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Dörte Wittenburg

Dörte Wittenburg
Research Institute for Farm Animal Biology (FBN) · Institute of Genetics and Biometry

Dr. rer. nat.

About

94
Publications
4,165
Reads
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335
Citations
Citations since 2016
55 Research Items
266 Citations
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20162017201820192020202120220102030405060
Introduction
I have a strong background in analysing mathematical models in livestock science, both from a Bayesian and Frequentist perspective. I push the development of statistical methods in animal breeding, thereby enjoying the own implementation of algorithms. Furthermore, I am available as a statistical consultant to other scientists seeking statistical solutions to biological questions.
Additional affiliations
October 2011 - present
University of Rostock
Position
  • Lecturer
Description
  • Contribution to lectures in the module "Linear and mixed models" which is part of the master programmes Animal Science and Plant Production at the University Rostock
February 2008 - present
Research Institute for Farm Animal Biology (FBN)
Position
  • Researcher
Description
  • - Considering population structure and different sources of genetic variation (additive, dominance, epistasis) for phenotype prediction - Inclusion of dependencies between genomic sites in penalised regression approaches - Analysis of population-genetic parameters (linkage disequilibrium and recombination rate) in non-random mating populations
Education
November 2021 - November 2021
University of Rostock
Field of study
  • Animal breeding and genetics
December 2005 - September 2008
University of Greifswald / FBN Dummerstorf
Field of study
  • Biomathematics
October 2000 - December 2005
University of Rostock
Field of study
  • Business Mathematics

Publications

Publications (94)
Article
Full-text available
Determination of sample size (the number of replications) is a key step in the design of an observational study or randomized experiment. Statistical procedures for this purpose are readily available. Their treatment in textbooks is often somewhat marginal, however, and frequently the focus is on just one particular method of inference (significanc...
Article
Full-text available
Creation of the bovine reference assembly paved the way to develop the high‐throughput genotyping arrays of the single nucleotide polymorphisms (SNPs) based on the available map coordinates that facilitated major advances in gene mapping and selection programs. The assembly flaws, however, may cause false results in the downstream gene mapping stud...
Article
Full-text available
In life sciences, high-throughput techniques typically lead to high-dimensional data and often the number of covariates is much larger than the number of observations. This inherently comes with multicollinearity challenging a statistical analysis in a linear regression framework. Penalization methods such as the lasso, ridge regression, the group...
Article
Full-text available
Pikeperch ( Sander lucioperca ) has emerged as a high value species to the aquaculture industry. However, its farming techniques are at an early stage and its production is often performed without a selective breeding program, potentially leading to high levels of inbreeding. In this study, we identified and characterized autozygosity based on geno...
Article
Full-text available
An amendment to this paper has been published and can be accessed via the original article.
Thesis
To study the genetic impact on a quantitative trait, molecular markers are used as predictor variables in a statistical model. This habilitation thesis elucidated challenges accompanied with such investigations. First, the usefulness of including different kinds of genetic effects, which can be additive or non-additive, was verified. Second, depend...
Conference Paper
The arrangement of markers on the genome can be defined either in physical or linkage terms. While a physical map represents the inter-marker distances in base pairs, a linkage map pictures the recombination frequency between pairs of markers. The rate by which two measures are correlated varies along the chromosomes and provides insights into the...
Conference Paper
Creation of the bovine reference assembly paved the way to develop the high-throughput genotyping arrays of the single nucleotide polymorphisms (SNPs) based on the available map coordinates that facilitated major advances in gene mapping and selection programs. The assembly flaws, however, may cause false positive results in the downstream gene map...
Article
The dairy cattle industry emits considerable amounts of nitrogen, contributing to eutrophication and greenhouse gas emissions. Therefore, breeding and selection of cattle with outstanding low nitrogen emission is investigated as a possible countermeasure. Since milk urea content (MUC) correlates with the amount of nitrogen emitted, this study aimed...
Article
Full-text available
Background Linkage and linkage disequilibrium (LD) between genome regions cause dependencies among genomic markers. Due to family stratification in populations with non-random mating in livestock or crop, the standard measures of population LD such as $$r^2$$ r 2 may be biased. Grouping of markers according to their interdependence needs to account...
Article
Full-text available
Pikeperch (Sander lucioperca) is a fish species with growing economic significance in the aquaculture industry. However, successful positioning of pikeperch in large-scale aquaculture requires advances in our understanding of its genome organization. In this study, an ultra-high density linkage map for pikeperch comprising 24 linkage groups and 1,0...
Conference Paper
The dairy cattle industry emits enormous amounts of nitrogen, which pollutes the environment. Therefore, breeding and selection of cattle with outstanding nitrogen efficiency could minimize environmental pollution. Since milk urea content (MUC) correlates with the amount of nitrogen emitted, this study aimed at estimating genetic parameters of MUC...
Article
Full-text available
Background: Single nucleotide polymorphisms (SNPs) which capture a significant impact on a trait can be identified with genome-wide association studies. High linkage disequilibrium (LD) among SNPs makes it difficult to identify causative variants correctly. Thus, often target regions instead of single SNPs are reported. Sample size has not only a...
Article
Full-text available
Background Recombination is a process by which chromosomes are broken and recombine to generate new combinations of alleles, therefore playing a major role in shaping genome variation. Recombination frequencies ( $$\theta$$ θ ) between markers are used to construct genetic maps, which have important implications in genomic studies. Here, we report...
Article
Full-text available
Background: Statistical analyses of biological problems in life sciences often lead to high-dimensional linear models. To solve the corresponding system of equations, penalization approaches are often the methods of choice. They are especially useful in case of multicollinearity, which appears if the number of explanatory variables exceeds the num...
Preprint
Full-text available
Background : Linkage and linkage disequilibrium (LD) between genome regions cause dependencies among genomic markers. Due to family stratification in populations with non-random mating in livestock or crop, the standard measures of population LD such as $r^2$ may be biased. Grouping of markers according to their interdependence needs to account for...
Preprint
Full-text available
Background: Linkage and linkage disequilibrium (LD) between genome regions cause dependencies among genomic markers. Due to family stratification in populations with non-random mating in livestock or crop, the standard measures of population LD such as r 2 may be biased. Grouping of markers according to their interdependence needs to account for th...
Preprint
Full-text available
Background : Linkage and linkage disequilibrium (LD) between genome regions cause dependencies among genomic markers. Due to family stratification in populations with non-random mating in livestock or crop, the standard measures of population LD such as r 2 may be biased. Grouping of markers according to their interdependence needs to account for t...
Article
Full-text available
Selective breeding can significantly improve the establishment of sustainable and profitable aquaculture fish farming. For rainbow trout (Oncorhynchus mykiss), one of the main aquaculture coldwater species in Europe, a variety of selected hatchery strains are commercially available. In this study, we investigated the genetic variation between the l...
Preprint
Full-text available
Statistical analyses of biological problems in life sciences often lead to high-dimensional linear models. To solve the corresponding system of equations, penalisation approaches are often the methods of choice. They are especially useful in case of multicollinearity which appears if the number of explanatory variables exceeds the number of observa...
Poster
Full-text available
Single nucleotide polymorphisms (SNPs) with significant impact on a trait can be identified with genome-wide association studies. High linkage disequilibrium (LD) among SNPs makes it difficult to identify causative variants correctly. Thus, often target regions instead of single SNPs are reported. Sample size has not only a crucial impact on the pr...
Preprint
Full-text available
Single nucleotide polymorphisms (SNPs) which capture a significant impact on a trait can be identified with genome-wide association studies. High linkage disequilibrium (LD) among SNPs makes it difficult to identify causative variants correctly. Thus, often target regions instead of single SNPs are reported. Sample size has not only a crucial impac...
Article
Full-text available
The pikeperch (Sander lucioperca) is a fresh and brackish water Percid fish natively inhabiting the northern hemisphere. This species is emerging as a promising candidate for intensive aquaculture production in Europe. Specific traits like cannibalism, growth rate and meat quality require genomics based understanding, for an optimal husbandry and d...
Conference Paper
Single nucleotide polymorphisms (SNPs) with significant impact on a trait can be identified with genome-wide association studies. The high linkage disequilibrium (LD) among SNPs makes it difficult to identify causative variants correctly. In contrast to a single-locus model, where single SNPs are investigated successively, a multi-locus model is th...
Article
Full-text available
Blood values of calcium (Ca), inorganic phosphorus (IP), and alkaline phosphatase activity (ALP) are valuable indicators for mineral status and bone mineralization. The mineral homeostasis is maintained by absorption, retention, and excretion processes employing a number of known and unknown sensing and regulating factors with implications on immun...
Poster
Full-text available
Modern genome-wide association studies as well as methods for genomic selection involve genetic data, derived either from the analysis of biological samples or from simulations, where the number of genetic markers (e.g. SNPs) vastly exceeds the number of individuals. In this high-dimensional setting, exploring the precision of SNP-effect estimates...
Conference Paper
Molecular markers can be used to assess the genetic variation in a livestock population. Not only are the physical but also the genetic position of markers important for characterising a livestock population and for planning mating decisions in livestock breeding. Though the physical position is available from the current genome assembly, the genet...
Conference Paper
For the genomic evaluation of domestic animals, whole-genome regression methods are applied which use extensive information about genomic markers (e.g. single nucleotide polymorphisms; SNPs). As the number of model parameters increases with a still growing number of SNPs, multicollinearity between covariates can affect the precision of marker-effec...
Poster
Full-text available
Modern genome-wide association studies as well as methods for genomic selection frequently involve linear models where the number of genetic markers vastly exceeds the number of observations. In this high-dimensional setting, exploring the precision of SNP-effect estimates leading to a reliable identification of causative variants is complicated. W...
Article
Full-text available
Genomic information can be used to study the genetic architecture of some trait. Not only the size of the genetic effect captured by molecular markers and their position on the genome but also the mode of inheritance, which might be additive or dominant, and the presence of interactions are interesting parameters. When searching for interacting loc...
Data
Estimates of paternal recombination rate for all autosomes using empirical bovine data. Pairwise recombination rates were obtained using the stepwise procedure EMDP.
Data
Validation of recombination-rate estimates using empirical bovine data on BTA4. Pairwise recombination rates were obtained using the stepwise procedure EMDP. BTA4 contained SNPs which were misplaced (A) within and (B) between chromosomes.
Data
MSE of estimated paternal recombination rate and maternal linkage disequilibrium for simulated scenarios. Start values were fixed (EMT0 and EMT05) or adapted (EMDP), 1,000 half-sibs were simulated with 10,000 replicates.
Data
Estimates of r2 for all autosomes using empirical bovine data. Pairwise r2's were obtained using the stepwise procedure EMDP.
Data
Bias of estimated paternal recombination rate and maternal linkage disequilibrium for simulated scenarios. Start values were fixed (EMT0 and EMT05) or adapted (EMDP), 1,000 half-sibs were simulated with 10,000 replicates.
Data
Investigations on the likelihood function and derivation of the Hessian matrix.
Data
Estimated vs. simulated recombination rate depending on start-value strategy. Start values were fixed (EMT0 and EMT05) or adapted (EMDP). Simulated maternal allele frequency and LD: (A) p1 = 0.5, Ddam = 0.05, (B) p1 = 0.5, Ddam = 0.10, (C) p1 = 0.4, Ddam = 0.05, and (D) p1 = 0.4, Ddam = 0.10. In total, 1,000 half-sibs were simulated with 1,000 repl...
Data
Estimates of maternal linkage disequilibrium for all autosomes using empirical bovine data. Pairwise linkage disequilibria were obtained using the stepwise procedure EMDP.
Data
Genotype data consisting of 39,780 SNPs (columns), and 265 progeny (rows).
Data
Assignment of genotypes to half-sib families.
Data
Physical position of SNPs based on assembly Btau 4.2 and UMD 3.1.1.
Article
Full-text available
A livestock population can be characterized by different population genetic parameters, such as linkage disequilibrium and recombination rate between pairs of genetic markers. The population structure, which may be caused by family stratification, has an influence on the estimates of these parameters. An expectation maximization algorithm has been...
Article
Full-text available
Quantifying the population stratification in genotype samples has become a standard procedure for data manipulation before conducting genome wide association studies, as well as for tracing patterns of migration in humans and animals, and for inference about extinct founder populations. The most widely used approach capable of providing biologicall...
Conference Paper
Population genetic parameters, such as linkage disequilibrium and recombination rate (theta), are parameters for characterising livestock populations. The population structure has an influence on these parameters. In half-sib families, which are a typical family structure in dairy cattle, the paternal theta and the linkage disequilibrium of materna...
Conference Paper
Identifying positions along the genome which affect a performance trait is of vast interest in quantitative genetics. Bayesian methods are among the most popular and successful mathematical approaches to estimate genetic effects captured by markers and to select the relevant loci, but their results strongly rely on proper choices of prior distribut...
Conference Paper
Half-sib family is a typical population structure in dairy cattle. The population structure has influence on population parameters such as linkage disequilibrium (LD) and recombination rate between pairs of genomic markers. Estimates of LD can be incorporated in extended models for genome-based phenotype prediction. The paternal contribution to LD...
Article
Full-text available
In livestock, current statistical approaches utilize extensive molecular data, e.g., single nucleotide polymorphisms (SNPs), to improve the genetic evaluation of individuals. The number of model parameters increases with the number of SNPs, so the multicollinearity between covariates can affect the results obtained using whole genome regression met...
Conference Paper
Modern genotyping techniques result in large amounts of molecular data, e.g. SNPs. Thus, multicollinearities between variables appear. These dependencies are not only a consequence of the high complexity, but are also due to linkage and linkage disequilibrium between SNPs and can mathematically be expressed as covariances, forming a high-dimensiona...
Conference Paper
In livestock, current statistical approaches involve extensive molecular data (e.g. SNPs) to reach an improved genetic evaluation of phenotypes. As the number of model parameters increases with a still growing number of SNPs, multicollinearity between covariates can affect the results of whole genome regression methods. The objective of this study...
Conference Paper
In livestock, current statistical approaches involve extensive molecular data (e.g. SNPs) to reach an improved genetic evaluation. As the number of model parameters increases with a still growing number of SNPs, multicollinearity between covariates can affect the results of whole genome regression methods. The objective of this study is to addition...
Conference Paper
Full-text available
Abstract Text: As the number of model parameters increases with still growing number of SNPs, multicollinearity between covariates can affect the results of whole genome prediction. Selecting appropriate SNPs may counteract this phenomenon. Additionally, dependencies between single SNPs or chromosome regions can directly be incorporated in predicti...
Article
Full-text available
Milk performance traits are likely influenced by both additive and non-additive (e.g. dominance) genetic effects. Genetic variation can be partitioned using genomic information. The objective of this study was to estimate genetic variance components of production and milk component traits (e.g. acetone, fatty acids), which are particularly importan...
Conference Paper
Genomic information can be used to study the genetic architecture of some trait. In particular, when searching for eQTL, genome-wide available SNP data are employed to identify loci with impact on mRNA expression levels which are analysed successively gene by gene. For processing such multitudes of information, a rapid algorithm is desired for esti...
Data
ADRB2 and flanking regions. Coding region is shown in blue, untranslated regions in yellow. Vertical arrows show position of polymorphisms. Horizontal double-headed arrows depict amplicons used for resequencing. STR – short tandem repeat, I – insertion/deletion, A – nonsynonymous variant
Article
Porcine adrenergic receptor beta 2 (ADRB2) gene exhibits differential allelic expression in skeletal muscle, and its genetic variation has been associated with muscle pH. Exploring the molecular-genetic background of expression variation for porcine ADRB2 will provide insight into the mechanisms driving its regulatory divergence and may also contri...
Article
Full-text available
In this study the benefit of metabolome level analysis for the prediction of genetic value of three traditional milk traits was investigated. Our proposed approach consists of three steps: First, milk metabolite profiles are used to predict three traditional milk traits of 1,305 Holstein cows. Two regression methods, both enabling variable selectio...
Data
Full-text available
Important SNP markers, occurring in more than seven cross-validation (CV) runs, for each milk trait obtained via the metabolite approach. For this analysis, the 10 training sets from the outer cross-validation was used. (PDF)
Data
Correlations between important milk metabolites for all investigated milk traits. The correlation values were adapted from [6]. (PDF)
Data
Known QTL regions or QTL peaks, which were filtered from the cattleQTL database [25]. The following criteria were applied: trait name equal to milk fat percentage and milk protein percentage, analysis type equal to QTL, breed equal to Holstein, and chromosome number and both flanking markers or peak markers had to be available. Based on the marker...
Article
Full-text available
Phenotypic variation can partly be explained by genetic variation, such as variation in single nucleotide polymorphism (SNP) genotypes. Genomic selection methods seek to predict genetic values (breeding values) based on SNP genotypes. To develop and to optimize these methods, simulated data are often used, which follow a rather simple genotype-phen...
Article
In the field of dairy cattle research, it is of great interest to improve the detection and prevention of diseases (e.g., mastitis and ketosis) and monitor specific traits related to the state of health and management. During the standard milk performance test, traditional milk traits are monitored, and quality and quantity are screened. In additio...
Article
Full-text available
The composition of milk is crucial to evaluate milk performance and quality measures. Milk components partly contribute to breeding scores, and they can be assessed to judge metabolic and energy status of the cow as well as to serve as predictive markers for diseases. In addition to the milk composition measures (e.g., fat, protein, lactose) tradit...
Conference Paper
The composition of milk is clue to evaluate milk performance and quality measures. Milk components partly contribute to breeding scores, and they can be assessed to judge metabolic and energy status of the cow as well as to serve as predictive markers for diseases. In addition to the milk composition measures (e.g. fat, protein, lactose) traditiona...