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ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Cell Wall Biology and Utilization Research » Research » Publications at this Location » Publication #377685

Research Project: Investigating Microbial, Digestive, and Animal Factors to Increase Dairy Cow Performance and Nutrient Use Efficiency

Location: Cell Wall Biology and Utilization Research

Title: The Bovine Pangenome Consortium

item Bickhart, Derek
item Rosen, Benjamin - Ben
item Smith, Timothy - Tim

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 9/1/2020
Publication Date: 10/5/2020
Citation: Bickhart, D.M., Rosen, B.D., Smith, T.P. 2020. The Bovine Pangenome Consortium. Meeting Abstract. Biodiversity Genomics Conference October 5-9, 2020, Virtual Meeting.

Interpretive Summary:

Technical Abstract: The “gold standard” for conducting genomic research in any organism has been to first create a usable draft reference genome. However, it is increasingly recognized that a single reference genome is inadequate to fully describe the extent of genetic variation, even in relatively low-diversity species such as humans. Efforts to characterize the majority of genetic variants in a population, also called the pangenome, have already begun in the field of human genomics. Fortunately, advances in sequencing technologies have enabled even livestock species such as cattle to achieve a similar goal. However, the paucity of non-European breeds in cattle genome assembly projects represents an untapped source of genetic variation that will need to be included in cattle pangenome efforts. Using comparative alignments of sequence data to the current Hereford cattle reference genome, ARS-UCD1.2, we demonstrate that the average individual of even highly characterized breeds such as Holstein and Angus has 606 kilobases of DNA that are missing from the reference. This is expected to be even higher in more genetically diverse cattle breeds and in other members of the Bovinae. We have started an initiative within the global cattle genomic research community to generate reference-quality genomes for as many members of the Bovinae as possible. Using the latest in long-read sequencing technologies and assembly approaches, we plan to assemble and characterize underrepresented cattle breeds from around the world. Our consortium consists of 55 participants from 18 research institutes, and our members have already submitted seven reference-quality cattle and Bovinae species assemblies.