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- Title
Accurate Genomic Predictions for Chronic Wasting Disease in U.S. White-Tailed Deer.
- Authors
Seabury, Christopher M.; Oldeschulte, David L.; Bhattarai, Eric K.; Legare, Dhruti; Ferro, Pamela J.; Metz, Richard P.; Johnson, Charles D.; Lockwood, Mitchell A.; Nichols, Tracy A.
- Abstract
The geographic expansion of chronic wasting disease (CWD) in U.S. white-tailed deer (Odocoileus virginianus) has been largely unabated by best management practices, diagnostic surveillance, and depopulation of positive herds. Using a custom Affymetrix Axiom single nucleotide polymorphism (SNP) array, we demonstrate that both differential susceptibility to CWD, and natural variation in disease progression, are moderately to highly heritable (h2 ¼ 0:337 6 0:079 ─ 0:637 6 0:070Þ among farmed U.S. white-tailed deer, and that loci other than PRNP are involved. Genome-wide association analyses using 123,987 quality filtered SNPs for a geographically diverse cohort of 807 farmed U.S. white-tailed deer (n = 284 CWD positive; n = 523 CWD non-detect) confirmed the prion gene (PRNP; G96S) as a largeeffect risk locus (P-value , 6.3E-11), as evidenced by the estimated proportion of phenotypic variance explained (PVE $ 0.05), but also demonstrated that more phenotypic variance was collectively explained by loci other than PRNP. Genomic best linear unbiased prediction (GBLUP; n = 123,987 SNPs) with k-fold cross validation (k = 3; k = 5) and random sampling (n = 50 iterations) for the same cohort of 807 farmed U.S. whitetailed deer produced mean genomic prediction accuracies $ 0.81; thereby providing the necessary foundation for exploring a genomically-estimated CWD eradication program.
- Subjects
CHRONIC wasting disease; WHITE-tailed deer; FORECASTING; SINGLE nucleotide polymorphisms; STATISTICAL sampling; BOVINE spongiform encephalopathy; LOCUS (Genetics)
- Publication
G3: Genes | Genomes | Genetics, 2020, Vol 10, Issue 4, p1433
- ISSN
2160-1836
- Publication type
Article
- DOI
10.1534/g3.119.401002