Genomic association with pathogen carriage in bighorn sheep ( Ovis canadensis )
Open Access
- 2 March 2021
- journal article
- research article
- Published by Wiley in Ecology and Evolution
- Vol. 11 (6), 2488-2502
- https://doi.org/10.1002/ece3.7159
Abstract
Genetic composition can influence host susceptibility to, and transmission of, pathogens, with potential population-level consequences. In bighorn sheep (Ovis canadensis), pneumonia epidemics caused by Mycoplasma ovipneumoniae have been associated with severe population declines and limited recovery across North America. Adult survivors either clear the infection or act as carriers that continually shed M. ovipneumoniae and expose their susceptible offspring, resulting in high rates of lamb mortality for years following the outbreak event. Here, we investigated the influence of genomic composition on persistent carriage of M. ovipneumoniae in a well-studied bighorn sheep herd in the Wallowa Mountains of Oregon, USA. Using 10,605 SNPs generated using RADseq technology for 25 female bighorn sheep, we assessed genomic diversity metrics and employed family-based genome-wide association methodologies to understand variant association and genetic architecture underlying chronic carriage. We observed no differences among genome-wide diversity metrics (heterozygosity and allelic richness) between groups. However, we identified two variant loci of interest and seven associated candidate genes, which may influence carriage status. Further, we found that the SNP panel explained similar to 55% of the phenotypic variance (SNP-based heritability) for M. ovipneumoniae carriage, though there was considerable uncertainty in these estimates. While small sample sizes limit conclusions drawn here, our study represents one of the first to assess the genomic factors influencing chronic carriage of a pathogen in a wild population and lays a foundation for understanding genomic influence on pathogen persistence in bighorn sheep and other wildlife populations. Future research should incorporate additional individuals as well as distinct herds to further explore the genomic basis of chronic carriage.Funding Information
- National Institutes of Health
- National Science Foundation
- U.S. Fish and Wildlife Service
- Morris Animal Foundation (D13ZO‐081)
- National Institute of General Medical Sciences
- National Institutes of Health (P20GM103474, P30GM110732, P30GM103324)
- National Science Foundation (DEB‐1316549)
This publication has 74 references indexed in Scilit:
- Genome-wide efficient mixed-model analysis for association studiesNature Genetics, 2012
- Fast gapped-read alignment with Bowtie 2Nature Methods, 2012
- QTL mapping for sexually dimorphic fitness-related traits in wild bighorn sheepHeredity, 2011
- BEDTools: a flexible suite of utilities for comparing genomic featuresBioinformatics, 2010
- How pathogens drive genetic diversity: MHC, mechanisms and misunderstandingsProceedings. Biological sciences, 2010
- The Sequence Alignment/Map format and SAMtoolsBioinformatics, 2009
- Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humansProceedings of the National Academy of Sciences of the United States of America, 2009
- ADZE: a rarefaction approach for counting alleles private to combinations of populationsBioinformatics, 2008
- PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage AnalysesAmerican Journal of Human Genetics, 2007
- The UCSC Table Browser data retrieval toolNucleic Acids Research, 2004