References of "Wagenaar, D"
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See detailResults of a whole genome scan targeting QTL for growth and carcass traits in a Pietrain x Large White intercross
Nezer, C.; Moreau, L.; Wagenaar, D. et al

in Genetics, Selection, Evolution (2002), 34(3, May-Jun), 371-387

We herein report the results of a whole genome scan performed in a Pietrain x Large White intercross counting 525 offspring to map QTL influencing economically important growth and carcass traits. We ... [more ▼]

We herein report the results of a whole genome scan performed in a Pietrain x Large White intercross counting 525 offspring to map QTL influencing economically important growth and carcass traits. We report experiment-wide significant lod scores (> 4.6) for meatiness and fat deposition on chromosome SSC2, and for average daily gain and carcass length on chromosome SSC7. Additional suggestive lod scores (> 3.3) for fat deposition are reported on chromosomes SSC1, SSC7 and SSC13. A significant dominance deviation was found for the QTL on SSC1, while the hypothesis of an additive QTL could not be rejected for the QTL on SSC7 and SSC13. No evidence for imprinted QTL could be found for QTL other than the one previously reported on SSC2. [less ▲]

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See detailSimultaneous 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
Farnir, Frédéric ULg; Grisart, B.; Coppieters, Wouter ULg et al

in Genetics (2002), 161(1), 275-287

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 ... [more ▼]

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. [less ▲]

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See detailHuman - ovine comparative sequencing of a 250 kilobase imprinted domain encompassing the callipyge (clpg) gene and identification of six imprinted transcripts: DLK1, DAT, GTL2, PEG11, antiPEG11 and MEG8
Charlier, Carole ULg; Segers, K.; Wagenaar, D. et al

in Genome Research (2001), 11

Two ovine BAC clones and a connecting long-range PCR product, jointly spanning ∼250 kb and representing most of theMULGE5-OY3 marker interval known to contain the clpglocus, were completely sequenced. The ... [more ▼]

Two ovine BAC clones and a connecting long-range PCR product, jointly spanning ∼250 kb and representing most of theMULGE5-OY3 marker interval known to contain the clpglocus, were completely sequenced. The resulting genomic sequence was aligned with its human ortholog and extensively annotated. Six transcripts, four of which were novel, were predicted to originate from within the analyzed region and their existence confirmed experimentally: DLK1, DAT, GTL2, PEG11, antiPEG11, and MEG8. RT-PCR experiments performed on a range of tissues sampled from an 8-wk-old animal demonstrated the preferential expression of all six transcripts in skeletal muscle, which suggests that they are under control of common regulatory elements. The six transcripts were also shown to be subject to parental imprinting: DLK1, DAT, andPEG11 were shown to be paternally expressed and GTL2,antiPEG11, and MEG8 to be maternally expressed. [less ▲]

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See detailExtensive Genome-Wide Linkage Disequilibrium in Cattle
Farnir, Frédéric ULg; Coppieters, Wouter ULg; Arranz, J. J. et al

in Genome Research (2000), 10(2), 220-7

A genome-wide linkage disequilibrium (LD) map was generated using microsatellite genotypes (284 autosomal microsatellite loci) of 581 gametes sampled from the dutch black-and-white dairy cattle population ... [more ▼]

A genome-wide linkage disequilibrium (LD) map was generated using microsatellite genotypes (284 autosomal microsatellite loci) of 581 gametes sampled from the dutch black-and-white dairy cattle population. LD was measured between all marker pairs, both syntenic and nonsyntenic. Analysis of syntenic pairs revealed surprisingly high levels of LD that, although more pronounced for closely linked marker pairs, extended over several tens of centimorgan. In addition, significant gametic associations were also shown to be very common between nonsyntenic loci. Simulations using the known genealogies of the studied sample indicate that random drift alone is likely to account for most of the observed disequilibrium. No clear evidence was obtained for a direct effect of selection ("Bulmer effect"). The observation of long range disequilibrium between syntenic loci using low-density marker maps indicates that LD mapping has the potential to be very effective in livestock populations. The frequent occurrence of gametic associations between nonsyntenic loci, however, encourages the combined use of linkage and linkage disequilibrium methods to avoid false positive results when mapping genes in livestock. [less ▲]

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See detailFine-Mapping of Quantitative Trait Loci by Identity by Descent in Outbred Populations: Application to Milk Production in Dairy Cattle
Riquet, J.; Coppieters, Wouter ULg; Cambisano, Nadine ULg et al

in Proceedings of the National Academy of Sciences of the United States of America (1999), 96(16), 9252-9257

We previously mapped a quantitative trait locus (QTL) affecting milk production to bovine chromosome 14. To refine the map position of this QTL, we have increased the density of the genetic map of ... [more ▼]

We previously mapped a quantitative trait locus (QTL) affecting milk production to bovine chromosome 14. To refine the map position of this QTL, we have increased the density of the genetic map of BTA14q11-16 by addition of nine microsatellites and three single nucleotide polymorphisms. Fine-mapping of the QTL was accomplished by a two-tiered approach. In the first phase, we identified seven sires heterozygous "Qq" for the QTL by marker-assisted segregation analysis in a Holstein-Friesian pedigree comprising 1,158 individuals. In a second phase, we genotyped the seven selected sires for the newly developed high-density marker map and searched for a shared haplotype flanking an hypothetical, identical-by-descent QTL allele with large substitution effect. The seven chromosomes increasing milk fat percentage were indeed shown to carry a common chromosome segment with an estimated size of 5 cM predicted to contain the studied QTL. The same haplotype was shown to be associated with increased fat percentage in the general population as well, providing additional support in favor of the location of the QTL within the corresponding interval. [less ▲]

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See detailA Qtl with Major Effect on Milk Yield and Composition Maps to Bovine Chromosome 14
Coppieters, Wouter ULg; Riquet, J.; Arranz, J. J. et al

in Mammalian Genome : Official Journal of the International Mammalian Genome Society (1998), 9(7), 540-4

A whole genome scan was undertaken in a granddaughter design comprising 1158 progeny-tested bulls in order to map QTL influencing milk yield and composition. In this paper we report the identification of ... [more ▼]

A whole genome scan was undertaken in a granddaughter design comprising 1158 progeny-tested bulls in order to map QTL influencing milk yield and composition. In this paper we report the identification of a locus on the centromeric end of bovine Chromosome (Chr) 14, with major effect on fat and protein percentage as well as milk yield. The genuine nature of this QTL was verified using the grand2-daughter design, that is, by tracing the segregating QTL alleles from heterozygous grandsires to their maternal grandsons and confirming the predicted QTL allele substitution effect. [less ▲]

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See detailA Qtl Affecting Milk Yield and Composition Maps to Bovine Chromosome 20: A Confirmation
Arranz, J. J.; Coppieters, Wouter ULg; Berzi, P. et al

in Animal Genetics (1998), 29(2), 107-15

As part of a whole genome scan undertaken to detect quantitative trait loci (QTL) affecting milk yield and composition, we have genotyped a granddaughter design comprising 1152 sons for six microsatellite ... [more ▼]

As part of a whole genome scan undertaken to detect quantitative trait loci (QTL) affecting milk yield and composition, we have genotyped a granddaughter design comprising 1152 sons for six microsatellite markers spanning bovine chromosome 20. An analysis performed across families provided strong evidence (experiment-wise P-values < 0.01) for the presence of a QTL affecting primarily protein percentage towards the telomeric end of the chromosome. A founder sire, shown in a previous study to segregate for a similar QTL in the corresponding chromosome region, was characterized by 29 and 57 sons and maternal grandsons, respectively, in the present design. Sorting corresponding sons and grandsons by paternal or grandpaternal allele provided significant evidence for the segregation of a QTL on chromosome 20. Altogether these results confirm the location of a QTL affecting milk production on bovine chromosome 20. [less ▲]

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