The Bovine Pangenome Consortium: Democratizing Production and Accessibility of Genome Assemblies for Global Cattle Breeds and Other Bovine Species
Open accessAbstract
The Bovine Pangenome Consortium (BPC) is an international collaboration dedicated to the assembly of cattle genomes to develop a more complete representation of cattle genomic diversity. The goal of the BPC is to provide genome assemblies and a community-agreed pangenome representation to replace breed-specific reference assemblies for cattle genomics. The BPC invites partners sharing our vision to participate in the production of these assemblies and the development of a common, community-approved, pangenome reference as a public resource for the research community ( https://bovinepangenome.github.io/ ). This community-driven resource will provide the context for comparison between studies and the future foundation for cattle genomic selection.
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The linear model inherently obscures sequences present in other individuals but absent in the reference, thereby introducing significant reference bias in variant calling and trait association.
“The linear model inherently obscures sequences present in other individuals but absent in the reference, thereby introducing significant reference bias in variant calling and trait association [180].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [180]
In “Why a pangenome?” (page unavailable), the paper says a single reference misses genetic variation, that insertions absent from the reference are difficult to detect, and that reference bias can cause mapping and genotyping errors. This supports the variant-calling part of the claim, but the passages do not establish reference bias in trait association. (LLM, conf=0.84)
Experimental — accuracy not yet measuredTraditional genomic studies have heavily relied on a single linear reference genome, such as ARS-UCD1.2, which is derived from Hereford.
“Traditional genomic studies have heavily relied on a single linear reference genome [180], such as ARS-UCD1.2, which is derived from an individual of a specific taurine breed, Hereford [181] (Table 3).”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [180]
The linear model fundamentally fails to capture the full genetic diversity, such as SVs and PAVs, particularly in non-reference populations like Bos indicus.
“While invaluable, this linear model fundamentally fails to capture the full genetic diversity, such as SVs and presence/absence variations (PAVs) [182], particularly in non-reference populations like Bos indicus [180].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [180]
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- [16]Null DJ VanRaden PM Rosen BD O’Connell JR Bickhart DM Using the ARS-UCD1.2 reference genome in U.S. evaluations Interbull Bulletin 2019 55 30 34
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Overcoming Limitations to Deep Learning in Domesticated Animals with TrioTrainPreprint
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Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrainPreprint
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Advancing the Indian Cattle Pangenome: Characterizing Non-Reference Sequences in Bos indicusPreprint
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Prospects for Utilization of Modern Technologies for Cattle Improvement in Africa
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- Authors
- Smith, T. P. L., Bickhart, D. M., Boichard, D., Chamberlain, A. J., Djikeng, A., Jiang, Y., Low, W. Y., Pausch, H., Demyda-Peyrás, S., Prendergast, J., Schnabel, R. D., Rosen, B. D., & Bovine Pangenome Consortium
- Affiliations
- United States Department of Agriculture (US)
- U.S. Dairy Forage Research Center (US)
- AgroParisTech (FR)
- La Trobe University (AU)
- International Livestock Research Institute (KE)
- Northwest A&F University (CN)
- The University of Adelaide (AU)
- ETH Zurich (CH)
- Roslin Institute (GB)
- University of Missouri (US)
- Agricultural Research Service (US)
- Corresponding author
- Rosen, Benjamin D.
- ORCID
- Venue
- Genome biology
- Published
- 2023-06-19
- Volume
- 24
- Issue
- 1
- Pages
- 139-139
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC10278262
- OpenAlex
- W4381251865
- Cited by
- 57
- References
- 40
- Citations by year
- 2026: 12 · 2025: 25 · 2024: 18 · 2023: 2
- FWCI
- 9.95
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion, cc-by)
- Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by)
- BORIS (University Library Bern) (submittedVersion, cc-by)
- CGSPace A Repository of Agricultural Research Outputs (Consultative Group for International Agricultural Research) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Universidad de Córdoba Insitutional Repository (Universidad de Córdoba) (submittedVersion, cc-by)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
- MELSpace (ICARDA (The International Center for Agricultural Research in Dry Areas)) (submittedVersion, cc-by)
- ETH Zürich Research Collection
- Funders
- Agricultural Research Service (3040-31000-100-00D, 5090-31000-026-00D, 8042-31000-001-00D)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- genome assembly, cattle breeds, genomic diversity
- MeSH terms
- Animals, Cattle, Genome, Polymorphism, Single Nucleotide, Genomics
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