An extensive resource of single nucleotide polymorphism markers associated with Atlantic salmon (Salmo salar) expressed sequences

Hayes, Ben J.; Laerdahl, Jon K.; Lien, Sigbjørn; Moen, Thomas; Berg, Paul R.; Hindar, Kjetil; Davidson, William S.; Koop, Ben F.; Adzhubei, Alexei A.; Høyheim, Bjørn

doi:10.1016/j.aquaculture.2007.01.037

Cited by 101 publications

(98 citation statements)

References 30 publications

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Section: Discussionsupporting

confidence: 67%

“…69 and 8.74% in human, 8.63 and 8.63% in mouse, 8.15 and 8.27% in cattle (our study), and 11 and 13% in Atlantic salmon (Hayes et al 2007). However, the A 4 T transversions were the least frequent in humans (7.42%) and cattle (6.14%), while the C 4 G substitutions were the least frequent in mouse (6.37%) and Atlantic salmon (8%) (Hayes et al 2007). Interestingly, when two immediate adjacent sites flanking the SNPs were A 1 T rich (A 1 T content of 2, in particular), the frequency of transversional mutations significantly increased in animals, such as cattle (38.56%), human (38.70%), and mouse (36.50%), and in plants, such as Arabidopsis (53%) (Zhang and Zhao 2004) and the rice and maize chloroplast noncoding regions (57%) (Morton 1995).…”

Section: Discussionsupporting

confidence: 67%

“…Nevertheless, transition is the most abundant form of SNP in both plants and animals. In addition, both C 4 T and A 4 G substitutions occur equally, for example, being 32.81 and 32.77% in human (Zhao and Boerwinkle 2002), 33.93 and 34.10% in mouse (Zhang and Zhao 2004), 35.13 and 34.63% in cattle (this study), and 29 and 29% in Atlantic salmon (Hayes et al 2007).…”

Section: Discussionsupporting

confidence: 48%

“…This number further increased to 68.13% in mouse (Zhang and Zhao, 2004) and 69.76% in cattle (this study), but decreased to 58% in Atlantic salmon among the coding SNPs derived from expressed sequences (Hayes et al 2007). Nevertheless, transition is the most abundant form of SNP in both plants and animals.…”

Section: Discussionmentioning

confidence: 48%

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The Complementary Neighborhood Patterns and Methylation-to-Mutation Likelihood Structures of 15,110 Single-Nucleotide Polymorphisms in the Bovine Genome

Jiang

Wu²,

Zhang

et al. 2008

Genetics

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Bayesian analysis was performed to examine the single-nucleotide polymorphism (SNPs) neighborhood patterns in cattle using 15,110 SNPs, each with a flanking sequence of 500 bp. Our analysis confirmed three well-known features reported in plants and/or other animals: (1) the transition is the most abundant type of SNPs, accounting for 69.8% in cattle; (2) the transversion occurs most frequently (38.56%) in cattle when the A 1 Tcontent equals two at their immediate adjacent sites; and (3) C 4 Tand A 4 G transitions have reverse complementary neighborhood patterns and so do A 4 C and G 4 T transversions. Our study also revealed several novel SNP neighborhood patterns that have not been reported previously. First, cattle and humans share an overall SNP pattern, indicating a common mutation system in mammals. Second, unlike C 4 T/ A 4 G and A 4 C/G 4 T, the true neighborhood patterns for A 4 T and C 4 G might remain mysterious because the sense and antisense sequences flanking these mutations are not actually recognizable. Third, among the reclassified four types of SNPs, the neighborhood ratio between A 1 T and G 1 C was quite different. The ratio was lowest for C 4 G, but increased for C 4 T/A 4 G, further for A 4 C/G 4 T, and the most for A 4 T. Fourth, when two immediate adjacent sites provide structures for CpG, it significantly increased transitions compared to the structures without the CpG. Finally, unequal occurrence between A 4 G and C 4 T in five paired neighboring structures indicates that the methylation-induced deamination reactions were responsible for $20% of total transitions. In addition, conversion can occur at both CpG sites and non-CpG sites. Our study provides new insights into understanding molecular mechanisms of mutations and genome evolution.

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Section: Discussionsupporting

confidence: 67%

Section: Discussionsupporting

confidence: 67%

Section: Discussionsupporting

confidence: 48%

Section: Discussionmentioning

confidence: 48%

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The Complementary Neighborhood Patterns and Methylation-to-Mutation Likelihood Structures of 15,110 Single-Nucleotide Polymorphisms in the Bovine Genome

Jiang

Wu²,

Zhang

et al. 2008

Genetics

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“…For instance, [26] reported a genetic variation map of the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNP) and [15] found 2507 putative SNP in the salmon genome that could be valuable for this purpose. In order to capture the information from historical recombinations, calculation of IBD probabilities simultaneously require information from LD and linkage information [18] at specific targeted regions.…”

mentioning

confidence: 99%

Further insights of the variance component method for detecting QTL in livestock and aquacultural species: relaxing the assumption of additive effects

Martínez¹

2008

Genet. Sel. Evol.

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-Complex traits may show some degree of dominance at the gene level that may influence the statistical power of simple models, i.e. assuming only additive effects to detect quantitative trait loci (QTL) using the variance component method. Little has been published on this topic even in species where relatively large family sizes can be obtained, such as poultry, pigs, and aquacultural species. This is important, when the idea is to select regions likely to be harbouring dominant QTL or in marker assisted selection. In this work, we investigated the empirical power and accuracy to both detect and localise dominant QTL with or without incorporating dominance effects explicitly in the model of analysis. For this purpose, populations with variable family sizes and constant population size and different values for dominance variance were simulated. The results show that when using only additive effects there was little loss in power to detect QTL and estimates of position, using or not using dominance, were empirically unbiased. Further, there was little gain in accuracy of positioning the QTL with most scenarios except when simulating an overdominant QTL.QTL / additive effect / dominance / power / REML

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Genomic Selection in Aquaculture: Methods and Practical Considerations

Ragavendran

Muir

2010

Next Generation Sequencing and Whole Genome Selection in Aquaculture

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An extensive resource of single nucleotide polymorphism markers associated with Atlantic salmon (Salmo salar) expressed sequences

Cited by 101 publications

References 30 publications

The Complementary Neighborhood Patterns and Methylation-to-Mutation Likelihood Structures of 15,110 Single-Nucleotide Polymorphisms in the Bovine Genome

The Complementary Neighborhood Patterns and Methylation-to-Mutation Likelihood Structures of 15,110 Single-Nucleotide Polymorphisms in the Bovine Genome

Further insights of the variance component method for detecting QTL in livestock and aquacultural species: relaxing the assumption of additive effects

Genomic Selection in Aquaculture: Methods and Practical Considerations

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