Analysis of 100 high-coverage genomes from a pedigreed captive baboon colony
- Jacqueline A. Robinson1,
- Saurabh Belsare1,
- Shifra Birnbaum2,
- Deborah E. Newman2,
- Jeannie Chan2,
- Jeremy P. Glenn2,
- Betsy Ferguson3,4,
- Laura A. Cox5,6 and
- Jeffrey D. Wall1
- 1Institute for Human Genetics, University of California, San Francisco, California 94143, USA;
- 2Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas 78245, USA;
- 3Division of Genetics, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA;
- 4Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA;
- 5Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, USA;
- 6Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas 78245, USA
Abstract
Baboons (genus Papio) are broadly studied in the wild and in captivity. They are widely used as a nonhuman primate model for biomedical studies, and the Southwest National Primate Research Center (SNPRC) at Texas Biomedical Research Institute has maintained a large captive baboon colony for more than 50 yr. Unlike other model organisms, however, the genomic resources for baboons are severely lacking. This has hindered the progress of studies using baboons as a model for basic biology or human disease. Here, we describe a data set of 100 high-coverage whole-genome sequences obtained from the mixed colony of olive (P. anubis) and yellow (P. cynocephalus) baboons housed at the SNPRC. These data provide a comprehensive catalog of common genetic variation in baboons, as well as a fine-scale genetic map. We show how the data can be used to learn about ancestry and admixture and to correct errors in the colony records. Finally, we investigated the consequences of inbreeding within the SNPRC colony and found clear evidence for increased rates of infant mortality and increased homozygosity of putatively deleterious alleles in inbred individuals.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.247122.118.
- Received December 3, 2018.
- Accepted March 21, 2019.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
