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Journal article
The graphical barley pangenome reveals micro- and macro-scale genetic variation
Agriculture Communications, Vol.4(1), 100131
2026
Abstract
Graphical pangenomes and orthologous gene clustering visualisations offer powerful tools to analyse, validate, and extract genomic variations within a species. For crop genomics, integrating these models and algorithms into complex and large genomes is essential to unlock the potential of genomic technology. Barley (Hordeum vulgare L.) is an important crop for the global malting industry, and faces increasing challenges from climate change and rising production demands. In this study, we integrated pangenome graph and orthologous gene clustering tools and applied them to multiple high-quality barley genome assemblies. This approach revealed a detailed and compact representation of genetic diversity, capturing variation from base-pair level to large structural rearrangements across the entire barley pangenome. Using pangenome graph and gene clustering analyses, we identified substantial structural variation (SV) between barley cultivars and landraces and characterised presence–absence variation (PAV) and copy number variation (CNV) patterns. Through hierarchical edge bundles, network plots, and sequence tube maps of genes controlling row-type, we identified haplotype blocks defined by single-nucleotide polymorphisms (SNPs) and InDels. Linearised genome graph visualisation via the Panache pangenome browser further enabled exploration of PAV regions. Together, these visualisation approaches demonstrate how multiple levels of resolution in a graphical pangenome can provide a unified view of genomic variation. The genomic resources and tools developed here expand the toolkit for barley breeding and genetic improvement.
•A graphical pangenome reveals extensive SNP and structural variation across 20 barley genomes.•Landraces show greater haplotype diversity than modern cultivars.•Key row-type genes are resolved into distinct haplotype blocks across a genome graph.•The genome graph exposes presence–absence variation affecting vitamin E pathways.•Interactive pangenome tools enable intuitive exploration of complex crop genomes.
Details
- Title
- The graphical barley pangenome reveals micro- and macro-scale genetic variation
- Authors/Creators
- Brett Chapman - Murdoch UniversityViet Dang - Murdoch UniversityTianhua He - Murdoch University, Centre for Crop and Food InnovationCamilla Hill - Murdoch UniversityHaifei Hu - Murdoch UniversityPenghao Wang - Murdoch University, School of Medical, Molecular and Forensic SciencesPhilipp E. Bayer - The University of Western AustraliaDavid Edwards - The University of Western AustraliaGabriel Keeble-Gagnère - Agriculture VictoriaJosquin Tibbits - Department of Primary Industries and Regional DevelopmentChengdao Li - Murdoch University, Centre for Crop and Food Innovation
- Publication Details
- Agriculture Communications, Vol.4(1), 100131
- Publisher
- Elsevier B.V. on behalf of Beijing Academy of Agriculture and Forestry Sciences.
- Number of pages
- 11
- Identifiers
- 991005869905007891
- Copyright
- Crown Copyright © 2026
- Murdoch Affiliation
- Western Crop Genetics Alliance; Centre for Crop and Food Innovation; School of Medical, Molecular and Forensic Sciences
- Language
- English
- Resource Type
- Journal article
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