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AlphaImpute is a flexible and accurate genotype imputation tool that was originally designed for the imputation of genotypes on autosomal chromosomes. In some species, sex chromosomes comprise a large portion ...
GC content varies greatly between different genomic regions in many eukaryotes. In order to determine whether this organization named isochore organization influences gene expression patterns, the relationship...
Outbreaks of infectious pancreatic necrosis (IPN) in Atlantic salmon can result in reduced growth rates in a fraction of the surviving fish (runts). Genetic and environmental variation also affects growth rate...
In China, the reference population of genotyped Holstein cattle is relatively small with to date, 80 bulls and 2091 cows genotyped with the Illumina 54 K chip. Including genotyped Holstein cattle from other co...
One method to improve durably animal welfare is to select, as reproducers, animals with the highest ability to resist or tolerate infection. To do so, it is necessary to distinguish direct and indirect mechani...
Genomic prediction uses two sources of information: linkage disequilibrium between markers and quantitative trait loci, and additive genetic relationships between individuals. One way to increase the accuracy ...
The original article was published in Genetics Selection Evolution 2012 44:21
Currently, genome-wide evaluation of cattle populations is based on SNP-genotyping using ~ 54 000 SNP. Increasing the number of markers might improve genomic predictions and power of genome-wide association st...
Several molecular and population genetic studies have focused on the native sheep breeds of Finland. In this work, we investigated their ancestral sheep populations from Iron Age, Medieval and Post-Medieval pe...
Effective population sizes of 140 populations (including 60 dog breeds, 40 sheep breeds, 20 cattle breeds and 20 horse breeds) were computed using pedigree information and six different computation methods. Si...
Today, genomic evaluations are an essential feature of dairy cattle breeding. Initially, genomic evaluation targeted young bulls but recently, a rapidly increasing number of females (both heifers and cows) are...
Using a multi-breed reference population might be a way of increasing the accuracy of genomic breeding values in small breeds. Models involving mixed-breed data do not take into account the fact that marker ef...
In national evaluations, direct genomic breeding values can be considered as correlated traits to those for which phenotypes are available for traditional estimation of breeding values. For this purpose, estim...
Single-step methods provide a coherent and conceptually simple approach to incorporate genomic information into genetic evaluations. An issue with single-step methods is compatibility between the marker-based ...
The Erratum to this article has been published in Genetics Selection Evolution 2014 46:20
In studies on parentage assignment with both parents unknown, the exclusion power of a marker set is generally computed under the hypothesis that the potential families tested are independent and unrelated sam...
Genotype by environment interactions are currently ignored in national genetic evaluations of dairy cattle. However, this is often questioned, especially when environment or herd management is wide-ranging. Th...
In recent decades, local varieties of domesticated animal species have been frequently crossed with economically superior breeds which has resulted in considerable genetic contributions from migrants. Optimum ...
Genomic predictions can be applied early in life without impacting selection candidates. This is especially useful for meat quality traits in sheep. Carcass and novel meat quality traits were predicted in a mu...
Spurious associations between single nucleotide polymorphisms and phenotypes are a major issue in genome-wide association studies and have led to underestimation of type 1 error rate and overestimation of the ...
Insect bite hypersensitivity is a common allergic disease in horse populations worldwide. Insect bite hypersensitivity is affected by both environmental and genetic factors. However, little is known about gene...
Simulation studies have shown that accuracy and genetic gain are increased in genomic selection schemes compared to traditional aquaculture sib-based schemes. In genomic selection, accuracy of selection can be...
Most Bayesian models for the analysis of complex traits are not analytically tractable and inferences are based on computationally intensive techniques. This is true of Bayesian models for genome-enabled selec...
It is commonly assumed that prediction of genome-wide breeding values in genomic selection is achieved by capitalizing on linkage disequilibrium between markers and QTL but also on genetic relationships. Here,...
In the past, pedigree relationships were used to control and monitor inbreeding because genomic relationships among selection candidates were not available until recently. The aim of this study was to understa...
Over the last ten years, genomic selection has developed enormously. Simulations and results on real data suggest that breeding values can be predicted with high accuracy using genetic markers alone. However, ...
Commercial breeding programs seek to maximise the rate of genetic gain while minimizing the costs of attaining that gain. Genomic information offers great potential to increase rates of genetic gain but it is ...
Milkability, primarily evaluated by measurements of milking speed and time, has an economic impact in milk production of dairy cattle. Recently the Italian Brown Swiss Breeders Association has included milking...
The focus in dairy cattle breeding is gradually shifting from production to functional traits and genetic parameters of calving traits are estimated more frequently. However, across countries, various statisti...
Infectious bovine keratoconjunctivitis (IBK) or ‘pinkeye’ is an economically important ocular disease that significantly impacts animal performance. Genetic parameters for IBK infection and its genetic and phe...
In spite of past controversies, the field of ancient DNA is now a reliable research area due to recent methodological improvements. A series of recent large-scale studies have revealed the true potential of an...
The Erratum to this article has been published in Genetics Selection Evolution 2013 45:4
A single-step blending approach allows genomic prediction using information of genotyped and non-genotyped animals simultaneously. However, the combined relationship matrix in a single-step method may need to ...
Over the past years, reports have indicated that honey bee populations are declining and that infestation by an ecto-parasitic mite (Varroa destructor) is one of the main causes. Selective breeding of resistant b...
Efficient, robust, and accurate genotype imputation algorithms make large-scale application of genomic selection cost effective. An algorithm that imputes alleles or allele probabilities for all animals in the...
Two atherosclerosis-susceptible and -resistant Japanese quail (Coturnix japonica) strains obtained by divergent selection are commonly used as models to study atherosclerosis, but no genetic characterization of t...
Many studies have provided evidence of the existence of genetic heterogeneity of environmental variance, suggesting that it could be exploited to improve robustness and uniformity of livestock by selection. Ho...
Multi-trait genomic models in a Bayesian context can be used to estimate genomic (co)variances, either for a complete genome or for genomic regions (e.g. per chromosome) for the purpose of multi-trait genomic ...
Cryopreservation of three endangered Belgian sheep breeds required to characterize their intra-breed genetic diversity. It is assumed that the genetic structure of a livestock breed depends mostly on gene flow...
In classical pedigree-based analysis, additive genetic variance is estimated from between-family variation, which requires the existence of larger phenotyped and pedigreed populations involving numerous famili...
In fish, the most studied production traits in terms of heritability are body weight or growth, stress or disease resistance, while heritability of cortisol levels, widely used as a measure of response to stre...
Independent studies have shown that several single nucleotide polymorphisms (SNP) in the human FTO (fat mass and obesity associated) gene are associated with obesity. SNP have also been identified in the pig FTO ...
Studies to detect associations between DNA markers and traits of interest in humans and livestock benefit from increasing the number of individuals genotyped. Performing association studies on pooled DNA sampl...
The risk of long-term unequal contribution of mating pairs to the gene pool is that deleterious recessive genes can be expressed. Such consequences could be alleviated by appropriately designing and optimizing...
Many methods for the genetic analysis of mastitis use a cross-sectional approach, which omits information on, e.g., repeated mastitis cases during lactation, somatic cell count fluctuations, and recovery proce...
A newly recognized type of genetic variation, Copy Number Variation (CNV), is detected in mammalian genomes, e.g. the cattle genome. This form of variation can potentially cause phenotypic variation. Our objec...
Ear size and shape are distinct conformation characteristics of pig breeds. Previously, we identified a significant quantitative trait locus (QTL) influencing ear surface on pig chromosome 5 in a White Duroc ×...
At present the Croatian Turopolje pig population comprises about 157 breeding animals. In Austria, 324 Turopolje pigs originating from six Croatian founder animals are registered. Multiple bottlenecks have occ...
The theory of genomic selection is based on the prediction of the effects of genetic markers in linkage disequilibrium with quantitative trait loci. However, genomic selection also relies on relationships betw...
Genomic selection has become an important tool in the genetic improvement of animals and plants. The objective of this study was to investigate the impacts of breeding value estimation method, reference popula...
Residual feed intake (RFI) and feed conversion ratio (FCR) can be incorporated into a breeding program as traits to select for feed efficiency. Alternatively, the direct measures used to calculate RFI and FCR ...
The prediction of the outcomes from multistage breeding schemes is especially important for the introduction of genomic selection in dairy cattle. Decorrelated selection indices can be used for the optimisatio...
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Genetics Selection Evolution