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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Different genomic relationship matrices for single-step analysis using phenotypic, pedigree and genomic information
TL;DR: Parameter estimates may be biased if the genomic relationship coefficients are in a different scale than pedigree-based coefficients, and a reasonable scaling may be obtained by using observed allele frequencies and re-scaling the genomes to obtain average diagonal elements of 1.
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Priors in Whole-Genome Regression: The Bayesian Alphabet Returns
TL;DR: It is concluded that members of the alphabet have a room in whole-genome prediction of phenotypes, but have somewhat doubtful inferential value, at least when sample size is such that n ≪ p.
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Genomic selection in forest tree breeding
Dario Grattapaglia,Dario Grattapaglia,Marcos Deon Vilela de Resende,Marcos Deon Vilela de Resende +3 more
TL;DR: The cautiously optimistic outlook is that GS has great potential to accelerate tree breeding, however, further simulation studies and proof-of-concept experiments of GS are needed before recommending it for operational implementation.
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Genomic prediction in CIMMYT maize and wheat breeding programs
José Crossa,Paulino Pérez,John M. Hickey,John M. Hickey,Juan Burgueño,Leonardo Ornella,J. Jesus Céron-Rojas,Xuecai Zhang,Susanne Dreisigacker,Raman Babu,Yongle Li,David Bonnett,Ky L. Mathews +12 more
TL;DR: Results show that pedigree (population structure) accounts for a sizeable proportion of the prediction accuracy when a global population is the prediction problem to be assessed, but when the prediction uses unrelated populations to train the prediction equations, prediction accuracy becomes negligible.
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Reconciling the analysis of IBD and IBS in complex trait studies
TL;DR: It is argued that the purpose of most IBD calculations is to predict IBS at unobserved loci, which leads to better methods to estimating IBD with benefits in mapping genes, estimating genetic variance and predicting inbreeding depression.
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.