Data from: Accurate genomic predictions for chronic wasting disease in North American elk

The geographic expansion of chronic wasting disease (CWD) in North
American elk (Cervus canadensis) has not been well-mitigated by best
management practices, diagnostic surveillance, and depopulation of
positive herds. Using a custom Affymetrix Axiom® genetic variant array, we
demonstrate that differential susceptibility to CWD is highly heritable (
among farmed North American elk; with loci other than PRNP involved.
Genome-wide association analyses using 173,674 quality filtered variants
for a geographically diverse cohort of 904 farmed North American elk (n =
357 CWD positive; n = 547 CWD non-detect) confirmed the prion gene (PRNP
codon 132 MetàLeu and promoter variants) as a large-effect risk locus
(P-value < 5.135E-08), as evidenced by the estimated proportion of
phenotypic variance explained (PVE ≥ 0.032). However, more phenotypic
variance was collectively explained by loci other than PRNP.** Genomic
best linear unbiased prediction (GBLUP; n = 173,674 markers) with k-fold
cross validation (k = 3; k = 5) and random sampling (n = 50 iterations)
for the same cohort of 904 farmed North American elk produced mean genomic
prediction accuracies ≥ 0.791; thereby providing a foundation to explore a
genomically-estimated CWD genetic improvement program.