Single nucleotide polymorphism (SNP) discovery in duplicated genomes: intron-primed exon-crossing (IPEC) as a strategy for avoiding amplification of duplicated loci in Atlantic salmon (Salmo salar) and other salmonid fishes

Genome characterization and analysis is an imperative step in identifying and selectively breeding for improved traits of agriculturally important species. Expressed sequence tags (ESTs) represent a transcribed portion of the genome and are an effective way to identify genes within a species. Downstream applications of EST projects include DNA microarray construction and interspecies comparisons. In this study, 694 ESTs were sequenced and analyzed from a library derived from a 24-day-old turkey embryo. The 437 unique sequences identified were divided into 76 assembled contigs and 361 singletons. The majority of significant comparative matches occurred between the turkey sequences and sequences reported from the chicken. Whole genome sequence from the chicken was used to identify potential exon–intron boundaries for selected turkey clones and intron-amplifying primers were developed for sequence analysis and single nucleotide polymorphism (SNP) discovery. Identified SNPs were genotyped for linkage analysis on two turkey reference populations. This study significantly increases the number of EST sequences available for the turkey.Key words: turkey, cDNA, expressed sequence tag, single nucleotide polymorphism.

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A New Single Nucleotide Polymorphism Database for North American Atlantic Salmon Generated Through Whole Genome Resequencing

Frontiers in Genetics ◽

10.3389/fgene.2020.00085 ◽

2020 ◽

Vol 11 ◽

Author(s):

Guangtu Gao ◽

Michael R. Pietrak ◽

Gary S. Burr ◽

Caird E. Rexroad ◽

Brian C. Peterson ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Atlantic Salmon ◽

North American ◽

Whole Genome ◽

Nucleotide Polymorphism ◽

Genome Resequencing ◽

Single Nucleotide ◽

Single Nucleotide Polymorphism Database ◽

Whole Genome Resequencing

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Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing

Plant Biotechnology Journal ◽

10.1111/j.1467-7652.2009.00401.x ◽

2009 ◽

Vol 7 (4) ◽

pp. 347-354 ◽

Cited By ~ 106

Author(s):

Peter C. Bundock ◽

Frances G. Eliott ◽

Gary Ablett ◽

Adam D. Benson ◽

Rosanne E. Casu ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Plant Species ◽

454 Sequencing ◽

Snp Discovery ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Polyploid Plant

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“Riverscape” genetics: river characteristics influence the genetic structure and diversity of anadromous and freshwater Atlantic salmon (Salmo salar) populations in northwest Russia

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f2012-114 ◽

2012 ◽

Vol 69 (12) ◽

pp. 1947-1958 ◽

Cited By ~ 32

Author(s):

Mikhail Yu. Ozerov ◽

Alexey E. Veselov ◽

Jaakko Lumme ◽

Craig R. Primmer

Keyword(s):

Genetic Diversity ◽

Atlantic Salmon ◽

Salmo Salar ◽

Carrying Capacity ◽

Salmonid Fishes ◽

Microsatellite Data ◽

Data Set ◽

Atlantic Salmon Salmo Salar ◽

Genetic Diversity And Structure ◽

Genetic Structure And Diversity

Combining population genetic and landscape ecology approaches provides an understanding of how environmental factors affect individual dispersal, population size, and structure. We first generated a set of predictions of the expected effect of “riverscape” characteristics on salmonid genetic diversity and divergence, based on the results of earlier research on this topic in salmonid fishes. We then tested these predictions in a data set consisting of the microsatellite data and riverscape characteristics of 39 Atlantic salmon ( Salmo salar ) populations from northwest Russia. The carrying capacity of the river was an important factor shaping the genetic diversity and differentiation of Atlantic salmon populations in the region: salmon in rivers with a larger carrying capacity tended to have higher genetic diversity and lower genetic differentiation. The importance of other riverscape characteristics often varied between anadromous and freshwater populations. Taken together, these associations demonstrate a high and complex level of river landscape influence on the genetic diversity and structure of Atlantic salmon populations and highlight the importance of spawning and nursery area maintenance for the conservation of salmonids.

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