Thirty‐two single nucleotide polymorphism markers for high‐throughput genotyping of sockeye salmon

Elfstrom, Carita M.; Smith, Christian T.; Seeb, James E.

doi:10.1111/j.1471-8286.2006.01507.x

Cited by 44 publications

(25 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Genotypes were obtained using the Fluidigm IFC thermal cyclers and the Fluidigm BioMark instrument, as detailed in Seeb et al (2009). All individuals were genotyped at 42 nuclear and 3 mitochondrial SNP loci (Table 2; Smith et al 2005;Elfstrom et al 2006;Habicht et al 2010). Genotypes were imported and organized in the International Program for Salmon Ecological Genetics Progeny database (Progeny Software, South Bend, Indiana).…”

Section: Methodsmentioning

confidence: 99%

Spawning Habitat and Geography Influence Population Structure and Juvenile Migration Timing of Sockeye Salmon in the Wood River Lakes, Alaska

et al. 2011

Self Cite

View full text Add to dashboard Cite

The strict homing of sockeye salmon Oncorhynchus nerka results in reproductively isolated populations that often spawn in close proximity and share rearing habitat. High spawning fidelity enables these populations to adapt to local conditions, resulting in a wide range of life history characteristics and genetic variation within individual watersheds. The Wood River system in southwestern Alaska provides a pristine, well‐studied system in which to examine fine‐scale population structure and its influences on juvenile life histories. Adult sockeye salmon spawn in lake beaches, rivers, and small tributaries throughout this watershed, and juveniles rear in five nursery lakes. We genotyped 30 spawning populations and 6,066 migrating smolts at 45 single nucleotide polymorphism loci, two of which are candidates for positive selection in the study system. We show that there is significant genetic structure (FST = 0.032) in the Wood River lakes and that divergence is generally related to spawning rather than nursery habitat (hierarchical analysis of molecular variance; P < 0.05). Four groups of populations were identified based on genetic structure and used to determine the composition of unknown mixtures of migrating smolts using a Bayesian modeling framework. We demonstrate that smolt migration timing is related to genetic structure; stream and river populations dominate catches in early June, while beach spawners and the populations in Lake Kulik are more prevalent from mid‐June to early September. Age‐2 smolts are primarily produced by the Lake Kulik and beach spawning populations, showing that genetic differences may reflect divergent freshwater and migration life history strategies. These results indicate that local adaptation to spawning habitat influences genetic divergence in the Wood River lakes, affecting both adult and juvenile life stages of sockeye salmon.

show abstract

Section: Methodsmentioning

confidence: 99%

Spawning Habitat and Geography Influence Population Structure and Juvenile Migration Timing of Sockeye Salmon in the Wood River Lakes, Alaska

et al. 2011

Self Cite

View full text Add to dashboard Cite

show abstract

“…All individuals were genotyped for 127 previously determined EST-based SNPs [64,69-71] following procedures for 5’ nuclease assays as described in Seeb et al [72]. Genotype calling was carried out using the SDS 2.3 software (Life Technologies, Carlsbad California) or the BioMark 3.0.2 software (Fluidigm, South San Francisco, California).…”

Section: Methodsmentioning

confidence: 99%

Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing

Everett

Miller²,

Seeb

2012

BMC Genomics

View full text Add to dashboard Cite

BackgroundMeiotic maps are a key tool for comparative genomics and association mapping studies. Next-generation sequencing and genotyping by sequencing are speeding the processes of SNP discovery and the development of new genetic tools, including meiotic maps for numerous species. Currently there are limited genetic resources for sockeye salmon, Oncorhynchus nerka. We develop the first dense meiotic map for sockeye salmon using a combination of novel SNPs found in restriction site associated DNA (RAD tags) and SNPs available from existing expressed sequence tag (EST) based assays.ResultsWe discovered and genotyped putative SNPs in 3,430 RAD tags. We removed paralogous sequence variants leaving 1,672 SNPs; these were combined with 53 EST-based SNP genotypes for linkage mapping. The map contained 29 male and female linkage groups, consistent with the haploid chromosome number expected for sockeye salmon. The female map contains 1,057 loci spanning 4,896 cM, and the male map contains 1,118 loci spanning 4,220 cM. Regions of conservation with rainbow trout and synteny between the RAD based rainbow trout map and the sockeye salmon map were established.ConclusionsUsing RAD sequencing and EST-based SNP assays we successfully generated the first high density linkage map for sockeye salmon.

show abstract

“…This approach to SNP discovery in non-model organisms is a reliable method that can be employed in most taxa (Aitken et al 2004;Lyons et al 1997;Palumbi 1996). The EPIC method works best when DNA sequence data are available for protein-coding regions of genes from organisms closely related to the focal species (for recent examples see Cappuccio et al 2006;Elfstrom et al 2006;Morin et al 2007; for a bioinformatics pipeline applicable to plants see Fredslund et al 2006). There are several variants on the EPIC approach, including amplification of exonic rather than intronic sequence (Elfstrom et al 2007;Ryynanen and Primmer 2004).…”

Section: Epic and Related Approachesmentioning

confidence: 99%

Gene mapping in the wild with SNPs: guidelines and future directions

et al. 2008

View full text Add to dashboard Cite

One of the biggest challenges facing evolutionary biologists is to identify and understand loci that explain fitness variation in natural populations. This review describes how genetic (linkage) mapping with single nucleotide polymorphism (SNP) markers can lead to great progress in this area. Strategies for SNP discovery and SNP genotyping are described and an overview of how to model SNP genotype information in mapping studies is presented. Finally, the opportunity afforded by new generation sequencing and typing technologies to map fitness genes by genome-wide association studies is discussed.

show abstract

Thirty‐two single nucleotide polymorphism markers for high‐throughput genotyping of sockeye salmon

Cited by 44 publications

References 17 publications

Spawning Habitat and Geography Influence Population Structure and Juvenile Migration Timing of Sockeye Salmon in the Wood River Lakes, Alaska

Spawning Habitat and Geography Influence Population Structure and Juvenile Migration Timing of Sockeye Salmon in the Wood River Lakes, Alaska

Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing

Gene mapping in the wild with SNPs: guidelines and future directions

Contact Info

Product

Resources

About