Change search
ReferencesLink to record
Permanent link

Direct link
SNP discovery in candidate adaptive genes using exon capture in a free-ranging alpine ungulate
US Geol Survey, Alaska Sci Ctr, 4210 Univ Dr, Anchorage, AK 99508 USA.;Univ Montana, Wildlife Biol Program, Dept Ecosyst Sci & Conservat, Coll Forestry & Conservat, Missoula, MT 59812 USA..ORCID iD: 0000-0002-8534-3664
Univ Montana, Fish & Wildlife Genom Grp, Div Biol Sci, Missoula, MT 59812 USA..
Univ Montana, Fish & Wildlife Genom Grp, Div Biol Sci, Missoula, MT 59812 USA..
Univ Montana, Fish & Wildlife Genom Grp, Div Biol Sci, Missoula, MT 59812 USA..
Show others and affiliations
2016 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 16, no 5, 1147-1164 p.Article in journal (Refereed) Published
Abstract [en]

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 (Oviscanadensis) exon capture data and directly from the domestic sheep genome (Ovisaries 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.

Place, publisher, year, edition, pages
2016. Vol. 16, no 5, 1147-1164 p.
Keyword [en]
candidate genes, exon capture, next-generation sequencing, Ovis dalli dalli, population genomics, SNP chip
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-305555DOI: 10.1111/1755-0998.12560ISI: 000383281400009PubMedID: 27327375OAI: oai:DiVA.org:uu-305555DiVA: diva2:1038871
Available from: 2016-10-20 Created: 2016-10-19 Last updated: 2016-10-20Bibliographically approved

Open Access in DiVA

fulltext(859 kB)13 downloads
File information
File name FULLTEXT01.pdfFile size 859 kBChecksum SHA-512
0137c677dd4919a4012a62ea54b64ea66ec7f5c1733a991497e0f18c2e6695663a0b4074cdbc63d0d8900c485c46ee68850144e537f171d3cd147e0109045a9c
Type fulltextMimetype application/pdf

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Roffler, Gretchen H.Kardos, Marty
By organisation
Evolutionary Biology
In the same journal
Molecular Ecology Resources
Biological Sciences

Search outside of DiVA

GoogleGoogle Scholar
Total: 13 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 54 hits
ReferencesLink to record
Permanent link

Direct link