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
Insights into the Maize Pan-Genome and Pan-Transcriptome
Candice N. Hirsch,Candice N. Hirsch,Jillian M. Foerster,James M. Johnson,Rajandeep S. Sekhon,Rajandeep S. Sekhon,German Muttoni,Brieanne Vaillancourt,Brieanne Vaillancourt,Francisco Peñagaricano,Erika Lindquist,Mary Ann Pedraza,Kerrie Barry,Natalia de Leon,Natalia de Leon,Shawn M. Kaeppler,Shawn M. Kaeppler,C. Robin Buell,C. Robin Buell +18 more
TL;DR: The dynamic nature of the maize pan-genome was revealed and it was demonstrated that a substantial portion of variation may lie outside the single reference genome for a species.
Journal ArticleDOI
Contrasting genetic architectures of schizophrenia and other complex diseases using fast variance-components analysis
Po-Ru Loh,Po-Ru Loh,Gaurav Bhatia,Gaurav Bhatia,Alexander Gusev,Alexander Gusev,Hilary K. Finucane,Brendan Bulik-Sullivan,Brendan Bulik-Sullivan,Samuela Pollack,Samuela Pollack,Teresa R de Candia,Sang Hong Lee,Sang Hong Lee,Naomi R. Wray,Kenneth S. Kendler,Michael Conlon O'Donovan,Benjamin M. Neale,Benjamin M. Neale,Nick Patterson,Alkes L. Price,Alkes L. Price +21 more
TL;DR: A fast algorithm for multicomponent, multi-trait variance-components analysis that overcomes prior computational barriers that made such analyses intractable at this scale is developed.
Journal ArticleDOI
Accuracy of genomic breeding values in multi-breed dairy cattle populations
TL;DR: Predicting genomic breeding values using a genomic relationship matrix is an attractive approach to implement genomic selection as expected accuracies of GEBV can be readily derived, however in multi-breed populations, Bayesian approaches give higher accuracies for some traits.
Journal ArticleDOI
Additive Genetic Variability and the Bayesian Alphabet
Daniel Gianola,Daniel Gianola,Daniel Gianola,Gustavo de los Campos,William G. Hill,Eduardo Manfredi,Rohan L. Fernando +6 more
TL;DR: The use of all available molecular markers in statistical models for prediction of quantitative traits has led to what could be termed a genomic-assisted selection paradigm in animal and plant breeding.
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The impact of genetic relationship information on genomic breeding values in German Holstein cattle
TL;DR: GEBV accuracy of current selection candidates varies due to different additive-genetic relationships relative to the training data, and accuracy of future candidates can be lower than reported in previous studies because information from close relatives will not be available when selection on GEBVs is applied.
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.