ARS | Publication request: Characterization of 22 novel single nucleotide polymorphism markers in steelhead and rainbow trout

Submitted to: Molecular Ecology Notes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 30, 2008
Publication Date: January 8, 2009
Repository URL: http://riley.nal.usda.gov/nal_web/digi/submission.html
Citation: Campbell, N.R., Overturf, K., Narum, S.R. 2009. Characterization of 22 novel single nucleotide polymorphism markers in steelhead and rainbow trout. Molecular Ecology Resources 9:318-322.

Interpretive Summary: From thirty-two individuals representing coastal and inland populations of the salmonids steelhead and rainbow trout (Oncorhynchus mykiss) 15 expressed sequences representing specific genes were sequenced. Nine regions of repeat sequence, also known as microsatellites loci were also sequenced. From the identified sequence obtained from isolated regions we were able to identify sixty-two single nucleotide polymorphisms (SNPs). After screening these sixty-two SNPS, thirteen were further developed in fluorescent detection assays. Genotypes from these fluorescent assays were compared to sequence data from individuals to confirm proper allele designations. These assays were then validated by testing them against 192 isolated salmonid samples from 6 different regions.

Technical Abstract: Thirty-two individuals representing coastal and inland populations of steelhead and rainbow trout (Oncorhynchus mykiss) were sequenced at 15 ESTs and 9 microsatellite loci to identify single nucleotide polymorphisms (SNPs). Sixty-two polymorphisms were discovered during the screen and 13 were developed into 5’ exonuclease assays (Taqman assays). Genotypes from TaqMan assays were compared to sequence data from individuals in the ascertainment panel to confirm proper allele designations. A larger number of samples (n = 192) from six regions were tested with the validated assays. Per locus FST values ranged from 0.000-0.414.