Journal
G3-GENES GENOMES GENETICS
Volume 10, Issue 4, Pages 1433-1441Publisher
GENETICS SOCIETY AMERICA
DOI: 10.1534/g3.119.401002
Keywords
genome-wide association; chronic wasting disease; white-tailed deer; genomic prediction; heritability
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Funding
- USDA-MIS-Animal and Plant Health Inspection Service [AP17VSSPRS00C126]
- Texas Parks and Wildlife Department [475613]
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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=0.337 +/- 0.079 & x2500;0.637 +/- 0.070) 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 large-effect 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. white-tailed deer produced mean genomic prediction accuracies >= 0.81; thereby providing the necessary foundation for exploring a genomically-estimated CWD eradication program.
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