Association mapping of genetic risk factors for chronic wasting disease in wild deer
Version of Record online: 30 AUG 2012
© 2012 The Authors. Evolutionary Applications published by Blackwell Publishing Ltd.
This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
Volume 6, Issue 2, pages 340–352, February 2013
How to Cite
Matsumoto, T., Samuel, M. D., Bollinger, T., Pybus, M. and Coltman, D. W. (2013), Association mapping of genetic risk factors for chronic wasting disease in wild deer. Evolutionary Applications, 6: 340–352. doi: 10.1111/eva.12003
- Issue online: 18 FEB 2013
- Version of Record online: 30 AUG 2012
- Manuscript Accepted: 11 JUL 2012
- Manuscript Received: 22 NOV 2011
- 2006. Prion diseases of humans and farm animals: epidemiology, genetics, and pathogenesis. Journal of Neurochemistry 97:1726–1739. .
- 2004. Mammalian prion biology: one century of evolving concepts. Cell 116:313–327. , and .
- 2008. The prion's elusive reason for being. Annual Review of Neuroscience 31:439–477. , , and .
- 2008. Linkage disequilibrium decay and haplotype block structure in the pig. Genetics 179:569–579. , , , , and .
- 2002. Patterns of linkage disequilibrium in the human genome. Nature Reviews Genetics 3:299–309. , , and .
- 2006. Levels of linkage disequilibrium in a wild bird population. Biology Letters 2:435–438. , , , and .
- 2004. Chronic wasting disease and potential transmission to humans. Emerging Infectious Diseases 10:977–984. , , , , , and .
- 2004. The economic impacts of chronic wasting disease (CWD) in Wisconsin. Human Dimensions of Wildlife 9:181–192.
- 1994. A genetic-linkage map for cattle. Genetics 136:619–639. , , , , , et al.
- 2009. Genetic susceptibility to chronic wasting disease in free-ranging white-tailed deer: complement component C1q and Prnp polymorphisms. Infection, Genetics and Evolution 9:1329–1335. , , , , , , et al.
- 2004. Role of cytokines and chemokines in prion infections of the central nervous system. International Journal of Developmental Neuroscience 22:497–505. , , , , , , and .
- 2011a. Broad and fine-scale genetic analysis of white-tailed deer populations: estimating the relative risk of chronic wasting disease spread. Evolutionary Applications 4:116–131. , , , , , and .
- 2011b. Multi-scale population genetic analysis of mule deer (Odocoileus hemionus hemionus) in western Canada sheds new light on chronic wasting disease spread. Canadian Journal of Zoology 89:134–147. , , , , , and .
- 2000. Enhanced levels of scrapie responsive gene mRNA in BSE-infected mouse brain. Molecular Brain Research 76:173–179. , , , , , , et al.
- 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics 12:499–510. , , , , , and .
- 2003. Genetic consequences of white-tailed deer (Odocoileus virginianus) restoration in Mississippi. Molecular Ecology 12:3237–3252. , , , , , and .
- 2005. Polygenic variation and transmission factors involved in the resistance/susceptibility to scrapie in a Romanov flock. Journal of General Virology 86:849–857. , , , , and .
- 2009. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 324:522–528. , , , , , , et al.
- 1990. Purification of Thermus aquaticus DNA polymerase expressed in Escherichia coli. Analytical Biochemistry 191:396–400. , , , and .
- 2000. Extensive genome-wide linkage disequilibrium in cattle. Genome Research 10:220–227. , , , , , , et al.
- 2005. A complete estimate of the phylogenetic relationships in Ruminantia: a dated species-level supertree of the extant ruminants. Biological Reviews 80:269–302. , and .
- 1954. Statistical Methods for Research Workers, 12th edn. Oliver & Boyd, Edinburgh, 356 pp. .
- 2006. Comparison of DNA variants in the PRNP and NF1 regions between bovine spongiform encephalopathy and control cattle. Animal Genetics 37:469–474. , , , , and .
- 2006. Infectious agent of sheep scrapie may persist in the environment for at least 16 years. Journal of General Virology 87:3737–3740. , , and .
- 1995. FSTAT (Version 1.2): a computer program to calculate F-statistics. Journal of Heredity 86:485–486. .
- 2009. Linkage disequilibrium and demographic history of wild and domestic canids. Genetics 181:1493–1505. , , , , , , et al.
- 2006. Demographic patterns and harvest vulnerability of chronic wasting disease infected white-tailed deer in Wisconsin. Journal of Wildlife Management 70:546–553. , , , and .
- 2006. Preliminary observations of genetic susceptibility of elk (Cervus elaphus nelsoni) to chronic wasting disease by experimental oral inoculation. Journal of Veterinary Diagnostic Investigation 18:110–114. , , , , , , et al.
- 2003. Molecular and morphological phylogenies of Ruminantia and the alternative position of the Moschidae. Systematic Biology 52:206–228. , and .
- 1987. Gametic disequilibrium measures: proceed with caution. Genetics 117:331–341.
- 2002. Genome-wide search for markers associated with bovine spongiform encephalopathy. Mammalian Genome 13:164–168. , , , , and .
- 2005. Genome-wide association studies for common diseases and complex traits. Nature Reviews Genetics 6:95–108. , and .
- 2007. Scrapie—Uncertainties, biology and molecular approaches. Biochimica et Biophysica Acta 1772:619–628. .
- 2004. A comprehensive genetic map of the cattle genome based on 3802 microsatellites. Genome Research 14:1987–1998. , , , , , , et al.
- 2009. Deer carcass decomposition and potential scavenger exposure to chronic wasting disease. Journal of Wildlife Management 73:655–662. , , , and .
- 2003. Chronic wasting disease in free-ranging Wisconsin white-tailed deer. Emerging Infectious Diseases 9:599–601. , , , , , , et al.
- 2006. Spatial epidemiology of chronic wasting disease in Wisconsin white-tailed deer. Journal of Wildlife Diseases 42:578–588. , , , , , , et al.
- 2004. Chronic wasting disease in Canada: part 1. Canadian Veterinary Journal 45:397–404. , , , and .
- 1982. Epidemiological Research. Van Nostrand Reinhold Publishers, New York. , , and .
- 2005. Chronic wasting disease of elk: transmissibility to humans examined by transgenic mouse models. Journal of Neuroscience 25:7944–7949. , , , , , , et al.
- 2008. Touchdown PCR for increased specificity and sensitivity in PCR amplification. Nature Protocols 3:1452–1456. , and .
- 1999. Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nature Genetics 22:139–144. .
- 1996. Transfer of bovine microsatellites to the cervine (Cervus elaphus). Animal Genetics 27:199–201. , , and .
- 2009. Species-wide phylogeography of North American mule deer (Odocoileus hemionus): cryptic glacial refugia and postglacial recolonization. Molecular Ecology 18:1730–1745. , , , and .
- 2007. Linkage disequilibrium in wild mice. PLoS Genetics 3:1487–1495. , , , , , , et al.
- 2010. Extensive linkage disequilibrium in a wild bird population. Heredity 104:600–610. , and .
- 2004. A polymorphism of the interleukin-1 beta gene at position + 3953 influences progression and neuro-pathological hallmarks of Alzheimer's disease. Neurobiology of Aging 25:1017–1022. , , , , and .
- 2005. Genetic susceptibility to prion diseases in humans and mice. Current Genomics 6:1–11. , and .
- 2001. Identification of multiple quantitative trait loci linked to prion disease incubation period in mice. Proceedings of the National Academy of Sciences of the United States of America 98:6279–6283. , , , , , , et al.
- 2002. Identification of genetic loci affecting mouse-adapted bovine spongiform encephalopathy incubation time in mice. Neurogenetics 4:77–81. , , , , and .
- 1996. A male linkage map of the cattle (Bos taurus) genome. Journal of Heredity 87:261–271. , , , , , , et al.
- 2001. Genetic and environmental factors modify bovine spongiform encephalopathy incubation period in mice. Proceedings of the National Academy of Sciences of the United States of America 98:7402–7407. , , , , , , et al.
- 2007. IL-1 family members as candidate genes modulating scrapie susceptibility in sheep: localization, partial characterization, and expression. Mammalian Genome 18:53–63. , , , , et al.
- 2006. Infectious prions in the saliva and blood of deer with chronic wasting disease. Science 314:133–136. , , , , , , et al.
- 2008. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nature Reviews Genetics 9:356–369. , , , , , , and .
- 2009. Genetic risk factors for variant Creutzfeldt–Jakob disease: a genome-wide association study. Lancet Neurology 8:57–66. , , , , , , and .
- 2005. Epidemiology of chronic wasting disease in free-ranging mule deer: spatial, temporal, and demographic influences on observed prevalence patterns. Journal of Wildlife Diseases 41:275–290. , and .
- 2003. Horizontal prion transmission in mule deer. Nature 425:35–36. , and .
- 2004. Environmental sources of prion transmission in mule deer. Emerging Infectious Diseases 10:1003–1006. , , , and .
- The International Sheep Genomics Consortium. 2011. A genome-wide set of SNPs detects population substructure and long range linkage disequilibrium in wild sheep. Molecular Ecology Resources 11:314–322. , , , , and
- 2003. Detection of new quantitative trait loci for susceptibility to transmissible spongiform encephalopathies in mice. Genetics 165:2085–2091. , , , , and .
- 2010. A 2cM genome-wide scan of European Holstein cattle affected by classical BSE. BMC Genetics 11:20. , , , , , , et al.
- 2004. Polymorphisms in the prion precursor functional gene but not the pseudogene are associated with susceptibility to chronic wasting disease in white-tailed deer. Journal of General Virology 85:1339–1346. , , , , , and .
- 2009. Spatial and temporal patterns of chronic wasting disease: fine-scale mapping of a wildlife epidemic in Wisconsin. Ecological Applications 19:1311–1322. , , , and .
- 2001. Trypanotolerance in West African cattle and the population genetic effects of selection. PhD Thesis, University of Dublin. .
- 2008. PrP genotypes of free-ranging wapiti (Cervus elaphus nelsoni) with chronic wasting disease. Journal of General Virology 89:1324–1328. , , , and .
- 2001. Linkage disequilibrium in humans: models and data. American Journal of Human Genetics 69:1–14. , and .
- 2000. Inference of population structure using multilocus genotype data. Genetics 155:945–959. , , and .
- 2010. MicroRNAs as a molecular basis for mental retardation, Alzheimer's and prion diseases. Brain Research 1338:58–66. .
- 1989. Scrapie prions. Annual Review of Microbiology 43:345–374.
- 2012a. Emerging prion disease drives host selection in a wildlife population. Ecological Applications 22:1050–1089. , , , , and .
- 2012b. The role of genetics in chronic wasting disease of North American cervids. Prion 6:155–164. , , , and .
- 2011. Diversity and distribution of white-tailed deer mtDNA lineages in chronic wasting disease (CWD) outbreak areas in southern Wisconsin, USA. Journal of Toxicology and Environmental Health-Part a-Current Issues 74:1521–1535. , , , and .
- 2008. GENEPOP ‘007: a complete re-implementation of the GENEPOP software for Windows and Linux. Molecular Ecology Resources 8:103–106. .
- 2010. Lipid rafts: keys to neurodegeneration. Brain Research Bulletin 82:7–17.
- 2000. An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology 18:233–234. .
- 2004. Role of Interleukin-1 in prion disease-associated astrocyte activation. American Journal of Pathology 165:671–678. , , , , , , et al.
- 2003. Interleukin-1B polymorphism is associated with age at onset of Alzheimer's disease. Neurobiology of Aging 24:927–931. , , , , , , et al.
- 2011. Genome-wide polymorphism and comparative analyses in the white-tailed deer (Odocoileus virginianus): a model for conservation genomics. PLoS ONE 6:e15811. , , , , , , et al.
- 2004. Potential economic impacts of chronic wasting disease in Colorado. Human Dimensions of Wildlife 9:241–245. , and .
- 2007. Admixture and patterns of linkage disequilibrium in a free-living vertebrate population. Journal of Evolutionary Biology 20:1415–1427. , and .
- 1998. Bovine microsatellite loci are highly conserved in red deer (Cervus elaphus), sika deer (Cervus nippon) and Soay sheep (Ovis aries). Animal Genetics 29:307–315. , , , , , and .
- 2002. A deer (subfamily Cervinae) genetic linkage map and the evolution of ruminant genomes. Genetics 160:1587–1597. , , , , , , et al.
- 2008. Linkage disequilibrium – understanding the evolutionary past and mapping the medical future. Nature Reviews Genetics 9:477–485. .
- 2010. Cellular roles of the prion protein in association with reggie/flotillin microdomains. Frontiers in Bioscience 15:1075–1085. , , , and .
- 2000. Quantitative trait loci affecting prion incubation time in mice. Genomics 69:47–53. , , , , , , and .
- 2006. Identification of prion protein binding proteins by combined use of far-Western immunoblotting, two dimensional gel electrophoresis and mass spectrometry. Proteomics 6:26–34. , , , and .
- 2004. Extensive and breed-specific linkage disequilibrium in Canis familiaris. Genome Research 14:2388–2396. , , , , , , and .
- 2006. Neurofibromin: a general outlook. Clinical Genetics 70:1–13. , and .
- 2002. Genetic variation at a major histocompatibility locus within and among populations of white-tailed deer (Odocoileus virginianus). Journal of Mammalogy 83:31–39. , , and .
- 2002. MapChart: software for the graphical presentation of linkage maps and QTLs. Journal of Heredity 93:77–78.
- 1979. Inferences about linkage disequilibrium. Biometrics 35:235–254.
- 1984. Estimating F-statistics for the analysis of population-structure. Evolution 38:1358–1370. , and .
- 2002. Linkage disequilibrium and the mapping of complex human traits. Trends in Genetics 18:19–24. , and .
- 2007. The cellular prion protein (PrPC): its physiological function and role in disease. Biochimica et Biophysica Acta 1772:629–644. , , and .
- 2009. Polymorphisms at the PRNP gene influence susceptibility to chronic wasting disease in two species of deer (Odocoileus spp.) in Western Canada. Journal of Toxicology and Environmental Health Part A 72:1025–1029. , , , , , and .
- 2008. Correlation-based inference for linkage disequilibrium with multiple alleles. Genetics 180:533–545. , , and
- 2004. Mapping of multiple quantitative trait loci affecting bovine spongiform encephalopathy. Genetics 167:1863–1872. , , , , , and .
- 2005. Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between markers and QTL. Genetics Research 86:77–87. , , , and .