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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 #364686

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: An improved pig reference genome to enable pig genetics and genomics research

Author
item WARR, AMANDA - Roslin Institute
item AFFARA, NABEEL - University Of Cambridge
item AKEN, BRONWEN - Embl-Ebi
item BEIKI, HAMID - Iowa State University
item Bickhart, Derek
item BILLIS, KONSTANTINOS - Embl-Ebi
item CHOW, WILLIAM - Wellcome Trust Sanger Institute
item EORY, LEL - Roslin Institute
item FINLAYSON, HEATHER - Roslin Institute
item FLICEK, PAUL - Embl-Ebi
item GIRON, CARLOS - Embl-Ebi
item GRIFFIN, DARREN - University Of Kent
item HALL, RICHARD - Pacific Biosciences Inc
item HANNUM, GREGORY - Denovium
item HOURLIER, THIBAUT - Embl-Ebi
item HOWE, KERSTIN - Wellcome Trust Sanger Institute
item HUME, DAVID - Roslin Institute
item IZUOGU, OSAGIE - Embl-Ebi
item KIM, KRISTI - Pacific Biosciences Inc
item KOREN, SERGEY - National Institutes Of Health (NIH)
item LIU, HAIBO - Iowa State University
item MANCHANDA, NANCY - Iowa State University
item MARTIN, FERGAL - Embl-Ebi
item Nonneman, Danny - Dan
item O'CONNOR, REBECCA - University Of Kent
item PHILLIPPY, ADAM - National Instiute Of Allergy And Infectious Diseases (NIAID, NIH)
item Rohrer, Gary
item Rosen, Benjamin
item RUND, LAURIE - University Of Illinois
item SARGENT, CAROLE - University Of Cambridge
item SCHOOK, LAWRENCE - University Of Illinois
item Schroeder, Steven - Steve
item SCHWATRZ, ARIEL - Denovium
item SKINNER, BENJAMIN - University Of Cambridge
item TALBOT, RICHARD - University Of Edinburgh
item TSENG, ELIZABETH - Pacific Biosciences Inc
item TUGGLE, CHRISTOPHER - Iowa State University
item WATSON, MICK - Roslin Institute
item Smith, Timothy - Tim
item ARCHIBALD, ALAN - Roslin Institute

Submitted to: Gigascience
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/22/2020
Publication Date: 6/16/2020
Citation: Warr, A., Affara, N., Aken, B., Beiki, H., Bickhart, D.M., Billis, K., Chow, W., Eory, L., Finlayson, H.A., Flicek, P., Giron, C.G., Griffin, D.K., Hall, R., Hannum, G., Hourlier, T., Howe, K., Hume, D.A., Izuogu, O., Kim, K., Koren, S., Liu, H., Manchanda, N., Martin, F.J., Nonneman, D.J., O'Connor, R.E., Phillippy, A.M., Rohrer, G.A., Rosen, B.D., Rund, L.A., Sargent, C.A., Schook, L.B., Schroeder, S.G., Schwatrz, A.S., Skinner, B.M., Talbot, R., Tseng, E., Tuggle, C.K., Watson, M., Smith, T.P., Archibald, A.L. 2020. An improved pig reference genome to enable pig genetics and genomics research. Nature Genetics. https://doi.org/10.1093/gigascience/giaa051.
DOI: https://doi.org/10.1093/gigascience/giaa051

Interpretive Summary: The domestic pig is an important species in US agriculture and medical research. We present a new reference genome for the pig that places it on par in quality with the human reference genome. This will enable better selective breeding for new pig lines. It will also allow more insight into shared genes that pigs have with human for future medical research. This result is due to an extensive collaboration between US and UK scientists.

Technical Abstract: The domestic pig is important both as a food source and as a biomedical model with high anatomical and immunological similarity to humans. The draft reference genome (Sscrofa10.2) represents a purebred female pig from a commercial pork production breed (Duroc), and was established using older clone-based sequencing methods. The Sscrofa10.2 assembly was incomplete and unresolved redundancies, short range order and orientation errors and associated misassembled genes limited its utility. We present two genome assemblies created with more recent long read technologies and a whole genome shotgun strategy, one for the same Duroc female (Sscrofa11.1) and one for an outbred, composite breed male animal commonly used for commercial pork production (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy compared to the earlier reference, and the availability of two independent assemblies provided an opportunity to identify large-scale variants and to error-check the accuracy of representation of the genome. We propose that the improved Duroc breed assembly (Sscrofa11.1) become the reference genome for genomic research in pigs