Data from: Development of a genotype-by-sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure

Pathogens are recognized as major drivers of local adaptation in wildlife
systems. By determining which gene variants are favored in local
interactions among populations with and without disease, spatially
explicit adaptive responses to pathogens can be elucidated. Much of our
current understanding of host responses to disease comes from a small
number of genes associated with an immune response. High-throughput
sequencing (HTS) technologies, such as genotype-by-sequencing (GBS),
facilitate expanded explorations of genomic variation among populations.
Hybridization-based GBS techniques can be leveraged in systems not well
characterized for specific variants associated with disease outcome to
“capture” specific genes and regulatory regions known to influence
expression and disease outcome. We developed a multiplexed, sequence
capture assay for red foxes to simultaneously assess ~300-kbp of genomic
sequence from 116 adaptive, intrinsic, and innate immunity genes of
predicted adaptive significance and their putative upstream regulatory
regions along with 23 neutral microsatellite regions to control for
demographic effects. The assay was applied to 45 fox DNA samples from
Alaska, where three arctic rabies strains are geographically restricted
and endemic to coastal tundra regions, yet absent from the boreal
interior. The assay provided 61.5% on-target enrichment with relatively
even sequence coverage across all targeted loci and samples (mean = 50×),
which allowed us to elucidate genetic variation across introns, exons, and
potential regulatory regions (4,819 SNPs). Challenges remained in
accurately describing microsatellite variation using this technique;
however, longer-read HTS technologies should overcome these issues. We
used these data to conduct preliminary analyses and detected genetic
structure in a subset of red fox immune-related genes between regions with
and without endemic arctic rabies. This assay provides a template to
assess immunogenetic variation in wildlife disease systems.