediated sugar and acid accumulation;
- The exploration of evolutionary history of peach fruit edibility.
PeachSNP170K is a natural outcome of these foundational studies—transforming long-term genomic insights into practical tools for molecular breeding.

What’s next for fruit tree breeding?

We are now collaborating with national breeding programs to integrate the PeachSNP170K array into:
- MAS pipelines for important traits like fruit acidity and flowering time;
- IBD-assisted parental design, leveraging shared haplotype blocks and kinship-based strategies;
- Pan-genomic integration across the Prunus genus to broaden marker applicability and trait tracking.

In the long term, we believe this framework—haplotype-driven, kinship-based, and function-informed—will accelerate genetic improvement in clonally propagated perennial fruit crops, such as peach, apricot, and plum. These crops typically face long generation times and complex pedigrees, highly heterozygous genomic backgrounds, and environmental adaptation challenges, making them ideal candidates for such precision tools.

By bridging high-resolution genotyping with trait-specific molecular insights, the PeachSNP170K platform not only enables precision breeding, but also illustrates a systematic framework for trait-driven, haplotype-informed breeding in perennial horticultural crops.

For more details：https://www.nature.com/articles/s42003-025-08144-2