20 Result(s)
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Open AccessIntegration of beef cattle international pedigree and genomic estimated breeding values into national evaluations, with an application to the Italian Limousin population
International evaluations combine data from different countries allowing breeders to have access to larger panels of elite bulls and to increase the accuracy of estimated breeding values (EBV). However, intern...
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Open AccessEfficient large-scale single-step evaluations and indirect genomic prediction of genotyped selection candidates
Single-step genomic best linear unbiased prediction (ssGBLUP) models allow the combination of genomic, pedigree, and phenotypic data into a single model, which is computationally challenging for large genotype...
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Open AccessValidation with single-step SNPBLUP shows that evaluations can continue using a single mean of genotyped individuals, even with multiple breeds
In genomic prediction, it is common to centre the genotypes of single nucleotide polymorphisms based on the allele frequencies in the current population, rather than those in the base generation. The mean bree...
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Open AccessInternational single-step SNPBLUP beef cattle evaluations for Limousin weaning weight
Compared to national evaluations, international collaboration projects further improve accuracies of estimated breeding values (EBV) by building larger reference populations or performing a joint evaluation us...
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Open AccessImpact of genomic preselection on subsequent genetic evaluations with ssGBLUP using real data from pigs
Empirically assessing the impact of preselection on genetic evaluation of preselected animals requires comparing scenarios that take different approaches into account, including scenarios without preselection....
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Open AccessEstimation of dam line composition of 3-way crossbred animals using genomic information
In genomic prediction including data of 3- or 4-way crossbred animals, line composition is usually fitted as a regression on expected line proportions, which are 0.5, 0.25 and 0.25, respectively, for 3-way cro...
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Open AccessConvergence behavior of single-step GBLUP and SNPBLUP for different termination criteria
The preconditioned conjugate gradient (PCG) method is the current method of choice for iterative solving of genetic evaluations. The relative difference between two successive iterates and the relative residua...
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Open AccessInvestigating the impact of preselection on subsequent single-step genomic BLUP evaluation of preselected animals
Preselection of candidates, hereafter referred to as preselection, is a common practice in breeding programs. Preselection can cause bias and accuracy loss in subsequent pedigree-based best linear unbiased pre...
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Article
Open AccessImpact of sub-setting the data of the main Limousin beef cattle population on the estimates of across-country genetic correlations
Cattle international genetic evaluations allow the comparison of estimated breeding values (EBV) across different environments, i.e. countries. For international evaluations, across-country genetic correlations (
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Article
Open AccessComputational strategies for the preconditioned conjugate gradient method applied to ssSNPBLUP, with an application to a multivariate maternal model
The single-step single nucleotide polymorphism best linear unbiased prediction (ssSNPBLUP) is one of the single-step evaluations that enable a simultaneous analysis of phenotypic and pedigree information of ge...
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Article
Open AccessA second-level diagonal preconditioner for single-step SNPBLUP
The preconditioned conjugate gradient (PCG) method is an iterative solver of linear equations systems commonly used in animal breeding. However, the PCG method has been shown to encounter convergence issues wh...
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Article
Open AccessImputation to whole-genome sequence using multiple pig populations and its use in genome-wide association studies
Use of whole-genome sequence data (WGS) is expected to improve identification of quantitative trait loci (QTL). However, this requires imputation to WGS, often with a limited number of sequenced animals for th...
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Article
Open AccessDeflated preconditioned conjugate gradient method for solving single-step BLUP models efficiently
The single-step single nucleotide polymorphism best linear unbiased prediction (ssSNPBLUP) method, such as single-step genomic BLUP (ssGBLUP), simultaneously analyses phenotypic, pedigree, and genomic informat...
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Open AccessSNPrune: an efficient algorithm to prune large SNP array and sequence datasets based on high linkage disequilibrium
High levels of pairwise linkage disequilibrium (LD) in single nucleotide polymorphism (SNP) array or whole-genome sequence data may affect both performance and efficiency of genomic prediction models. Thus, th...
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Article
Open AccessCorrection to: Genomic evaluation for a three-way crossbreeding system considering breed-of-origin of alleles
After publication of our article [1], we found a typo in the formula to build the genomic relationship matrix using allele frequencies across all genotyped pigs (matrix) and the genomic relationship matrix usi...
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Open AccessGenomic evaluation for a three-way crossbreeding system considering breed-of-origin of alleles
Genomic prediction of purebred animals for crossbred performance can be based on a model that estimates effects of single nucleotide polymorphisms (SNPs) in purebreds on crossbred performance. For crossbred pe...
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Open AccessPrediction of the reliability of genomic breeding values for crossbred performance
In crossbreeding programs, various genomic prediction models have been proposed for using phenotypic records of crossbred animals to increase the selection response for crossbred performance in purebred animal...
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Open AccessAssigning breed origin to alleles in crossbred animals
For some species, animal production systems are based on the use of crossbreeding to take advantage of the increased performance of crossbred compared to purebred animals. Effects of single nucleotide polymorp...
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Open AccessEmpirical determination of breed-of-origin of alleles in three-breed cross pigs
Although breeding programs for pigs and poultry aim at improving crossbred performance, they mainly use training populations that consist of purebred animals. For some traits, e.g. residual feed intake, the ge...
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Open AccessUnified method to integrate and blend several, potentially related, sources of information for genetic evaluation
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...
