Location: Genetics and Animal BreedingTitle: Genome assemblies of global cattle breeds to create a cattle Pangenome
Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 10/30/2019
Publication Date: 1/2/2020
Citation: Smith, T.P.L, Bickhart, D.M., Rosen, B.D. 2020. Genome assemblies of global cattle breeds to create a cattle Pangenome [abstract]. International Plant & Animal Genome XXVIII Conference, January 11-15, 2020, San Diego, California. Poster Number PE0318. Available at: https://plan.core-apps.com/pag_2020/abstracts
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, while very useful, is inadequate to fully describe the extent of genetic variation, even in relatively low-diversity species such as humans. This observation is the basis of the recently-announced Human Pangenome Reference Sequence Project (HPRSP), which aims to generate high-quality assemblies of the diversity of human genomes. Fortunately, advances in sequencing technologies have reduced the cost of creating assemblies to the point where even livestock species could reasonably achieve a similar goal if global resources can be marshalled to this end. The other big challenge to creating a useful Pangenome resource from these assemblies, is a way to represent genomes in such a way as to serve as a comprehensive reference map of genetic variation that includes all DNA segments existing in all members of the species. This latter challenge is a major initiative within HPRSP, and the tools developed there should be applicable to other species. We propose an initiative within the global cattle genomic research community, to generate reference-quality genomes for as many cattle breeds as possible. We suggest that the best strategy will make use of F1 crosses of breeds using the trio binning approach, and will outline a proposed framework to achieve a cattle pangenome in a time frame to coincide with development of visualization and analysis tools in the human genome community.