Data from: Discovery and characterization of a large number of diagnostic markers to discriminate Oncorhynchus mykiss and O. clarkii

Hybridization of cutthroat trout and steelhead/rainbow trout is ubiquitous
where they are sympatric, either naturally or due to introductions. The
ability to detect hybridization between them has been hampered by a
paucity of genetic markers that have been validated across the many
phylogenetic lineages in the two species. Here, we describe 81 novel
genetic markers and associated assays for discriminating the genomes of
these sister species. These diagnostic nucleotide polymorphisms were
discovered by sequencing of rainbow trout expressed sequence tags (ESTs)
in a diverse panel of both cutthroat trout and steelhead/rainbow trout.
The resulting markers were validated in a large number of lineages of both
species, including all extant subspecies of cutthroat trout and most of
the lineages of rainbow trout that are found in natural sympatry with
cutthroat trout or used in stocking practices. Most of these markers (79%)
distinguish genomic regions for all lineages of the two species, but a
small number do not reliably diagnose coastal, westslope, and/or other
subspecies of cutthroat trout. Surveys of natural populations and hatchery
strains of trout and steelhead found rare occurrences of the alternative
allele, which may be due to either previous introgression or shared
polymorphism. The availability of a large number of genetic markers for
distinguishing genomic regions originating in these sister species will
allow the detection of both recent and more distant hybridization events,
facilitate the study of the evolutionary dynamics of hybridization and
provide a powerful set of tools for the conservation and management of
both species.