A5032535221- Genetic and phenotypic traits in livestock
- Genetic Mapping and Diversity in Plants and Animals
- Cancer-related molecular mechanisms research
- Genetics and Plant Breeding
- Animal Behavior and Welfare Studies
- Milk Quality and Mastitis in Dairy Cows
- Reproductive Physiology in Livestock
- Animal Genetics and Reproduction
- Gene expression and cancer classification
- Animal Nutrition and Physiology
- Effects of Environmental Stressors on Livestock
- Genomics and Phylogenetic Studies
- Molecular Biology Techniques and Applications
- Wheat and Barley Genetics and Pathology
- Ruminant Nutrition and Digestive Physiology
- Livestock Farming and Management
- Genetic Associations and Epidemiology
- Animal Disease Management and Epidemiology
- Agricultural Economics and Policy
- Bioinformatics and Genomic Networks
- RNA and protein synthesis mechanisms
- Genetic diversity and population structure
- Agriculture Sustainability and Environmental Impact
- Meat and Animal Product Quality
- Economics of Agriculture and Food Markets
Aarhus University
2016-2025
Genomics (United Kingdom)
2015-2020
Norwegian Institute of Bioeconomy Research
2016-2019
Institut thématique Génétique, génomique et bioinformatique
2000-2018
Génétique Animale et Biologie Intégrative
2018
Université Paris-Saclay
2018
University of Copenhagen
2007-2011
Danish Cattle Research Centre
1999-2009
Epilepsy Society
2009
Danish Ministry of Food, Agriculture and Fisheries
2004
The use of genomic selection in breeding programs may increase the rate genetic improvement, reduce generation time, and provide higher accuracy estimated values (EBVs). A number different methods have been developed for prediction values, but many them assume that all animals genotyped. In practice, not are genotyped, to be adapted this situation.In paper we an extension a linear mixed model method situation with non-genotyped animals. specifies value is sum polygenic random effect, where...
Non-additive genetic variation is usually ignored when genome-wide markers are used to study the architecture and genomic prediction of complex traits in human, wild life, model organisms or farm animals. However, non-additive effects may have an important contribution total traits. This presented a BLUP including additive effects, which relation matrices were constructed from information dense single nucleotide polymorphism (SNP) markers. In addition, this for first time proposed method...
Size of the reference population and reliability phenotypes are crucial factors influencing genomic predictions. It is therefore useful to combine closely related populations. Increased accuracies predictions depend on number individuals added population, their phenotypes, relatedness populations that combined. This paper assesses increase in achieved when combining four Holstein 4000 bulls each, from European breeding organizations, i.e. UNCEIA (France), VikingGenetics (Denmark, Sweden,...
Recent developments in sequencing technology have facilitated widespread investigations of genomic variants, including continuous stretches homozygous regions. For cattle, a large proportion these runs homozygosity (ROH) are likely the result inbreeding due to accumulation elite alleles from long-term selective breeding programs. In present study, ROH were characterized four cattle breeds with whole genome sequence data and distribution predicted functional variants was detected regions...
The functional annotation of livestock genomes is crucial for understanding the molecular mechanisms that underpin complex traits economic importance, adaptive evolution and comparative genomics. Here, we provide most comprehensive catalogue to date regulatory elements in pig (Sus scrofa) by integrating 223 epigenomic transcriptomic data sets, representing 14 biologically important tissues. We systematically describe dynamic epigenetic landscape across tissues functionally annotating 15...
Abstract The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been established to develop a public resource of genetic regulatory variants in livestock, which is essential for linking polymorphisms variation phenotypes, helping fundamental biological discovery and exploitation animal breeding human biomedicine. Here we show results from the pilot phase PigGTEx by processing 5,457 RNA-sequencing 1,602 whole-genome sequencing samples passing quality control pigs. We build pig...
Selection for total number of piglets born (TNB) since 1992 has led to a significant increase in this trait Danish Landrace and Yorkshire but also been accompanied by an piglet mortality. The objective study was estimate the genetic phenotypic parameters litter size survival find alternative selection criteria improve at weaning. Data from (9,300 litters) (6,861 were analyzed using REML based on linear model including effects sow service-sire. estimates heritability (based component) TNB,...
In dairy cattle, the widespread use of artificial insemination has resulted in increased selection intensity, which led to spectacular increase productivity. However, cow fertility concomitantly severely declined. It is generally assumed that this reduction primarily due negative energy balance high-producing cows at peak lactation. We herein describe fine-mapping a major QTL Nordic Red and identify 660-kb deletion encompassing four genes as causative variant. show recessive embryonically...
Abstract Background A single-step blending approach allows genomic prediction using information of genotyped and non-genotyped animals simultaneously. However, the combined relationship matrix in a method may need to be adjusted because marker-based pedigree-based matrices not on same scale. The apply when GBLUP model includes both breeding values residual polygenic effects. objective this study was compare methods with without adjustment for 16 traits Nordic Holstein population. Methods...
<h2>Abstract</h2> This study investigated genomic prediction using medium-density (∼54,000; 54K) and high-density marker panels (∼777,000; 777K), based on data from Nordic Holstein Red Dairy Cattle (RDC). The comprised 4,539 progeny-tested bulls, the RDC 4,403 bulls. were divided into reference test October 1, 2001, as a cut-off date (birth of bulls). resulted in about 25% genotyped bulls 20% data. For each breed, 3 sets markers used to predict breeding values: (1) 54K set with missing...
This study investigated the reliability of genomic estimated breeding values (GEBV) in Danish Holstein population. The data analysis included 3,330 bulls with both published conventional EBV and single nucleotide polymorphism (SNP) markers. After editing, 38,134 SNP markers were available. In analysis, all fitted simultaneously as random effects a Bayesian variable selection model, which allows heterogeneous variances for different response variables official EBV. Direct GEBV calculated sum...
Many genome variants shaping mammalian phenotype are hypothesized to regulate gene transcription and/or be under selection. However, most of the evidence support this hypothesis comes from human studies. Systematic for regulatory and evolutionary signals contributing complex traits in a different model is needed. Sequence associated with expression (expression quantitative trait loci [eQTLs]) concentration metabolites (metabolic [mQTLs]) histone-modification marks several tissues were...
This study investigated the accuracy of direct genomic breeding values (DGV) using a BLUP model, enhanced (GEBV) one-step blending approach, and GEBV selection index approach for 15 traits Nordic Red Cattle. The data comprised 6,631 bulls which 4,408 were genotyped Illumina Bovine SNP50 BeadChip (Illumina, San Diego, CA). To validate reliability predictions, about 20% youngest taken as test set. Deregressed proofs (DRP) used response variables predictions. Reliabilities predictions in...
Mastitis is a mammary disease that frequently affects dairy cattle. Despite considerable research on the development of effective prevention and treatment strategies, mastitis continues to be significant issue in bovine veterinary medicine. To identify major genes affect cattle, 6 chromosomal regions Bos taurus autosome (BTA) 6, 13, 16, 19, 20 were selected from genome scan for 9 phenotypes using imputed high-density single nucleotide polymorphism arrays. Association analyses sequence-level...
The advent of low cost next generation sequencing has made it possible to sequence a large number dairy and beef bulls which can be used as reference for imputation whole genome data. aim this study was investigate the accuracy speed from high density SNP marker panel level. Data contained 132 Holstein, 42 Jersey, 52 Nordic Red 16 Brown Swiss with data; 27 Jersey 29 Reds had previously been typed bovine were validation. We investigated effect enlarging population by combining data across...
Various models have been used for genomic prediction. Bayesian variable selection often predict more accurate breeding values than BLUP (GBLUP), but GBLUP is generally preferred routine evaluations because of low computational demand. The objective this study was to achieve the benefits both using results from and genome-wide association studies as weights on single nucleotide polymorphism (SNP) markers when constructing matrix (G-matrix) data comprised 5,221 progeny-tested bulls Nordic...
The reaction norm model is becoming a popular approach for the analysis of genotype × environment interactions. In classical model, expression in different environments described as linear function (a norm) an environmental gradient or value. An value typically defined mean performance all genotypes environment, which usually unknown. One approximation to estimate phenotypic each and then treat these estimates known covariates model. However, more satisfactory alternative infer values...
A genome-wide association study was conducted using a mixed model analysis for QTL fertility traits in Danish and Swedish Holstein cattle. The incorporated 2,531 progeny tested bulls, total of 36,387 SNP markers on 29 bovine autosomes were used. Eleven analyzed association. Furthermore, used analyses where polygenic effect fitted as random effect, genotypes at single SNPs successively included fixed the model. Bonferroni correction multiple testing applied to adjust significance threshold....
This study investigated the possibility of increasing reliability direct genomic values (DGV) by combining reference populations. The data were from 3,735 bulls Danish, Swedish, and Finnish Red dairy cattle Single nucleotide polymorphism markers fitted as random variables in a Bayesian model, using published estimated breeding response variables. In total, 17 index traits analyzed. Reliabilities 5-fold cross validation, calculated within-year squared correlation between DGV. Marker effects...
Abstract Background Genome-wide association study (GWAS) is a powerful tool for revealing the genetic basis of quantitative traits. However, studies using GWAS conformation traits cattle comparatively less. This aims to use find candidates genes body Results The Illumina BovineSNP50 BeadChip was used identify single nucleotide polymorphisms (SNPs) that are associated with A least absolute shrinkage and selection operator (LASSO) applied detect multiple SNPs simultaneously 29 1,314 Chinese...
In order to obtain accurate genomic breeding values a large number of reference animals with both phenotype and genotype data are needed. This poses challenge for breeds small populations. One option overcome this obstacle is use multi-breed population. However, combining populations across not straightforward due differences in linkage disequilibrium structure weak relationships between breeds. study offers review the available literature on compiled from different cattle Results show that...
This study investigated the imputation accuracy of different methods, considering both minor allele frequency and relatedness between individuals in reference test data sets. Two sets from combined population Swedish Finnish Red Cattle were used to influence these factors on imputation. Data set 1 consisted 2,931 bulls 971 bulls, was for validation 3,000 markers (3K) 54,000 (54K). 2 contained 341 117 set, 54K high density [777,000 (777K)]. Both divided into 4 groups according their...