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B Guldbrandtsen

Publications and source records attributed to B Guldbrandtsen.

5 recordsLinked to original sources
PubMed2003

Multitrait fine mapping of quantitative trait loci using combined linkage disequilibria and linkage analysis.

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.

Chromosome Mapping↗
PubMed2000

A polymorphic major histocompatibility complex class II-like locus maps outside of both the chicken B-system and Rfp-Y-system.

Chickens have two major regions encoding major histocompatibility complex (MHC) class Ialpha genes and MHC class IIss genes, the serological and functional B-system and the Rfp-Y-system. Recently, they have been shown to assort in a genetically independent way although still located on the same microchromosome. Moreover, the monomorphic MHC class IIalpha gene maps at a third locus located 5 cM from the nearest class IIss genes, located in the B-system (Kaufman et al., 1995). A pedigree family was studied in three generations in order to assign MHC class IIss restriction fragments observed in Southern blot analyses to either the B-system, the Rfp-Y-system or the B-Lalpha locus. In this study, we demonstrate by classical genetic testing of chickens within this fully pedigreed family the existence of an MHC class II-like polymorphic restriction fragment that segregates independently of the B-system, the Rfp-Y-system and of the B-Lalpha locus.

Alleles↗
PubMed1998

Population differentiation through mutation and drift--a comparison of genetic identity measures.

Different genetic identity or distance measures are compared that consider allelic variation within and between populations. Particularily we analyse those suggested by Nei (IS, DS), Rogers (DR), Reynolds, Weir and Cockerham (D theta), Nei, Tajima and Tateno (DA), Tomiuk and Loeschcke (ITL, DTL) and Goldstein et al. ((delta mu)2). The simulations focus on the influence of non-equilibrium conditions on the stability of these measures. The degree of homozygosity of an ancestral population before it splits into two sister populations is most important for the stability of the different estimates of genetic identity. If populations are not close to their equilibrium homozygosity, a considerable bias can occur and, thereby, provide very misleading estimates of the time span since divergence. The ITL-measure based on estimates of ancestral alleles is more robust than other measures of genetic identity, especially for large population sizes and high mutation rates. For the infinite allele model, the analysis shows that more precise estimates of the frequency of ancestral alleles can greatly improve the reliability of the estimate of genetic identity in the case of ITL. For the stepwise mutation model, the TL-measure combines the attributes of the DA- and (delta mu)2-measures. The TL-measure is efficient for the construction of the correct tree topology of related populations as well as for the estimation of the branch length when protein or microsatellite data are analysed.

Alleles↗
PubMedDate not supplied

Sampling genotypes in large pedigrees with loops.

Markov chain Monte Carlo (MCMC) methods have been proposed to overcome computational problems in linkage and segregation analyses. This approach involves sampling genotypes at the marker and trait loci. Scalar-Gibbs is easy to implement, and it is widely used in genetics. However, the Markov chain that corresponds to scalar-Gibbs may not be irreducible when the marker locus has more than two alleles, and even when the chain is irreducible, mixing has been observed to be slow. These problems do not arise if the genotypes are sampled jointly from the entire pedigree. This paper proposes a method to jointly sample genotypes. The method combines the Elston-Stewart algorithm and iterative peeling, and is called the ESIP sampler. For a hypothetical pedigree, genotype probabilities are estimated from samples obtained using ESIP and also scalar-Gibbs. Approximate probabilities were also obtained by iterative peeling. Comparisons of these with exact genotypic probabilities obtained by the Elston-Stewart algorithm showed that ESIP and iterative peeling yielded genotypic probabilities that were very close to the exact values. Nevertheless, estimated probabilities from scalar-Gibbs with a chain of length 235 000, including a burn-in of 200 000 steps, were less accurate than probabilities estimated using ESIP with a chain of length 10 000, with a burn-in of 5 000 steps. The effective chain size (ECS) was estimated from the last 25 000 elements of the chain of length 125 000. For one of the ESIP samplers, the ECS ranged from 21 579 to 22 741, while for the scalar-Gibbs sampler, the ECS ranged from 64 to 671. Genotype probabilities were also estimated for a large real pedigree consisting of 3 223 individuals. For this pedigree, it is not feasible to obtain exact genotype probabilities by the Elston-Stewart algorithm. ESIP and iterative peeling yielded very similar results. However, results from scalar-Gibbs were less accurate.

Algorithms↗