scholarly journals Linkage Disequilibrium Grouping of Single Nucleotide Polymorphisms (SNPs) Reflecting Haplotype Phylogeny for Efficient Selection of Tag SNPs

Genetics ◽  
2005 ◽  
Vol 170 (1) ◽  
pp. 291-304 ◽  
Author(s):  
Fumihiko Takeuchi ◽  
Kazuyuki Yanai ◽  
Toshiyuki Morii ◽  
Yuji Ishinaga ◽  
Keiko Taniguchi-Yanai ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Tag Snps ◽  
Efficient Selection ◽  
Selection Of

Efficient selection of tagging single-nucleotide polymorphisms in multiple populations

2006 ◽  
Vol 120 (1) ◽  
pp. 58-68 ◽  
Author(s):  
Bryan N. Howie ◽  
Christopher S. Carlson ◽  
Mark J. Rieder ◽  
Deborah A. Nickerson
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Multiple Populations ◽  
Efficient Selection ◽  
Selection Of

scholarly journals Assessment of linkage disequilibrium patterns between structural variants and single nucleotide polymorphisms in three commercial chicken populations

2021 ◽  
Author(s):  
Johannes Geibel ◽  
Nora Paulina Praefke ◽  
Steffen Weigend ◽  
Henner Simianer ◽  
Christian Reimer
Keyword(s):  
Linkage Disequilibrium ◽  
Single Nucleotide Polymorphisms ◽  
Phenotypic Traits ◽  
Strong Linkage Disequilibrium ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Single Nucleotide ◽  
Tag Snps ◽  
Commercial Chicken ◽  
Translocation Breakpoints

Abstract BackgroundStructural variants (SV) are causative for some prominent phenotypic traits of livestock as different comb types in chickens or color patterns in pigs. Their effects on production traits are also increasingly studied. Nevertheless, accurately calling SV remains challenging. It is therefore of interest, whether close-by single nucleotide polymorphisms (SNPs) are in strong linkage disequilibrium (LD) with SVs and can serve as markers. Literature comes to different conclusions on whether SVs are in LD to SNPs on the same level as SNPs to other SNPs. The present study aimed to generate a precise SV callset from whole-genome short-read sequencing (WGS) data for three commercial chicken populations and to evaluate LD patterns between the called SV and surrounding SNPs.ResultsThe final callset consisted of 12,294,329 bivariate SNPs, 4,301 deletions (DEL), 224 duplications (DUP), 218 inversions (INV) and 117 translocation breakpoints (BND). While average LD between DELs and SNPs was at the same level as between SNPs and SNPs, LD between other SVs and SNPs was strongly reduced (DUP: 40 %, INV: 27 %, BND: 19 % of between-SNP LD). A main factor for the reduced LD was the presence of local minor allele frequency differences, which accounted for 50 % of the difference between SNP – SNP and DUP – SNP LD. This was potentially accompanied by lower genotyping accuracies for DUP, INV and BND compared with SNPs and DELs. An evaluation of the presence of tag SNPs (SNP in highest LD to the variant of interest) further revealed DELs to be slightly less tagged by WGS SNPs than WGS SNPs by other SNPs. This difference, however, was no longer present when reducing the pool of potential tag SNPs to SNPs located on four different chicken genotyping arrays.ConclusionsThe results imply that genomic variance due to DELs in the chicken populations studied can be captured by different SNP marker sets as good as variance from WGS SNPs, whereas separate SV calling might be advisable for DUP, INV, and BND effects.

Protein Variation in ADH and ADH-RELATED in Drosophila pseudoobscura: Linkage Disequilibrium Between Single Nucleotide Polymorphisms and Protein Alleles

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 673-687
Author(s):  
Stephen W Schaeffer ◽  
C Scott Walthour ◽  
Donna M Toleno ◽  
Anna T Olek ◽  
Ellen L Miller
Keyword(s):  
Linkage Disequilibrium ◽  
Single Nucleotide Polymorphisms ◽  
Drosophila Pseudoobscura ◽  
Linkage Disequilibrium Mapping ◽  
Nucleotide Polymorphisms ◽  
Neutral Model ◽  
Significant Linkage Disequilibrium ◽  
Single Nucleotide ◽  
Synonymous Sites ◽  
Significant Linkage

Abstract A 3.5-kb segment of the alcohol dehydrogenase (Adh) region that includes the Adh and Adh-related genes was sequenced in 139 Drosophila pseudoobscura strains collected from 13 populations. The Adh gene encodes four protein alleles and rejects a neutral model of protein evolution with the McDonald-Kreitman test, although the number of segregating synonymous sites is too high to conclude that adaptive selection has operated. The Adh-related gene encodes 18 protein haplotypes and fails to reject an equilibrium neutral model. The populations fail to show significant geographic differentiation of the Adh-related haplotypes. Eight of 404 single nucleotide polymorphisms (SNPs) in the Adh region were in significant linkage disequilibrium with three ADHR protein alleles. Coalescent simulations with and without recombination were used to derive the expected levels of significant linkage disequilibrium between SNPs and 18 protein haplotypes. Maximum levels of linkage disequilibrium are expected for protein alleles at moderate frequencies. In coalescent models without recombination, linkage disequilibrium decays between SNPs and high frequency haplotypes because common alleles mutate to haplotypes that are rare or that reach moderate frequency. The implication of this study is that linkage disequilibrium mapping has the highest probability of success with disease-causing alleles at frequencies of 10%.

The effect of linkage disequilibrium on the estimates of Single Nucleotide Polymorphic effects

2009 ◽  
Vol 2009 ◽  
pp. 44-44
Author(s):  
K Moore ◽  
J Gibson ◽  
D Johnston
Keyword(s):  
Linkage Disequilibrium ◽  
Single Nucleotide Polymorphisms ◽  
Genetic Improvement ◽  
Dairy Herd ◽  
Physical Distance ◽  
Causative Mutation ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Single Nucleotide Polymorphic ◽  
Single Nucleotide

The identification and exploitation of single nucleotide polymorphisms (SNP) associated with production traits present new opportunities for livestock genetic improvement. Often the identified SNP is not the causative mutation but rather is in some degree of linkage disequilibrium (LD). LD markers within 5cM can be considered as direct markers for the causative mutation because they are located close to the causative mutation (Dekkers, 2004). In a dairy herd, Farnir et al., (2000) estimated that the average LD, measured as D′ was 0.5 for loci pairs positioned within 5cM. Goddard et al., (2006) estimated that LD measured as r2 decreased rapidly as the physical distance between loci increased; at a separating distance of 0.5Mb the LD (r2) was only approximately 0.2. The aim of this work was to use stochastic simulation to investigate the effect that the distance between the SNP and causative mutation had on the accuracy of estimating additive and dominance effects of the causative mutation.

scholarly journals Identification of tag single-nucleotide polymorphisms in regions with varying linkage disequilibrium

BMC Genetics ◽  
2005 ◽  
Vol 6 (Suppl 1) ◽  
pp. S73 ◽  
Author(s):  
Priya Duggal ◽  
Elizabeth M Gillanders ◽  
Rasika A Mathias ◽  
Grace P Ibay ◽  
Alison P Klein ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide

scholarly journals Accuracy of marker-assisted selection with single markers and marker haplotypes in cattle

2007 ◽  
Vol 89 (4) ◽  
pp. 215-220 ◽  
Author(s):  
B. J. HAYES ◽  
A. J. CHAMBERLAIN ◽  
H. McPARTLAN ◽  
I. MACLEOD ◽  
L. SETHURAMAN ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Quantitative Trait Loci ◽  
Single Nucleotide Polymorphisms ◽  
Quantitative Trait ◽  
Marker Assisted Selection ◽  
Nucleotide Polymorphisms ◽  
Data Set ◽  
Single Nucleotide ◽  
Angus Cattle ◽  
Genome Wide

SummaryA key question for the implementation of marker-assisted selection (MAS) using markers in linkage disequilibrium with quantitative trait loci (QTLs) is how many markers surrounding each QTL should be used to ensure the marker or marker haplotypes are in sufficient linkage disequilibrium (LD) with the QTL. In this paper we compare the accuracy of MAS using either single markers or marker haplotypes in an Angus cattle data set consisting of 9323 genome-wide single nucleotide polymorphisms (SNPs) genotyped in 379 Angus cattle. The extent of LD in the data set was such that the average marker–marker r2 was 0·2 at 200 kb. The accuracy of MAS increased as the number of markers in the haplotype surrounding the QTL increased, although only when the number of markers in the haplotype was 4 or greater did the accuracy exceed that achieved when the SNP in the highest LD with the QTL was used. A large number of phenotypic records (>1000) were required to accurately estimate the effects of the haplotypes.

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