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Since the pig is one of the most important livestock animals worldwide, mapping loci that are associated with economically important traits and/or traits that influence animal welfare is extremely relevant for...
The major obstacles for the implementation of genomic selection in Australian beef cattle are the variety of breeds and in general, small numbers of genotyped and phenotyped individuals per breed. The Australi...
No abstract
The original article was published in Genetics Selection Evolution 2014 46:30
No abstract
The original article was published in Genetics Selection Evolution 2013 45:32
The one-step blending approach has been suggested for genomic prediction in dairy cattle. The core of this approach is to incorporate pedigree and phenotypic information of non-genotyped animals. The objective...
Genotype imputation from low-density (LD) to high-density single nucleotide polymorphism (SNP) chips is an important step before applying genomic selection, since denser chips tend to provide more reliable gen...
Genomic prediction is based on the accurate estimation of the genomic relationships among and between training animals and selection candidates in order to obtain accurate estimates of the genomic estimated br...
A cost-effective strategy to increase the density of available markers within a population is to sequence a small proportion of the population and impute whole-genome sequence data for the remaining population...
The prediction accuracy of several linear genomic prediction models, which have previously been used for within-line genomic prediction, was evaluated for multi-line genomic prediction.
A condition to predict unbiased estimated breeding values by best linear unbiased prediction is to use simultaneously all available data. However, this condition is not often fully met. For example, in dairy c...
The accuracy of genomic prediction depends largely on the number of animals with phenotypes and genotypes. In some industries, such as sheep and beef cattle, data are often available from a mixture of breeds, ...
Seven donkey breeds are recognized by the French studbook. Individuals from the Pyrenean, Provence, Berry Black, Normand, Cotentin and Bourbonnais breeds are characterized by a short coat, while those from the...
Genomic prediction requires estimation of variances of effects of single nucleotide polymorphisms (SNPs), which is computationally demanding, and uses these variances for prediction. We have developed models w...
To obtain predictions that are not biased by selection, the conditional mean of the breeding values must be computed given the data that were used for selection. When single nucleotide polymorphism (SNP) effec...
Efficient methodologies based on animal models are widely used to estimate breeding values in farm animals. These methods are not applicable in honey bees because of their mode of reproduction. Observations ar...
While much attention has focused on the development of high-density single nucleotide polymorphism (SNP) assays, the costs of developing and running low-density assays have fallen dramatically. This makes it f...
Genotyping accounts for a substantial part of the cost of genomic selection (GS). Using both dense and sparse SNP chips, together with imputation of missing genotypes, can reduce these costs. The aim of this s...
The major prolificacy gene FecL was first described in the Lacaune sheep meat breed Ovi-Test in 1998. A few studies estimated the effect of this gene on prolificacy but little data is available. In 2010, the Ovi-...
With the advent of genomic selection, alternative relationship matrices are used in animal breeding, which vary in their coverage of distant relationships due to old common ancestors. Relationships based on pe...
Although the X chromosome is the second largest bovine chromosome, markers on the X chromosome are not used for genomic prediction in some countries and populations. In this study, we presented a method for co...
The use of whole-genome sequence data can lead to higher accuracy in genome-wide association studies and genomic predictions. However, to benefit from whole-genome sequence data, a large dataset of sequenced i...
Numerous methods have been developed over the last decade to predict allelic identity at unobserved loci between pairs of chromosome segments along the genome. These loci are often unobserved positions tested ...
Antimicrobial peptides (AMP) are important elements of the first line of defence against pathogens in animals. NK-lysin is a cationic AMP that plays a critical role in innate immunity. The chicken NK-lysin gene h...
The absence of horns, called polled phenotype, is the favored trait in modern cattle husbandry. To date, polled cattle are obtained primarily by dehorning calves. Dehorning is a practice that raises animal wel...
Experience from progeny-testing indicates that the mating of popular bull sires that have high estimated breeding values with excellent dams does not guarantee the production of offspring with superior breedin...
Estimates of dominance variance in dairy cattle based on pedigree data vary considerably across traits and amount to up to 50% of the total genetic variance for conformation traits and up to 43% for milk produ...
Social interactions often occur among living organisms, including aquatic animals. There is empirical evidence showing that social interactions may genetically affect phenotypes of individuals and their group ...
“Foie gras” is produced predominantly in France and about 90% of the commercialized product is obtained from male mule ducks. The melting rate (percentage of fat released during cooking) is the main criterion ...
Accuracy of genomic prediction depends on number of records in the training population, heritability, effective population size, genetic architecture, and relatedness of training and validation populations. Ma...
Genomic selection estimates genetic merit based on dense SNP (single nucleotide polymorphism) genotypes and phenotypes. This requires that SNPs explain a large fraction of the genetic variance. The objectives ...
To better understand the genetic determination of udder health, we performed a genome-wide association study (GWAS) on a population of 2354 German Holstein bulls for which daughter yield deviations (DYD) for s...
Recombination events tend to occur in hotspots and vary in number among individuals. The presence of recombination influences the accuracy of haplotype phasing and the imputation of missing genotypes. Genes th...
Feather pecking is a major welfare issue in laying hen industry that leads to mortality. Due to a ban on conventional cages in the EU and on beak trimming in some countries of the EU, feather pecking will beco...
Determining an animal’s genetic merit using genomic information can improve estimated breeding value (EBV) accuracy; however, the magnitude of the accuracy improvement must be large enough to recover the costs...
The present availability of sequence data gives new opportunities to narrow down from QTL (quantitative trait locus) regions to causative mutations. Our objective was to decrease the number of candidate causat...
Since the recommendations on group housing of mink (Neovison vison) were adopted by the Council of Europe in 1999, it has become common in mink production in Europe. Group housing is advantageous from a productio...
The Erratum to this article has been published in Genetics Selection Evolution 2014 46:70
The maintenance of lactation in mammals is the result of a balance between competing signals from mammary development, prolactin signalling and involution pathways. Dairy cattle are an interesting case study t...
Fat content and fatty acid composition in swine are becoming increasingly studied because of their effect on sensory and nutritional quality of meat. A QTL (quantitative trait locus) for fatty acid composition...
The original article was published in Genetics Selection Evolution 2014 46:7
The original article was published in Genetics Selection Evolution 2012 44:37
Iran is an area of particular interest for investigating goat diversity. Archaeological remains indicate early goat domestication (about 10 000 years ago) in the Iranian Zagros Mountains as well as in the high...
The molecular mechanisms that underlie sex determination and differentiation are conserved and diversified. In fish species, temperature-dependent sex determination and differentiation seem to be ubiquitous an...
Improving digestive efficiency is a major goal in poultry production, to reduce production costs, make possible the use of alternative feedstuffs and decrease the volume of manure produced. Since measuring dig...
Since both the number of SNPs (single nucleotide polymorphisms) used in genomic prediction and the number of individuals used in training datasets are rapidly increasing, there is an increasing need to improve...
For a two-breed crossbreeding system, Wei and van der Werf presented a model for genetic evaluation using information from both purebred and crossbred animals. The model provides breeding values for both pureb...
The extent of linkage disequilibrium (LD) between molecular markers impacts genome-wide association studies and implementation of genomic selection. The availability of high-density single nucleotide polymorph...
Signatures of selection are regions in the genome that have been preferentially increased in frequency and fixed in a population because of their functional importance in specific processes. These regions can ...
Host genetics has been shown to play a role in porcine reproductive and respiratory syndrome (PRRS), which is the most economically important disease in the swine industry. A region on Sus scrofa chromosome (SSC)...
Nellore cattle play an important role in beef production in tropical systems and there is great interest in determining if genomic selection can contribute to accelerate genetic improvement of production and f...
Identifying the relevant environmental variables that cause GxE interaction is often difficult when they cannot be experimentally manipulated. Two statistical approaches can be applied to address this question...
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Genetics Selection Evolution