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Identification
of Novel Single-Nucleotide Polymorphisms in Chinook Salmon and Variation
among Life History Types
Abstract |
| Single-nucleotide
polymorphisms (SNPs) are simple base substitutions of small indels
in otherwise conserved regions of nuclear or mitochondrial DNA. Assays
detecting these genetic maerkers have been a powerful tool for conserving
and managing fish populations. In nonmodel species, however, available
DNA sequence data are limited and inventive techniques must be employed
in screening for SNPs. In this study, we used expressed sequence tags
from rainbow trout Oncorhynchus mykiss) to design primers
for amplification of genomic DNA fragments from Chinook salmon O.
tchawytscha. The regions flanking the repeat sequence of published
microsatellite loci in Chinook salmon were also chosen to examine
nucleotide variation. Thirty-two individuals representing the majority
of the species' range from Russia to California were sequenced at
19 loci to identify SNPs. We discovered 58 polymorphisms during the
screen and chose 13 for development into 5' exonuclease assays (TaqMan
assays). The genotypes from the TaqMan assays were compared with sequence
data from individuals from the ascertainment panel to confirm proper
allele designations. To evaluate the power of these markers to differentiate
populations and life history types, we typed 91 individuals representing
the major lineages of Chinook salmon with 11 validated assays. Significant
allele frequency differences were observed among life history types
of Chinook salmon at seven SNP loci, demonstrating the power of these
markers to differentiate lineages. |
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