A relationship matrix including full pedigree and genomic information [PDF]
Journal of Dairy Science, 2009 Dense molecular markers are being used in genetic evaluation for parts of the population. This requires a two-step procedure where pseudo-data (for instance, daughter yield deviations) are computed from full records and pedigree data and later used for genomic evaluation. This results in bias and loss of information.
A Legarra, I Aguilar, I Misztal
exaly +9 more sources
Using recursion to compute the inverse of the genomic relationship matrix [PDF]
Journal of Dairy Science, 2014 Computing the inverse of the genomic relationship matrix using recursion was investigated. A traditional algorithm to invert the numerator relationship matrix is based on the observation that the conditional expectation for an additive effect of 1 animal given the effects of all other animals depends on the effects of its sire and dam only, each with a
I Misztal, A Legarra, I Aguilar
exaly +7 more sources
A novel linkage-disequilibrium corrected genomic relationship matrix for SNP-heritability estimation and genomic prediction. [PDF]
Heredity (Edinb), 2018 Single nucleotide polymorphism (SNP)-heritability estimation is an important topic in several research fields, including animal, plant and human genetics, as well as in ecology. Linear mixed model estimation of SNP-heritability uses the structures of genomic relationships between individuals, which is constructed from genome-wide sets of SNP-markers ...
Mathew B, Léon J, Sillanpää MJ.
europepmc +8 more sources
Forensic use of the genomic relationship matrix to validate and discover livestock pedigrees. [PDF]
J Anim Sci, 2019 Correct pedigree is essential to produce accurate genetic evaluations of livestock populations. Pedigree validation has traditionally been undertaken using microsatellites and more recently, based on checks on opposing homozygotes using single nucleotide polymorphisms (SNPs). In this study, the genomic relationship matrix was examined to see whether it
Moore KL +4 more
europepmc +8 more sources
A recursive algorithm for decomposition and creation of the inverse of the genomic relationship matrix [PDF]
Journal of Dairy Science, 2012 Some genomic evaluation models require creation and inversion of a genomic relationship matrix (G). As the number of genotyped animals increases, G becomes larger and thus requires more time for inversion. A single-step genomic evaluation also requires inversion of the part of the pedigree relationship matrix for genotyped animals (A(22)).
N Gengler, I Misztal
exaly +7 more sources
A Weighted Genomic Relationship Matrix Based on Fixation Index (FST) Prioritized SNPs for Genomic Selection. [PDF]
Genes (Basel), 2019 A dramatic increase in the density of marker panels has been expected to increase the accuracy of genomic selection (GS), unfortunately, little to no improvement has been observed. By including all variants in the association model, the dimensionality of the problem should be dramatically increased, and it could undoubtedly reduce the statistical power.
Chang LY +4 more
europepmc +5 more sources
Discovery of hidden pedigree errors combining genomic information with the genomic relationship matrix in Texel sheep [PDF]
Animal, 2022 Genomic variants such as Single Nucleotide Polymorphisms and animal pedigree are now used widely in routine genetic evaluations of livestock in many countries.
K. Kaseja +5 more
doaj +5 more sources
Implication of the order of blending and tuning when computing the genomic relationship matrix in single-step GBLUP. [PDF]
J Anim Breed Genet, 2023 AbstractSingle‐step genomic BLUP (ssGBLUP) relies on the combination of the genomic () and pedigree relationship matrices for all () and genotyped () animals. The procedure ensures and are compatible so that both matrices refer to the same genetic base (‘tuning’).
McWhorter TM +6 more
europepmc +5 more sources
The use of a genomic relationship matrix for breed assignment of cattle breeds: comparison and combination with a machine learning method. [PDF]
J Anim Sci, 2023 Abstract To develop a breed assignment model, three main steps are generally followed: 1) The selection of breed informative single nucleotide polymorphism (SNP); 2) The training of a model, based on a reference population, that allows to classify animals to their breed of origin; and 3) The validation of the developed model on external ...
Wilmot H +4 more
europepmc +5 more sources
Genomic selection for QTL-MAS data using a trait-specific relationship matrix [PDF]
BMC Proceedings, 2011 The genomic estimated breeding values (GEBV) of the young individuals in the XIV QTL-MAS workshop dataset were predicted by three methods: best linear unbiased prediction with a trait-specific marker-derived relationship matrix (TABLUP), ridge regression best linear unbiased prediction (RRBLUP), and BayesB.The TABLUP method is identical to the ...
Zhang, Zhe +4 more
core +4 more sources