scholarly journals Evaluation of a New Fine-mapping Method Exploiting Linkage Disequilibrium: a Case Study Analysing a QTL with Major Effect on Milk Composition on Bovine Chromosome 14

2002 ◽  
Vol 15 (9) ◽  
pp. 1250-1256 ◽  
Author(s):  
JongJoo Kim ◽  
Michel Georges
Keyword(s):  
Linkage Disequilibrium ◽  
Fine Mapping ◽  
Milk Composition ◽  
Major Effect ◽  
Mapping Method ◽  
Bovine Chromosome ◽  
Chromosome 14

scholarly journals Simultaneous Mining of Linkage and Linkage Disequilibrium to Fine Map Quantitative Trait Loci in Outbred Half-Sib Pedigrees: Revisiting the Location of a Quantitative Trait Locus With Major Effect on Milk Production on Bovine Chromosome 14

Genetics ◽  
2002 ◽  
Vol 161 (1) ◽  
pp. 275-287 ◽  
Author(s):  
Frédéric Farnir ◽  
Bernard Grisart ◽  
Wouter Coppieters ◽  
Juliette Riquet ◽  
Paulette Berzi ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Quantitative Trait ◽  
Milk Fat ◽  
Haplotype Analysis ◽  
Major Effect ◽  
Mapping Method ◽  
Substitution Effects ◽  
Marker Interval ◽  
Chromosome 14 ◽  
Trait Locus

Abstract A maximum-likelihood QTL mapping method that simultaneously exploits linkage and linkage disequilibrium and that is applicable in outbred half-sib pedigrees is described. The method is applied to fine map a QTL with major effect on milk fat content in a 3-cM marker interval on proximal BTA14. This proximal location is confirmed by applying a haplotype-based association method referred to as recombinant ancestral haplotype analysis. The origin of the discrepancy between the QTL position derived in this work and that of a previous analysis is examined and shown to be due to the existence of distinct marker haplotypes associated with QTL alleles having large substitution effects.

scholarly journals Haplotype Sharing Refines the Location of an Imprinted Quantitative Trait Locus With Major Effect on Muscle Mass to a 250-kb Chromosome Segment Containing the Porcine IGF2 Gene

Genetics ◽  
2003 ◽  
Vol 165 (1) ◽  
pp. 277-285
Author(s):  
Carine Nezer ◽  
Catherine Collette ◽  
Laurence Moreau ◽  
Benoît Brouwers ◽  
Jong-Joo Kim ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Linkage Disequilibrium ◽  
Muscle Mass ◽  
Fine Mapping ◽  
Segregation Analysis ◽  
Major Effect ◽  
Chromosome Segment ◽  
Haplotype Sharing ◽  
Igf2 Gene ◽  
Trait Locus

Abstract We herein describe the fine mapping of an imprinted QTL with major effect on muscle mass that was previously assigned to distal SSC2p in the pig. The proposed approach exploits linkage disequilibrium in combination with QTL genotyping by marker-assisted segregation analysis. By identifying a haplotype shared by all “Q” chromosomes, we map the QTL to an ∼250-kb chromosome segment containing INS and IGF2 as the only known paternally expressed genes. This considerably reinforces the candidacy of these genes, justifying their detailed analysis.

A QTL with major effect on milk yield and composition maps to bovine Chromosome 14

1998 ◽  
Vol 9 (7) ◽  
pp. 540-544 ◽  
Author(s):  
Wouter Coppieters ◽  
Juliette Riquet ◽  
Juan-José Arranz ◽  
Paulette Berzi ◽  
Nadine Cambisano ◽  
...  
Keyword(s):  
Milk Yield ◽  
Major Effect ◽  
Bovine Chromosome ◽  
Chromosome 14

A mammary gland EST showing linkage disequilibrium to a milk production QTL on bovine Chromosome 14

2001 ◽  
Vol 12 (8) ◽  
pp. 646-650 ◽  
Author(s):  
Christian Looft ◽  
Norbert Reinsch ◽  
Christina Karall-Albrecht ◽  
Sven Paul ◽  
Maren Brink ◽  
...  
Keyword(s):  
Mammary Gland ◽  
Linkage Disequilibrium ◽  
Milk Production ◽  
Bovine Chromosome ◽  
Chromosome 14

scholarly journals Multitrait Fine Mapping of Quantitative Trait Loci Using Combined Linkage Disequilibria and Linkage Analysis

Genetics ◽  
2003 ◽  
Vol 163 (1) ◽  
pp. 405-410 ◽  
Author(s):  
M S Lund ◽  
P Sørensen ◽  
B Guldbrandtsen ◽  
D A Sorensen
Keyword(s):  
Linkage Disequilibrium ◽  
Linkage Analysis ◽  
Fine Mapping ◽  
First Generation ◽  
Mapping Method ◽  
Linkage Disequilibria ◽  
Identical By Descent ◽  
Pleiotropic Qtl ◽  
Marker Information ◽  
Qtl Effects

Abstract A novel multitrait fine-mapping method is presented. The method is implemented by a model that treats QTL effects as random variables. The covariance matrix of allelic effects is proportional to the IBD matrix, where each element is the probability that a pair of alleles is identical by descent, given marker information and QTL position. These probabilities are calculated on the basis of similarities of marker haplotypes of individuals of the first generation of genotyped individuals, using “gene dropping” (linkage disequilibrium) and transmission of markers from genotyped parents to genotyped offspring (linkage). A small simulation study based on a granddaughter design was carried out to illustrate that the method provides accurate estimates of QTL position. Results from the simulation also indicate that it is possible to distinguish between a model postulating one pleiotropic QTL affecting two traits vs. one postulating two closely linked loci, each affecting one of the traits.

Case study: Comparison of milk composition from adjacent organic and conventional farms in the USA

2015 ◽  
Vol 69 (1) ◽  
pp. 137-142 ◽  
Author(s):  
Michael H Tunick ◽  
Diane L Van Hekken ◽  
Moushumi Paul ◽  
Elaine R Ingham ◽  
Hubert J Karreman
Keyword(s):  
Milk Composition ◽  
Conventional Farms ◽  
The Usa
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