Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout

The increased numbers of genetic markers produced by genomic techniques have the potential to both identify hybrid individuals and localize chromosomal regions responding to selection and contributing to introgression. We used restriction-site-associated DNA sequencing to identify a dense set of can...

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Bibliographic Details
Published in:Molecular ecology resources 2011-03, Vol.11 (s1), p.117-122
Main Authors: HOHENLOHE, PAUL A, AMISH, STEPHEN J, CATCHEN, JULIAN M, ALLENDORF, FRED W, LUIKART, GORDON
Format: Article
Language:English
Subjects:
Animals
Chromosome Mapping
conservation biology
Fish
Gene Library
Genetic Carrier Screening
genome duplication
Genomes
Genomics
Genotype
homeolog
Hybridization
Hybridization, Genetic
invasive species
Likelihood Functions
Oncorhynchus
Oncorhynchus - genetics
Oncorhynchus mykiss
Polymorphism, Single Nucleotide
population genomics
Sequence Analysis, DNA - methods
Species Specificity
threatened salmonids
Trout
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Summary:The increased numbers of genetic markers produced by genomic techniques have the potential to both identify hybrid individuals and localize chromosomal regions responding to selection and contributing to introgression. We used restriction-site-associated DNA sequencing to identify a dense set of candidate SNP loci with fixed allelic differences between introduced rainbow trout (Oncorhynchus mykiss) and native westslope cutthroat trout (Oncorhynchus clarkii lewisi). We distinguished candidate SNPs from homeologs (paralogs resulting from whole-genome duplication) by detecting excessively high observed heterozygosity and deviations from Hardy-Weinberg proportions. We identified 2923 candidate species-specific SNPs from a single Illumina sequencing lane containing 24 barcode-labelled individuals. Published sequence data and ongoing genome sequencing of rainbow trout will allow physical mapping of SNP loci for genome-wide scans and will also provide flanking sequence for design of qPCR-based TaqMan® assays for high-throughput, low-cost hybrid identification using a subset of 50-100 loci. This study demonstrates that it is now feasible to identify thousands of informative SNPs in nonmodel species quickly and at reasonable cost, even if no prior genomic information is available.
ISSN:1755-0998
1755-098X
1755-0998
DOI:10.1111/j.1755-0998.2010.02967.x