ArticleNature communications2022
Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 30 citations in OpenAlex.
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- Cucurbitacins in Plant-Insect Interactions: Biosynthesis, Regulation, Ecological Functions, and Prospects for Crop Protection.Plants (Basel, Switzerland) · 2026Review
- Harnessing the untapped genetic diversity of local landraces: omics technologies as a gateway to horticultural breeding.Frontiers in plant science · 2026Review
- Developing pangenomes for large and complex plant genomes and their representation formats.Journal of advanced research · 2025Review
- Chromosome-level haplotype-resolved genome assembly provides insights into the highly heterozygous genome of Italian ryegrass (Lolium multiflorum Lam.).The plant genome · 2025Article
- Integrating parental genomes to reduce reference bias and identify intramuscular fat genes in Qinchuan Black pigs.Journal of animal science and biotechnology · 2025Article
- Nuclear and organelle genome assemblies of 5 Cucumis melo L. accessions, Ananas, Canton, PI 414723, Vedrantais, and Zhimali, belonging to diverse botanical groups.G3 (Bethesda, Md.) · 2025Article
- Evolution and comparison of the expression of TCP genes in the benincaseae and cucurbiteae tribes.Scientific reports · 2025Article
- Current and future pangenomic research in cucurbit crops.Breeding science · 2025Article
- Toward a standardized framework for pangenome graph evaluation: assessing crop plant pangenome variation graph construction from multiple assemblies.GigaScience · 2025Article
- From map to blueprint: the plant pan-genome unraveling genetic mysteries and powering precision breeding.Frontiers in plant science · 2025Review
- Complexity welcome: Pangenome graphs for comprehensive population genomics.Quantitative plant biology · 2025Review
- Technological Development and Advances for Constructing and Analyzing Plant Pangenomes.Genome biology and evolution · 2024Review
- Two haplotype-resolved genomes reveal important flower traits in bigleaf hydrangea (Horticulture research · 2023Article
- Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes.Biomolecules · 2023Review
- Representing true plant genomes: haplotype-resolved hybrid pepper genome with trio-binning.Frontiers in plant science · 2023Article
- The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics.Frontiers in fungal biology · 2023Review
- Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance in melon.Nature communications · 2022Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The genomic sequences segregating in experimental populations are often highly divergent from the community reference and from one another. Such divergence is problematic under various short-read-based genotyping strategies. In addition, large structural differences are often invisible despite being strong candidates for causal variation. These issues are exacerbated in specialty crop breeding programs with fewer, lower-quality sequence resources. Here, we examine the benefits of complete genomic information, based on long-read assemblies, in a biparental mapping experiment segregating at numerous disease resistance loci in the non-model crop, melon (Cucumis melo). We find that a graph-based approach, which uses both parental genomes, results in 19% more variants callable across the population and raw allele calls with a 2 to 3-fold error-rate reduction, even relative to single reference approaches using a parent genome. We show that structural variation has played a substantial role in shaping two Fusarium wilt resistance loci with known causal genes. We also report on the genetics of powdery mildew resistance, where copy number variation and local recombination suppression are directly interpretable via parental genome alignments. Benefits observed, even in this low-resolution biparental experiment, will inevitably be amplified in more complex populations.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.