SNP discovery in candidate adaptive genes using exon capture in a free-ranging alpine ungulate.
Identification of genes underlying genomic signatures of natural selection is key to understanding adaptation to local conditions. We used targeted resequencing to identify SNP markers in 5321 candidate adaptive genes associated with known immunological, metabolic and growth functions in ovids and other ungulates. We selectively targeted 8161 exons in protein-coding and nearby 5' and 3' untranslated regions of chosen candidate genes. Targeted sequences were taken from bighorn sheep (Ovis canadensis) exon capture data and directly from the domestic sheep genome (Ovis aries v. 3; oviAri3). The bighorn sheep sequences used in the Dall's sheep (Ovis dalli dalli) exon capture aligned to 2350 genes on the oviAri3 genome with an average of 2 exons each. We developed a microfluidic qPCR-based SNP chip to genotype 476 Dall's sheep from locations across their range and test for patterns of selection. Using multiple corroborating approaches (lositan and bayescan), we detected 28 SNP loci potentially under selection. We additionally identified candidate loci significantly associated with latitude, longitude, precipitation and temperature, suggesting local environmental adaptation. The three methods demonstrated consistent support for natural selection on nine genes with immune and disease-regulating functions (e.g. Ovar-DRA, APC, BATF2, MAGEB18), cell regulation signalling pathways (e.g. KRIT1, PI3K, ORRC3), and respiratory health (CYSLTR1). Characterizing adaptive allele distributions from novel genetic techniques will facilitate investigation of the influence of environmental variation on local adaptation of a northern alpine ungulate throughout its range. This research demonstrated the utility of exon capture for gene-targeted SNP discovery and subsequent SNP chip genotyping using low-quality samples in a nonmodel species.
Alaska Science Center, U.S. Geological Survey, 4210 University Drive, Anchorage, AK, 99508, USA.|Wildlife Biology Program, Department of Ecosystem Sciences and Conservation, College of Forestry and Conservation, University of Montana, Missoula, MT, 59812, USA.
Gretchen H
http://orcid.org/0000-0002-8534-3664
GH
Roffler
Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA.
Stephen J
SJ
Amish
Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA.
Seth
S
Smith
Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA.
Ted
T
Cosart
Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA.|Evolutionary Biology Centre, Uppsala University, SE-75236, Uppsala, Sweden.
Marty
M
Kardos
Evolutionary Biology Centre, Uppsala University, SE-75236, Uppsala, Sweden.|US Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, 800 E. Beckwith Ave., Missoula, MT, 59801, USA.
Michael K
MK
Schwartz
Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA.|Flathead Lake Biological Station, University of Montana, Polson, MT, 59860, USA.
Gordon
G
Luikart
D000220:Adaptation, Biological; D000818:Animals; D005091:Exons; D005828:Genetics, Population / Q000379:methods*; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D044085:Microfluidics / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D012756:Sheep / Q000145:classification* / Q000235:genetics*
Ovis dalli dalli; SNP chip; candidate genes; exon capture; next-generation sequencing; population genomics