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

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