A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus
Open accessAbstract
Genomics research has relied principally on the establishment and curation of a reference genome for the species. However, it is increasingly recognized that a single reference genome cannot fully describe the extent of genetic variation within many widely distributed species. Pangenome representations are based on high-quality genome assemblies of multiple individuals and intended to represent the broadest possible diversity within a species. A Bovine Pangenome Consortium (BPC) has recently been established to begin assembling genomes from more than 600 recognized breeds of cattle, together with other related species to provide information on ancestral alleles and haplotypes. Previously reported de novo genome assemblies for Angus, Brahman, Hereford, and Highland breeds of cattle are part of the initial BPC effort. The present report describes a complete single haplotype assembly at chromosome-scale for a fullblood Simmental cow from an F1 bison-cattle hybrid fetus by trio binning. Simmental cattle, also known as Fleckvieh due to their red and white spots, originated in central Europe in the 1830s as a triple-purpose breed selected for draught, meat, and dairy production. There are over 50 million Simmental cattle in the world, known today for their fast growth and beef yields. This assembly (ARS_Simm1.0) is similar in length to the other bovine assemblies at 2.86 Gb, with a scaffold N50 of 102 Mb (max scaffold 156.8 Mb) and meets or exceeds the continuity of the best Bos taurus reference assemblies to date.
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The Simmental breed emerged in the Middle Ages in the Simme Valley of Switzerland and resulted from the crossbreeding of large German cattle with smaller Swiss indigenous cattle.
“For example, the Simmental breed, which emerged in the Middle Ages in the Simme Valley of Switzerland, resulted from the crossbreeding of large German cattle with smaller Swiss indigenous cattle [43,44].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [44]
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The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution
Liu, Y., Dao, W., Gao, R., Fan, X., Yang, R., & Miao, Y. (2026) · Animals · doi:10.3390/ani16050776 · Cited by 1 · see citing works
- Authors
- Heaton, M. P., Smith, T. P. L., Bickhart, D. M., Vander Ley, B. L., Kuehn, L. A., Oppenheimer, J., Shafer, W. R., Schuetze, F. T., Stroud, B., McClure, J. C., Barfield, J. P., Blackburn, H. D., Kalbfleisch, T. S., Davenport, K. M., Kuhn, K. L., Green, R. E., Shapiro, B., & Rosen, B. D.
- Affiliations
- Agricultural Research Service (US)
- U.S. Dairy Forage Research Center (US)
- Great Plains Veterinary Educational Center, University of Nebraska-Lincoln, Lincoln, NE
- University of California, Santa Cruz (US)
- American Simmental Association, Bozeman, MT
- Simmentals of Texas, Granbury, TX
- Stroud Veterinary Embryo Services, Weatherford, TX
- Colorado State University (US)
- Gluck Equine Research Center, University of Kentucky, Lexington, KY
- University of Idaho (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Heaton, Michael P
- Rosen, Benjamin D
- ORCID
- Venue
- Journal of Heredity
- Publisher
- Oxford University Press (OUP)
- Published
- 2021-01-13
- Volume
- 112
- Issue
- 2
- Pages
- 184-191
- ISSN
- 0022-1503 (ISSN-L)
- 1465-7333
- PMC
- PMC8006815
- OpenAlex
- W3120222892
- Cited by
- 52
- References
- 24
- Citations by year
- 2026: 3 · 2025: 3 · 2024: 16 · 2023: 17 · 2022: 10 · 2021: 3
- FWCI
- 6.79
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of Heredity (publishedVersion, public-domain)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Lincoln (University of Nebraska) (submittedVersion, public-domain)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- U.S. Department of Agriculture (3040-31000-100-00D, 5090-31000-026-00D, 5438-32000-034-00D)
- Agricultural Research Service
- Nebraska Beef Industry Endowment (2662390323001)
- National Institutes of Health (T32 HG008345-01)
- National Science Foundation (DEB-1754451)
- American Simmental Association
- 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
- Simmental cattle, Bos taurus taurus, reference genome, chromosome-level genome assembly, trio binning, cattle breeds
- MeSH terms
- Animals, Cattle, Chromosome Mapping, Female, Haplotypes, Male, Bison, Genome
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