A reference genome assembly of Simmental cattle, Bos taurus taurus

Authors: Heaton, Michael - Mike; Smith, Timothy - Tim; Bickhart, Derek; VANDER LEY, BRIAN - University Of Nebraska; Kuehn, Larry; OPPENHEIMER, JONAS - University Of California Santa Cruz; SHAFER, WADE - American Simmental Association; SCHUETZE, FRED - Simmentals Of Texas; STROUD, BRAD - Stroud Veterinary Embryo Services; McClure, Jennifer; BARFIELD, JENNIFER - Colorado State University; Blackburn, Harvey; KALBFLEISCH, THEODORE - University Of Kentucky; DAVENPORT, KIMBERLY - University Of Idaho; Kuhn, Kristen; GREEN, RICHARD - University Of California Santa Cruz; SHAPIRO, BETH - University Of California Santa Cruz; Rosen, Benjamin - Ben

Submitted to: Journal of Heredity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/18/2020
Publication Date: 3/1/2021
Citation: 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. 2021. A reference genome assembly of Simmental cattle, Bos taurus taurus. Journal of Heredity. 112(2):184-191. https://doi.org/10.1093/jhered/esab002.
DOI: https://doi.org/10.1093/jhered/esab002

Interpretive Summary: Bovine genome assemblies represent genetic blueprints for building and maintaining cattle. These blueprints advance our understanding of the genomic elements affecting important traits and aid in identification of genetic differences between animals that contributes to variation in individual performance. A pangenome represents a set of high-quality genome assemblies of multiple individuals and is intended to represent the broadest possible diversity within a species. An international Bovine Pangenome Consortium (BPC) has recently been established to begin assembling genomes from more than 600 recognized breeds of cattle and closely related species. Previously reported genome assemblies for Angus, Brahman, Hereford, and Highland breeds of cattle and yak, gaur, and bison species are part of the initial BPC effort. The present report describes assembly of a fullblood Simmental cow from an F1 bison-cattle hybrid fetus in a process called “trio binning”, that results in an improved product compared to sequencing a purebred Simmental individual. The quality of this genome meets or exceeds that of the best cattle assemblies to date. This approach allows reference assemblies to be readily produced for all breeds of cattle and would pave the way for understanding functional genetic differences between breeds.

Technical Abstract: 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.