Efficient Methods to Compute Genomic Predictions
TLDR
Efficient methods for processing genomic data were developed to increase reliability of estimated breeding values and to estimate thousands of marker effects simultaneously, and a blend of first- and second-order Jacobi iteration using 2 separate relaxation factors converged well for allele frequencies and effects.About:
This article is published in Journal of Dairy Science.The article was published on 2008-11-01 and is currently open access. It has received 4196 citations till now. The article focuses on the topics: Best linear unbiased prediction & Allele frequency.read more
Citations
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Journal ArticleDOI
A Genomic Bayesian Multi-trait and Multi-environment Model
Osval A. Montesinos-López,Abelardo Montesinos-López,José Crossa,Fernando H. Toledo,Oscar Pérez-Hernández,Kent M. Eskridge,Jessica Rutkoski +6 more
TL;DR: A Bayesian model for analyzing multiple traits and multiple environments for whole-genome prediction (WGP) model with unstructured variance–covariance structures is proposed and it is found that when the correlation between traits was high (>0.5), the proposed model improved prediction accuracy compared to the model with diagonal and standard variance-covarance structures.
Journal ArticleDOI
Estimation of Genetic Correlation via Linkage Disequilibrium Score Regression and Genomic Restricted Maximum Likelihood
TL;DR: It is suggested that any interesting findings from massive LDSC analysis for a large number of complex traits should be followed up, where possible, with more detailed analyses with GREML methods, even if sample sizes are lesser.
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Genome scan for meat quality traits in Nelore beef cattle.
Polyana C. Tizioto,Jared E. Decker,Jeremy F. Taylor,Robert D. Schnabel,Maurício A. Mudadu,Fabiane de Lima Silva,Gerson Barreto Mourão,Luiz Lehmann Coutinho,P. Tholon,Tad S. Sonstegard,A. N. Rosa,Maurício Mello de Alencar,Rymer Ramiz Tullio,Sérgio Raposo de Medeiros,Renata Tieko Nassu,G. L. D. Feijo,Luiz Otávio Campos da Silva,R.A.A. Torres,F. Siqueira,R. H. Higa,Luciana Correia de Almeida Regitano +20 more
TL;DR: Meat quality traits in Nelore are controlled by numerous QTL of small effect, except for a small number of large-effect QTL identified for a*fat, CL, and pH, which appear to differ from those identified in taurine cattle for meat quality traits.
Journal ArticleDOI
Preliminary investigation on reliability of genomic estimated breeding values in the Danish Holstein population
TL;DR: The results indicate that genomic selection can greatly improve the accuracy of preselection for young bulls compared with traditional selection based on parent average information.
Journal ArticleDOI
Estimation of SNP Heritability from Dense Genotype Data
S. Hong Lee,Jian Yang,Guo-Bo Chen,Stephan Ripke,Stephan Ripke,Eli A. Stahl,Christina M. Hultman,Pamela Sklar,Peter M. Visscher,Patrick F. Sullivan,Michael E. Goddard,Michael E. Goddard,Naomi R. Wray +12 more
TL;DR: The URLs for data presented herein are as follows: GCTA, http://www.complextraitgenomics.com/software/gcta/LDAK, http-www.ldak.org.
References
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Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps
TL;DR: It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants, especially if combined with reproductive techniques to shorten the generation interval.
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Coefficients of Inbreeding and Relationship
TL;DR: The importance of having a coefficient by means of which the degree of inbreeding may be expressed has been brought out by Pearl' in a number of papers published between 1913 and 1917.
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Strategy for applying genome-wide selection in dairy cattle.
TL;DR: Genome-wide selection may become a popular tool for genetic improvement in livestock after a strategy that utilizes these advantages was compared with a traditional progeny testing strategy under a typical Canadian-like dairy cattle situation.
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Derivation, calculation, and use of national animal model information.
Paul M. VanRaden,G.R. Wiggans +1 more
TL;DR: New terms and definitions were developed to explain national USDA genetic evaluations computed by an animal model, whereiability is the squared correlation of predicted and true transmitting ability.
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Accuracy of Genomic Selection Using Different Methods to Define Haplotypes
TL;DR: It was concluded that genomic selection is considerably more accurate than traditional selection, especially for a low-heritability trait.