ArticleGenome biology2021
Genome structure variation analyses of peach reveal population dynamics and a 1.67 Mb causal inversion for fruit shape.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers, 1 of them a synthesis that pooled it.
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Who cites it
71 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Research evolution of flat peach (Frontiers in plant science · 2025Pooled it
- Genome-wide variation analysis of two Salvia hispanica L. genotypes and implication for associations with metabolic and adaptive traits.Journal, genetic engineering & biotechnology · 2026Article
- A transposable element-derived regulatory variation inHorticulture research · 2026Article
- Genome-Wide Dissection of the TCP Gene Family in Peach and Expression Analysis Under Drought Stress.International journal of molecular sciences · 2026Article
- Analysis of deep-resequencing data of 984 soybean accessions reveals structural variations underlying agronomic traits.Nature communications · 2026Article
- Pan-Genome-Wide Analysis and Expression Profiling of the Potato GST Gene Family.Plants (Basel, Switzerland) · 2026Article
- De Novo Chromosome-Level Genome Assembly of 'Qing Zhou Mi' Landrace Peach and Analysis of Late Maturity and Fruit Weight Traits in Peach.Plants (Basel, Switzerland) · 2026Article
- Identification and comprehensive characterization of the OVATE family protein in litchi.BMC plant biology · 2026Article
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- Pangenome-driven discovery and comparative genomics of glycosyltransferase genes inFrontiers in plant science · 2026Article
- Chromosome-scale assembly of European flax (Linum usitatissimum L.) genotypes and pangenomic analysis provide genomic tools to improve breeding.BMC genomics · 2025Article
- Assembling the chromosome-level genome of Arctium Lappa L. provides new insights into carotenoid biosynthesis.BMC plant biology · 2025Article
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- Pan-genome identification and expression analysis of the ARF gene family in potato.BMC plant biology · 2025Article
- Haplotype-resolved genome and pan-genome graphs reveal the impacts of structural variation on functional genome and feather colors in chickens.iMetaOmics · 2025Article
- Structural Variations Associated with Adaptation and Coat Color in Qinghai-Tibetan Plateau Cattle.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- PeachMD: a multi-omics database for peach.Molecular horticulture · 2025Article
- The PeachSNP170K array facilitates insights into a large-scale population relatedness and genetic impacts on citrate content and flowering time.Communications biology · 2025Article
- GKNnet: an relational graph convolutional network-based method with knowledge-augmented activation layer for microbial structural variation detection.Briefings in bioinformatics · 2025Article
- Major Facilitator Superfamily transporters balance sugar metabolism in peach.Plant physiology · 2025Article
11 more citing papers are in PubMed but not listed here.
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10 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundStructural variations (SVs), a major resource of genomic variation, can have profound consequences on phenotypic variation, yet the impacts of SVs remain largely unexplored in crops.
resultsHere, we generate a high-quality de novo genome assembly for a flat-fruit peach cultivar and produce a comprehensive SV map for peach, as a high proportion of genomic sequence is occupied by heterozygous SVs in the peach genome. We conduct population-level analyses that indicate SVs have undergone strong purifying selection during peach domestication, and find evidence of positive selection, with a significant preference for upstream and intronic regions during later peach improvement. We perform a SV-based GWAS that identifies a large 1.67-Mb heterozygous inversion that segregates perfectly with flat-fruit shape. Mechanistically, this derived allele alters the expression of the PpOFP2 gene positioned near the proximal breakpoint of the inversion, and we confirm in transgenic tomatoes that PpOFP2 is causal for flat-fruit shape.
conclusionsThus, beyond introducing new genomics resources for peach research, our study illustrates how focusing on SV data can drive basic functional discoveries in plant science.
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