10.5061/DRYAD.KK466
Roffler, Gretchen H.
University of Montana
Amish, Stephen J.
University of Montana
Smith, Seth
University of Montana
Cosart, Ted
University of Montana
Kardos, Marty
Uppsala University
University of Montana
Schwartz, Michael K.
Uppsala University
US Forest Service
Luikart, Gordon
University of Montana
Data from: SNP discovery in candidate adaptive genes using exon capture in
a free-ranging alpine ungulate
Dryad
dataset
2016
candidate genes
Next-generation sequencing
exon capture
Ovis dalli dalli
SNP chip
2016-06-14T14:22:00Z
2016-06-14T14:22:00Z
en
https://doi.org/10.1111/1755-0998.12560
366814 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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 5,321 candidate adaptive genes
associated with known immunological, metabolic, and growth functions in
ovids and other ungulates. We selectively targeted 8,161 exons in
protein-coding and nearby 5′ and 3′ untranslated regions of chosen
candidate genes. Targeted sequences were taken from bighorn sheep (O.
canadensis) exon capture data and directly from the domestic sheep genome
(O. aries v. 3; oviAri3). The bighorn sheep sequences used in the
Dall's sheep (Ovis dalli dalli) exon capture aligned to 2,350 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 3 methods
demonstrated consistent support for natural selection on 9 genes with
immune and disease-regulating functions (e.g., Ovar-DRA, APC, BATF2,
MAGEB18), cell regulation signaling 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 non-model species.
SNP dataSNPdata.txt