Evaluation of a Single Nucleotide Polymorphism Baseline for Genetic Stock Identification of Chinook Salmon (Oncorhynchus tshawytscha) in the California Current Large Marine Ecosystem

Chinook Salmon (Oncorhynchus tshawytscha) is an economically and ecologically important species, and populations from the west coast of North America are a major component of fisheries in the North Pacific Ocean. The anadromous life history strategy of this species generates populations (or stocks) that typically are differentiated from neighboring populations. In many cases, it is desirable to discern the stock of origin of an individual fish or the stock composition of a mixed sample to monitor the stock-specific effects of anthropogenic impacts and alter management strategies accordingly. Genetic stock identification (GSI) provides such discrimination, and we describe here a novel GSI baseline composed of genotypes from more than 8000 individual fish from 69 distinct populations at 96 single nucleotide polymorphism (SNP) loci. The populations included in this baseline represent the likely sources for more than 99% of the salmon encountered in ocean fisheries of California and Oregon. This new genetic baseline permits GSI with the use of rapid and cost-effective SNP genotyping, and power analyses indicate that it provides very accurate identification of important stocks of Chinook Salmon. In an ocean fishery sample, GSI assignments of more than 1000 fish, with our baseline, were highly concordant (98.95%) at the reporting unit level with information from the physical tags recovered from the same fish. This SNP baseline represents an important advance in the technologies available to managers and researchers of this species

Heterogeneous genetic basis of age at maturity in salmonid fishes

Understanding the genetic basis of repeated evolution of the same phenotype across taxa is a fundamental aim in evolutionary biology and has applications in conservation and management. However, the extent to which interspecific life-history trait polymorphisms share evolutionary pathways remains underexplored. Here, we address this gap by studying the genetic basis of a key life-history trait, age at maturity, in four species of Pacific salmonids (genus Oncorhynchus) that exhibit intra- and interspecific variation in this trait-Chinook Salmon, Coho Salmon, Sockeye Salmon, and Steelhead Trout. We tested for associations in all four species between age at maturity and two genome regions, six6 and vgll3, that are strongly associated with the same trait in Atlantic Salmon (Salmo salar). We also conducted a genome-wide association analysis in Steelhead to assess whether additional regions were associated with this trait. We found the genetic basis of age at maturity to be heterogeneous across salmonid species. Significant associations between six6 and age at maturity were observed in two of the four species, Sockeye and Steelhead, with the association in Steelhead being particularly strong in both sexes (p = 4.46 x 10(-9) after adjusting for genomic inflation). However, no significant associations were detected between age at maturity and the vgll3 genome region in any of the species, despite its strong association with the same trait in Atlantic Salmon. We discuss possible explanations for the heterogeneous nature of the genetic architecture of this key life-history trait, as well as the implications of our findings for conservation and management.Peer reviewe

Validation of a New Method for Population Assessment of Pacific Salmonids Using Genetic Markers

The goal of the proposed research project is to evaluate a novel method of efficient genetic tagging through an experiment with Chinook salmon (Oncorhynchus tshawytscha) from California’s Central Valley. The proposed parentage-based tagging (PBT) experiment has four components: marker discovery, development of analysis tools, implementation of the parent database, and assignment of known offspring and mixed fishery samples. Utilizing new methods for large scale parentage assignment, the collection of genetic information from a parental breeding generation can be used to “tag” the offspring cohort. When this is done at a hatchery or at a weir, the entire breeding population of a stock or population can be sampled, and the entire next generation tagged. Offspring can be non-lethally sampled during their seaward migration, in fisheries, and upon return to spawn (at hatcheries or instream). Genotyping is followed by high confidence parentage assignment wherein the inherited genetic tags are used to locate the parents of sampled individuals in the parent database, thereby identifying the stock and cohort of origin. Additionally, we will evaluate whether the same set of genetic markers for PBT are also effective for genetic stock identification (GSI). While PBT can identify the specific parents of an unknown individual (as long as their genetic data is in the parent database), GSI employs baseline samples from each population to which an unknown individual can be assigned

Validation of a New Method for Population Assessment of Pacific Salmonids Using Genetic Markers

The goal of the proposed research project is to evaluate a novel method of efficient genetic tagging through an experiment with Chinook salmon (Oncorhynchus tshawytscha) from California’s Central Valley. The proposed parentage-based tagging (PBT) experiment has four components: marker discovery, development of analysis tools, implementation of the parent database, and assignment of known offspring and mixed fishery samples. Utilizing new methods for large scale parentage assignment, the collection of genetic information from a parental breeding generation can be used to “tag” the offspring cohort. When this is done at a hatchery or at a weir, the entire breeding population of a stock or population can be sampled, and the entire next generation tagged. Offspring can be non-lethally sampled during their seaward migration, in fisheries, and upon return to spawn (at hatcheries or instream). Genotyping is followed by high confidence parentage assignment wherein the inherited genetic tags are used to locate the parents of sampled individuals in the parent database, thereby identifying the stock and cohort of origin. Additionally, we will evaluate whether the same set of genetic markers for PBT are also effective for genetic stock identification (GSI). While PBT can identify the specific parents of an unknown individual (as long as their genetic data is in the parent database), GSI employs baseline samples from each population to which an unknown individual can be assigned

Genetic Markers for Detecting Population Structure of West Coast Chinook Salmon

Scientists have identified 117 new single nucleotide polymorphisms (SNPs) for detecting the genetic relatedness of Chinook salmon.The most basic genetic variation possible, a SNP (pronounced “snip”) refers to a single difference in one base pair of a nucleotide. The major outcome of this project is the identification of an optimal panel of 96 SNPs that is capable of detecting both the parentage of hatchery-born Chinook and the origin (i.e., stock) of Chinook caught off California and Oregon.SNPs are fast becoming the tool of choice for population genetics studies of nonmodel organisms such as Pacific salmon, because of their low rates of error (mutation) and high resolving power. The detailed resolution of SNPs is particularly well suited for studies of anadromous fishes such as Chinook salmon (Oncorhynchus tshawytscha), as their fidelity to their natal rivers leads to a hierarchical population structure. This project demonstrates applications and advantages of SNP markers for California’s most commercially important salmon species

Genetic Markers for Detecting Population Structure of West Coast Chinook Salmon

Scientists have identified 117 new single nucleotide polymorphisms (SNPs) for detecting the genetic relatedness of Chinook salmon.The most basic genetic variation possible, a SNP (pronounced “snip”) refers to a single difference in one base pair of a nucleotide. The major outcome of this project is the identification of an optimal panel of 96 SNPs that is capable of detecting both the parentage of hatchery-born Chinook and the origin (i.e., stock) of Chinook caught off California and Oregon.SNPs are fast becoming the tool of choice for population genetics studies of nonmodel organisms such as Pacific salmon, because of their low rates of error (mutation) and high resolving power. The detailed resolution of SNPs is particularly well suited for studies of anadromous fishes such as Chinook salmon (Oncorhynchus tshawytscha), as their fidelity to their natal rivers leads to a hierarchical population structure. This project demonstrates applications and advantages of SNP markers for California’s most commercially important salmon species

Tree file for Supplemental Figure 1

NEXML tree file for the ten validation populations genotyped with the 91 SNP markers described in the paper

Data from: Discovery and characterization of single nucleotide polymorphisms in coho salmon, Oncorhynchus kisutch

Molecular population genetic analyses have become an integral part of ecological investigation and population monitoring for conservation and management. Microsatellites have been the molecular marker of choice for such applications over the last several decades, but single nucleotide polymorphism (SNP) markers are rapidly expanding beyond model organisms. Coho salmon (Oncorhynchus kisutch) is native to the north Pacific Ocean and its tributaries, where it is the focus of intensive fishery and conservation activities. As it is an anadromous species, coho salmon typically migrate across multiple jurisdictional boundaries, complicating management and requiring shared data collection methods. Here, we describe the discovery and validation of a suite of novel SNPs and associated genotyping assays which can be used in the genetic analyses of this species. These assays include 91 that are polymorphic in the species and one that discriminates it from a sister species, Chinook salmon. We demonstrate the utility of these SNPs for population assignment and phylogeographic analyses, and map them against the draft trout genome. The markers constitute a large majority of all SNP markers described for coho salmon and will enable both population- and pedigree-based analyses across the southern part of the species native range