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To reduce the predation pressure in the natural habitats and ensure that some fry survived the year, 135 resident coho smolts and 2 cutthroat trout (O. clarkii) were trapped in the natural habitat areas and released into the wild.
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During these initial analyses, we suspected that some of the putative steelhead samples were steelhead x cutthroat hybrids because for three of these loci (Oke4 [37], Ots3 [38], Ots100 [39]), cutthroat trout showed genetic markers (alleles) that were distinguishable from those of steelhead.
We also compiled sequence data from an additional 95 cutthroat trout samples (Yellowstone cutthroat trout [n = 71], Lahontan cutthroat trout [n = 4], Rio Grande cutthroat trout [n = 10], Colorado River cutthroat trout [n = 6], and greenback cutthroat trout [n = 4]) deposited in the GenBank database [ 27, 40, 41]; providing an additional 38 haplotypes.
A total of 43,558 putative SNPs were identified, and of those, 125 SNP primers were developed that successfully amplified 96 cutthroat trout and rainbow trout individuals.
The parallel pyrosequencing technology, commercialized by 454 pyrosequencing, is another next generation sequencing technology and has been used to identify gene-associated SNPs derived from ESTs, e.g. in the blunt snout bream [ 11], lake whitefish [ 12], cutthroat trout [ 13], Atlantic herring [ 14] and Atlantic cod [ 15].
During the three study years, 14 of the 66 putative cutthroat smolts (21.2%) were genetically identified as hybrids, and 28 of the 117 putative steelhead smolts (23.9%) were identified as hybrids.
We initially designed parallel studies of steelhead [34] and cutthroat [35] but took fin clips for DNA analysis to validate the visual identification of the species.
Of the 14
Examples include the migratory grayling (Thymallus thymallus; Meldgaard et al. 2003) and brown trout (Salmo trutta; Van Houdt et al. 2005; Heggenes and Røed 2006), coastal cutthroat trout (Oncorhynchus clarki clarki; Wofford et al. 2005) and the residential bullhead (Cottus gobio; Hänfling et al. 2002; Hänfling and Weetman 2006).
Genome maps have also been constructed for coho salmon O. kisutch (McClelland and Naish 2008), sockeye salmon O. nerka (Everett et al. 2012), pink salmon O. gorbuscha (Lindner et al. 2000), and cutthroat trout O. clarkii and rainbow trout hybrids (Ostberg et al. 2013).
All 125 validated SNPs are listed with the minor allele frequencies and the subspecies that carried the minor allele in Additional file 2. Westslope cutthroat trout had the lowest number of polymorphic SNPs with 20, whereas greenback cutthroat trout had the highest number of polymorphic SNPs with 75 (Table 3).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com