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This work was supported by the National Key Research and Development Program (2023YFE0105400), National Natural Science Foundation of China (32341042), Central Public-Interest Scientific Institution Basal Research Fund (Y2022QC23), National Key Laboratory & Zhongyuan Research Center ‘Xinyi’ Project (ZYZX20240304), Agricultural Science and Technology Innovation Program (CAAS-ASTIP-2024-ZFRI-01), Natural Science Foundation of Henan (232300421042), and National Science and Technology Major Project of Yunan (202302AE090005-3).

Analysis of institutional authors

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July 21, 2025
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Panvariome and pangenome of 1,020 global peach accessions shed light on evolution patterns, hidden natural variations, and efficient gene discovery

Publicated to:Molecular Plant. 18 (6): 995-1013 - 2025-06-02 18(6), DOI: 10.1016/j.molp.2025.04.009

Authors: Li, Y; Arús, P; Wu, JL; Zhu, GR; Fang, WC; Chen, CW; Wang, XW; Cao, K; Wang, LR

Affiliations

Chinese Acad Agr Sci, Inst Western Agr, Changji - Author
Chinese Acad Agr Sci, Zhengzhou Fruit Res Inst, Natl Hort Germplasm Resources Ctr China NPGRC, Zhengzhou 450000 - Author
Ctr Res Agr Genom CRAG CSIC, IRTA, UAB, UB, , Catalonia, Barcelona 08193 - Author
Genòmica i Biotecnologia . IRTA Investigación y Tecnología Agroalimentarias - Author
Genòmica i Biotecnologia . Producció Vegetal - Author
Producció Vegetal. IRTA Investigación y Tecnología Agroalimentarias - Author
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Abstract

Natural variations are the foundation of crop improvement. However, genomic variability remains largely understudied. Here, we present the full-spectrum integrated panvariome and pangenome of 1,020 peach accessions, including 10.5 million single-nucleotide polymorphisms, insertions, deletions, duplications, inversions, translocations, copy-number variations, transposon-insertion polymorphisms, and presence- absence variations, uncovering 70.6% novel variants and 3,289 novel genes. Analysis of the panvariome recapitulated the global evolutionary history of the peach and identified several novel trait-causally rare variants. We found that landraces and improved accessions encode more genes than the wild accessions, implying gene gains during peach domestication and improvement. Analysis of global introgression patterns revealed their value in phenotype prediction and gene mining, and suggested that the most likely wild progenitor of the domesticated peach is Prunus mira and that almond was involved in the origin of Prunus davidiana. Furthermore, we developed a novel panvariome-based one-step solution for association study, GWASPV, which was used to identify several trait-conferring genes and over 2,000 novel associations.. Collectively, our study reveals new insights into peach evolution and genomic variations, providing a novel method for plant gene mining and important targets for peach breeding.

Keywords

AlmondDomesticationEvolutionGene discoveryGenome analysisGenotypeIntrogressionsLinkage mapMutationPangenomePanvariomePeachProteinResistanceTraitVariant

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Molecular Plant due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2025, it was in position 2/273, thus managing to position itself as a Q1 (Primer Cuartil), in the category Plant Sciences. Notably, the journal is positioned above the 90th percentile.

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-08-07:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 3.

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 5.45.
  • The number of mentions on the social network X (formerly Twitter): 10 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.
  • Assignment of a Handle/URN as an identifier within the deposit in the Institutional Repository: http://hdl.handle.net/20.500.12327/4682

Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: China.