Salmonid fishes exhibit extensive local adaptations owing to abundant environmental variation and precise natal homing. This extensive local adaptation makes conservation and restoration of salmonids a challenge. For example, defining unambiguous units of conservation is difficult, and restoration attempts often fail owing to inadequate adaptive matching of translocated populations. A better understanding of the genetic architecture of local adaptation in salmonids could provide valuable information to assist in conserving and restoring natural populations of these important species. Here, we use a combination of laboratory crosses and next-generation sequencing to investigate the genetic architecture of the parallel adaptation of rapid development rate in two geographically and genetically distant populations of rainbow trout (Oncorhynchus mykiss). Strikingly, we find that not only is a parallel genetic mechanism used but that a conserved haplotype is responsible for this intriguing adaptation. The repeated use of adaptive genetic variation across distant geographical areas could be a general theme in salmonids and have important implications for conservation and restoration.

The timing and propensity for migration between fresh-and seawater is a key theme in the diversity of life histories within the salmonid fishes. Across salmonid species, life-history strategies range from wholly freshwater-resident populations, to migratory and nonmigratory variation within populations, to populations and species that are primarily migratory. Despite the central theme of migration to the evolution of these fishes, the genetic architecture of migration-related processes is poorly understood. Using a genetic cross of clonal lines derived from migratory and nonmigratory life-history types of Onchorhynchus mykiss (steelhead and rainbow trout, respectively), we have dissected the genetic architecture of the complex physiological and morphological transformation that occurs immediately prior to seaward migration (termed smoltification). Quantitative trait loci (QTL) analyses were used to identify the number, effects, and genomic location of loci associated with smoltification-related traits, including growth and condition factor, body coloration, morphology, and osmoregulatory enzymes during the smoltification period. Genetic analyses revealed numerous QTL, but one locus in particular is associated with multiple traits in single and joint analyses. Dissecting the genetic architecture of this highly complex trait has profound implications for understanding the genetic and evolutionary basis of life-history diversity within and among migratory fishes.

Androgenetic doubled haploid progeny produced from a cross between the Oregon State University and Arlee clonal rainbow trout (Oncorhynchus mykiss) lines, used for a previous published rainbow trout map, were used to update the map with the addition of more amplified fragment length polymorphic (AFLP) markers, microsatellites, type I and allozyme markers. We have added more than 900 markers, bringing the total number to 1359 genetic markers and the sex phenotype including 799 EcoRI AFLPs, 174 PstI AFLPs, 226 microsatellites, 72 VNTR, 38 SINE markers, 29 known genes, 12 minisatellites, five RAPDs, and four allozymes. Thirty major linkage groups were identified. Synteny of linkage groups in our map with the outcrossed microsatellite map has been established for all except one linkage group in this doubled haploid cross. Putative homeologous relationships among linkage groups, resulting from the autotetraploid nature of the salmonid genome, have been revealed based on the placement of duplicated microsatellites and type I loci.

Covalently functionalized Laponite clay was synthesized through a condensation reaction of the clay's silanol groups with mono- and trifunctional alkoxy silanes. Most of the work focuses on primary-amine-containing modifications because that group offers a wide range of derivitization options. Various 3-aminopropyltrimethoxy silane (APS) treatments yielded 4−14 wt % of organic material bound to the clay. APS-treated clay was further reacted to yield attached methacrylate, benzophenone, and tertiary bromine groups capable of polymerization, photoinitiation, and atom transfer radical polymerization initiation, respectively. Studies using a monoalkoxy analogue of APS, aminopropyldimethylethoxysilane (APES), are consistent with the hypothesis that multifunctional alkoxy silanes can cause the clay sheets to link together, hindering the clay's dispersibility and the efficiency of subsequent surface ion-exchange reactions. The attached amines were further reacted to 40 and 80% conversion in the APS- and APES-treated Laponites. Quantification studies show that there are about 200 siloxane-reactive sites per clay sheet at a concentration of 11 mequiv per 100 g of clay. All products were characterized with thermogravimetric analysis and solid-state 13C NMR to study the organic content and composition. 29Si solid-state NMR was also used to compare the treated clay with untreated sodium Laponite. Changes in the 29Si spectra were consistent with the expected silanol reaction.

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