Northwest Fisheries Science Center

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Document Type: Journal Article
Center: NWFSC
Document ID: 4726
Title: Evaluating adaptive divergence between migratory and nonmigratory ecotypes of a salmonid fish, Oncorhynchus mykiss
Author: M. Hale, Frank P. Thrower, E. A. Berntson, Michael Miller, Krista M. Nichols
Publication Year: 2013
Journal: Genes, Genomes, Genetics
Volume: 3
Pages: 1273-1285
DOI: 10.1534/g3.113.006817
Keywords: Smoltification, life history variation, genomics, SNP, salmonids,

 Next generation sequencing and the application of population genomic and association approaches have made it possible to detect selection and unravel the genetic basis to variable phenotypic traits. Using the two approaches in parallel is an especially attractive approach in non-models organisms that lack a sequenced and annotated genome, but only works well when population structure is not confounded with the phenotype of interest. Herein, we use population genomics in a non-model fish species, rainbow trout (Oncorhynchus mykiss), to better understand adaptive divergence between migratory and non-migratory ecotype, and to further our understanding about the genetic basis of migration. RAD tag sequencing was used to identify Single Nucleotide Polymorphisms (SNPs) in migrant and resident O. mykiss from two systems, one in Alaska and the other in Oregon, USA. A total of 7,920 and 6,755 SNPs met filtering criteria in the Alaska and Oregon, data sets respectively. Population genetic tests determined that 1,423 SNPs were candidates for selection when loci were compared between resident and migrant samples. Prior linkage mapping studies using RAD tag SNPs were available to determine the position of 1,990 markers. Several significant SNPs are located in genome regions that contain QTL for migratory related traits, reinforcing the importance of these regions in the genetic basis of migration/residency. Annotation of genome regions linked to significant SNPs revealed genes involved in processes known to be important in migration (such as osmoregulatory function). This study adds to our growing knowledge on adaptive divergence between migratory and non-migratory ecotypes of this species; across studies, this complex trait appears to be controlled by many loci of small effect, with some in common, but many loci not shared between populations studied.

Theme: Recovery, Rebuilding and Sustainability of Marine and Anadromous Species
Foci: Characterize vital rates and other demographic parameters for key species, and develop and improve methods for predicting risk and viability/sustainability from population dynamics and demographic information.