ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Breeding
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1702527
Whole-genome sequencing reveals genetic diversity, population structure, and core collection construction in Korean peach (Prunus persica) germplasm
Provisionally accepted
- Rural Development Administration, Jeonju-si, Republic of Korea
Select one of your emails
You have multiple emails registered with Frontiers:
Notify me on publication
Please enter your email address:
If you already have an account, please login
You don't have a Frontiers account ? You can register here
Peach (Prunus persica) is an important temperate fruit crop and a model species for genomic research due to its diploid genome, short juvenile period, and relatively small genome size. Despite advances in next-generation sequencing (NGS), most peach genome-wide studies focused on a limited number of elite cultivars, and thus, the diversity of conserved germplasm is underrepresented. In Korea, a large number of peach genetic resources are maintained at the National Institute of Horticultural and Herbal Science (NIHHS), a branch of the Rural Development Administration (RDA), but no genome-scale core collection has been developed to date. This study aimed to perform whole-genome sequencing (WGS) on 445 peach accessions conserved in Korea between 2020 and 2025 using the Illumina NovaSeq 6000 platform, with the primary objective of constructing a representative genome-scale core collection and secondary objectives of identifying genome-wide single-nucleotide polymorphisms (SNPs) and assessing genetic diversity, population structure, and phylogenetic relationships.A total of 944,670 high-confidence SNPs were identified, with chromosomes 2 (G2) and 4 (G4) showing the highest variant density. Analyses using fastSTRUCTURE, principal component analysis (PCA), and phylogenetic reconstruction revealed a complex population structure and substantial genetic variation. From this data, a representative core collection was established, effectively capturing the majority of the genetic diversity present in the Korean peach germplasm. These results offer valuable genomic resources for peach improvement, marker development, pan-genome construction, and comparative genomics within the Rosaceae family.
Keywords: Prunus persica, Whole-genome sequencing, SNP, population structure, genetic diversity, core collection
Received: 10 Sep 2025; Accepted: 20 Oct 2025.
Copyright: © 2025 Bae, Jeong, Kwon, Lee, Hwang, Hur and Lee. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: So Jin Lee, dlthwls324@korea.kr
Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.