ArticleBioinformatics (Oxford, England)2022
The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- The MexMAGIC population reveals the genetic architecture of traits exhibiting clinal variation in Mexican native maize.The New phytologist · 2026Article
- Dissecting genetic variance structure and evaluating genomic prediction models for single-cross hybrids derived from Stiff Stalk and Non-Stiff Stalk maize heterotic groups.G3 (Bethesda, Md.) · 2026Article
- Prioritization of deleterious mutations informs genomic prediction and increases the rate of gain in common bean (Phaseolus vulgaris L.), a simulation study.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- 2NPLGBM: a genomic model that merges the strengths of classical and machine learning methods in genomic prediction.Plant methods · 2026Article
- Accessing crop genetic diversity via pangenomics.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Potato dihaploids uncover diverse alleles to facilitate diploid potato breeding.The plant genome · 2026Article
- Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize.Genome research · 2026Article
- Haplotype applications in genomic selection.Genome biology · 2026Review
- Predicting maize hybrid performance with machine learning and a locus-specific weighted degree of dominance transformation.Frontiers in plant science · 2026Article
- Pan-genomics of polyploid crops: from complexity to breeding.Frontiers in plant science · 2026Review
- Pangenome-based genome inference using integer programming.Genome research · 2025Article
- Developing pangenomes for large and complex plant genomes and their representation formats.Journal of advanced research · 2025Review
- A global assembly of landrace oat (Avena sativa L.) accessions is a discovery resource for adaptive variation, association mapping, and trait deployment.G3 (Bethesda, Md.) · 2025Article
- The phased pan-genome of tetraploid European potato.Nature · 2025Article
- Genomic selection: Essence, applications, and prospects.The plant genome · 2025Review
- The genetic architecture of cell type-specific cis regulation in maize.Science (New York, N.Y.) · 2025Article
- Using genotype imputation to integrate Canola populations for genome-wide association and genomic prediction of blackleg resistance.BMC genomics · 2025Article
- Article
- Comparison of Recombination Rate, Reference Bias, and Unique Pangenomic Haplotypes inInternational journal of molecular sciences · 2025Article
- BrAPI v2: real-world applications for data integration and collaboration in the breeding and genetics community.Database : the journal of biological databases and curation · 2025Article
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Authors and funding
9 authors.
Funding
Abstract
motivationPangenomes provide novel insights for population and quantitative genetics, genomics and breeding not available from studying a single reference genome. Instead, a species is better represented by a pangenome or collection of genomes. Unfortunately, managing and using pangenomes for genomically diverse species is computationally and practically challenging. We developed a trellis graph representation anchored to the reference genome that represents most pangenomes well and can be used to impute complete genomes from low density sequence or variant data.
resultsThe Practical Haplotype Graph (PHG) is a pangenome pipeline, database (PostGRES & SQLite), data model (Java, Kotlin or R) and Breeding API (BrAPI) web service. The PHG has already been able to accurately represent diversity in four major crops including maize, one of the most genomically diverse species, with up to 1000-fold data compression. Using simulated data, we show that, at even 0.1× coverage, with appropriate reads and sequence alignment, imputation results in extremely accurate haplotype reconstruction. The PHG is a platform and environment for the understanding and application of genomic diversity. AVAILABILITY AND IMPLEMENTATION: All resources listed here are freely available. The PHG Docker used to generate the simulation results is https://hub.docker.com/ as maizegenetics/phg:0.0.27. PHG source code is at https://bitbucket.org/bucklerlab/practicalhaplotypegraph/src/master/. The code used for the analysis of simulated data is at https://bitbucket.org/bucklerlab/phg-manuscript/src/master/. The PHG database of NAM parent haplotypes is in the CyVerse data store (https://de.cyverse.org/de/) and named/iplant/home/shared/panzea/panGenome/PHG_db_maize/phg_v5Assemblies_20200608.db. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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