scholarly journals Fine Mapping of a Quantitative Trait Locus for Twinning Rate Using Combined Linkage and Linkage Disequilibrium Mapping

Genetics ◽  
2002 ◽  
Vol 161 (1) ◽  
pp. 373-379 ◽  
Author(s):  
Theo H E Meuwissen ◽  
Astrid Karlsen ◽  
Sigbjørn Lien ◽  
Ingrid Olsaker ◽  
Mike E Goddard
Keyword(s):  
Quantitative Trait Locus ◽  
Linkage Disequilibrium ◽  
Quantitative Trait ◽  
Complex Traits ◽  
Middle Part ◽  
Linkage Disequilibrium Mapping ◽  
Chromosome 5 ◽  
Linkage Information ◽  
Linkage Disequilibrium Information ◽  
Trait Locus

Abstract A novel and robust method for the fine-scale mapping of genes affecting complex traits, which combines linkage and linkage-disequilibrium information, is proposed. Linkage information refers to recombinations within the marker-genotyped generations and linkage disequilibrium to historical recombinations before genotyping started. The identity-by-descent (IBD) probabilities at the quantitative trait locus (QTL) between first generation haplotypes were obtained from the similarity of the marker alleles surrounding the QTL, whereas IBD probabilities at the QTL between later generation haplotypes were obtained by using the markers to trace the inheritance of the QTL. The variance explained by the QTL is estimated by residual maximum likelihood using the correlation structure defined by the IBD probabilities. Unlinked background genes were accounted for by fitting a polygenic variance component. The method was used to fine map a QTL for twinning rate in cattle, previously mapped on chromosome 5 by linkage analysis. The data consisted of large half-sib families, but the method could also handle more complex pedigrees. The likelihood of the putative QTL was very small along most of the chromosome, except for a sharp likelihood peak in the ninth marker bracket, which positioned the QTL within a region <1 cM in the middle part of bovine chromosome 5. The method was expected to be robust against multiple genes affecting the trait, multiple mutations at the QTL, and relatively low marker density.

Quantitative trait locus for seizure susceptibility on mouse chromosome 5 confirmed with reciprocal congenic strains

2007 ◽  
Vol 31 (3) ◽  
pp. 458-462 ◽  
Author(s):  
Thomas N. Ferraro ◽  
George G. Smith ◽  
Candice L. Schwebel ◽  
Falk W. Lohoff ◽  
Patrick Furlong ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Quantitative Trait ◽  
Genetic Background ◽  
Seizure Threshold ◽  
Maximal Electroshock ◽  
Seizure Susceptibility ◽  
Chromosome 5 ◽  
Congenic Strains ◽  
Combining Data ◽  
Trait Locus

Multiple quantitative trait locus (QTL) mapping studies designed to localize seizure susceptibility genes in C57BL/6 (B6, seizure resistant) and DBA/2 (D2, seizure susceptible) mice have detected a significant effect originating from midchromosome 5. To confirm the presence and refine the position of the chromosome 5 QTL for maximal electroshock seizure threshold (MEST), reciprocal congenic strains between B6 and D2 mice were created by a DNA marker-assisted backcross breeding strategy and studied with respect to changes in MEST. A genomic interval delimited by marker D5Mit75 (proximal to the acromere) and D5Mit403 (distal to the acromere) was introgressed for 10 generations. A set of chromosome 5 congenic strains produced by an independent laboratory was also studied. Comparison of MEST between congenic and control (parental genetic background) mice indicates that genes influencing this trait were captured in all strains. Thus, mice from strains having D2 alleles from chromosome 5 on a B6 genetic background exhibit significantly lower MEST compared with control littermates, whereas congenic mice harboring B6 chromosome 5 alleles on a D2 genetic background exhibit significantly higher MEST compared with control littermates. Combining data from all congenic strains, we conclude that the gene(s) underlying the chromosome 5 QTL for MEST resides in the interval between D5Mit108 (26 cM) and D5Mit278 (61 cM). Generation of interval-specific congenic strains from the primary congenic strains described here may be used to achieve high-resolution mapping of the chromosome 5 gene(s) that contributes to the large difference in seizure susceptibility between B6 and D2 mice.

Two closely linked interactive blood pressure QTL on rat chromosome 5 defined using congenic Dahl rats

2002 ◽  
Vol 8 (2) ◽  
pp. 81-86 ◽  
Author(s):  
Michael R. Garrett ◽  
John P. Rapp
Keyword(s):  
Blood Pressure ◽  
Quantitative Trait Locus ◽  
Quantitative Trait ◽  
Congenic Strain ◽  
Major Effect ◽  
Large Region ◽  
Chromosome 5 ◽  
Low Blood Pressure ◽  
Trait Locus

Previously we reported the construction of a congenic strain, S.LEW( 5 ), spanning a large region of rat chromosome 5. The Lewis (LEW) strain was the donor, and the Dahl salt-sensitive (S) strain was the recipient. The congenic strain included a blood pressure quantitative trait locus (QTL). In the present work, a series of nine congenic substrains were constructed from S.LEW( 5 ) which defined two closely linked blood pressure QTL in the region previously thought to contain only one. LEW low-blood-pressure alleles at both QTL were required for a major effect on blood pressure. Neither LEW allele alone had a significant effect on blood pressure. The two QTL were localized to regions 6.3 and 4.6 cM, and these were 1.0 cM apart.

scholarly journals An annotated consensus genetic map forPinus taedaL. and extent of linkage disequilibrium in three genotype-phenotype discovery populations

2014 ◽  
Author(s):  
Jared W. Westbrook ◽  
Vikram E. Chhatre ◽  
Le-Shin Wu ◽  
Srikar Chamala ◽  
Leandro Gomide Neves ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Linkage Disequilibrium ◽  
Genetic Map ◽  
Loblolly Pine ◽  
Quantitative Trait Locus Mapping ◽  
Quantitative Trait ◽  
Consensus Map ◽  
Family Pedigree ◽  
Trait Locus ◽  
Locus Mapping

A consensus genetic map forPinus taeda(loblolly pine) was constructed by merging three previously published maps with a map from a pseudo-backcross betweenP. taedaandP. elliottii(slash pine). The consensus map positioned 4981 markers via genotyping of 1251 individuals from four pedigrees. It is the densest linkage map for a conifer to date. Average marker spacing was 0.48 centiMorgans and total map length was 2372 centiMorgans. Functional predictions for 4762 markers for expressed sequence tags were improved by alignment to full-lengthP. taedatranscripts. Alignments to theP. taedagenome mapped 4225 scaffold sequences onto linkage groups. The consensus genetic map was used to compare the extent of genome-wide linkage disequilibrium in an association population of distantly relatedP. taedaindividuals (ADEPT2), a multiple-family pedigree used for genomic selection studies (CCLONES), and a full-sib quantitative trait locus mapping population (BC1). Weak linkage disequilibrium was observed in CCLONES and ADEPT2. Average squared correlations, R2, between genotypes at SNPs less than one centiMorgan apart was less than 0.05 in both populations and R2 did not decay substantially with genetic distance. By contrast, strong and extended linkage disequilibrium was observed among BC1 full-sibs where average R2 decayed from 0.8 to less than 0.1 over 53 centiMorgans. The consensus map and analysis of linkage disequilibrium establish a foundation for comparative association and quantitative trait locus mapping between genotype-phenotype discovery populations. 

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