10.5061/DRYAD.XD2547DCW
Seabury, Christopher M.
0000-0001-7104-0032
Texas A&M University
Oldeschulte, David L.
Texas A&M University
Bhattarai, Eric K.
Texas A&M University
Legare, Dhruti
Texas A&M University System
Ferro, Pamela J.
Texas A&M University System
Metz, Richard P.
0000-0002-9876-3385
Texas A&M University System
Johnson, Charles D.
Texas A&M University System
Lockwood, Mitchell A.
Texas Parks and Wildlife Department
Nichols, Tracy A.
National Health Law Program
Data from: Accurate genomic predictions for chronic wasting disease in
U.S. white-tailed deer
Dryad
dataset
2019
genome-wide association
Genomic prediction
2020-03-04T00:00:00Z
2020-03-04T00:00:00Z
en
https://doi.org/10.1534/g3.119.401002
657401405 bytes
8
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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 ( 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.
The geographic expansion of chronic wasting disease (CWD) in U.S.
white-tailed deer has been largely unabated by best management practices,
diagnostic surveillance, and depopulation of positive herds. Using a
custom SNP array, we show that differential susceptibility to CWD is
heritable, and that loci other than PRNP are involved. Genomic prediction
with k-fold cross validation for a geographically diverse cohort of farmed
U.S. white-tailed deer produced prediction accuracies ≥ 0.81.