Atlantic herring, Atlantic cod, Atlantic salmon ). For example, several recent studies have found that the use of outlier loci can reveal fine-scale population structure beyond what was previously inferred from conventional neutral markers (e.g. The combined signal from high density neutral and putatively adaptive SNPs throughout the genome offers great potential for investigating evolutionary and ecological questions in natural populations. Central to a population genomic approach is the identification of statistical outlier loci that exhibit locus-specific patterns that are highly divergent from the rest of the genome, representing candidate regions under selection.

The emerging field of population genomics has evolved in tandem with these novel technologies, incorporating genome-wide sequence data into the study of systems that historically would have been limited to a small number of neutral markers. The efficiency of SNP discovery and validation may be further increased through targeting of the transcriptome (RNAseq ) or restriction-site associated DNA tags (RAD ). Due to their broad genomic distribution, direct association with functional significance, and ease of genotyping, SNPs represent an improvement over conventional markers such as amplified length polymorphisms (AFLPs) and expressed sequence tag (EST)-linked microsatellites. Single nucleotide polymorphisms (SNPs) have emerged as a marker of choice for population-level studies in the genomics era. The result is an exponential increase in the abundance of genomic resources available for studying non-model organisms. With the increasing ubiquity of next-generation sequencing technology, it is now possible to rapidly generate millions of base pairs of DNA sequence data for a fraction of the per-base cost required for chain-termination Sanger sequencing. While this RNAseq approach was successful at identifying a large number of new SNP loci, we found that the frequency of alleles present in the pooled transcriptome data was not an accurate predictor of population allele frequencies.īiology is currently undergoing a genomics revolution. This study provides novel genomic resources to support population genetic and genomic studies of both kokanee and anadromous sockeye salmon, and has the potential to produce markers capable of fine-scale stock assessment. In addition, we found some evidence for greater pathogen load among the kokanee sampled in stream-spawning habitats, suggesting a possible evolutionary advantage to shore-spawning that warrants further study. We also identified a number of contigs that were composed entirely of reads from a single ecotype, which may indicate regions of differential gene expression between the two reproductive ecotypes. A subset of these putative SNPs was validated using high-resolution melt analysis and Sanger resequencing to genotype independent samples of kokanee and anadromous sockeye salmon. These raw data were assembled into 11,074 high coverage contigs from which we identified 32,699 novel single nucleotide polymorphisms.

We used pooled cDNA samples from both ecotypes of kokanee to generate 750 million base pairs of transcriptome sequence data. The development of genome-wide SNP markers is an essential step towards fine-scale stock identification, and may enable a direct investigation of the genetic basis of ecotype divergence. Current conservation and management strategies may treat these ecotypes as discrete stocks, however their recent divergence and low levels of gene flow make in-season genetic stock identification a challenge. Kokanee salmon are recently diverged freshwater populations of sockeye salmon ( Oncorhynchus nerka) that exhibit reproductive ecotypes (stream-spawning and shore-spawning) in lakes throughout western North America and northeast Asia. When analyzed within a population genomics framework, SNP-based genotypic data may be used to investigate questions of evolutionary, ecological, and conservation significance in natural populations of non-model organisms. High throughput next-generation sequencing technology has enabled the collection of genome-wide sequence data and revolutionized single nucleotide polymorphism (SNP) discovery in a broad range of species.

Clc genomics workbench 5.5