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
Phenotypic and genetic associations of milk traits with milk coagulation properties.
TL;DR: Examination of milk composition and rennet-induced coagulation properties of milk from 892 individual Danish Holstein and Danish Jersey cows and determine the genetic influences on these properties by determining heritability and genomic correlations with single nucleotide polymorphisms identified by the bovine HD Beadchip suggest that potential for changing MCP through breeding exists, but the genetic background of the MCP traits might be different in different breeds.
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Comparing genomic prediction accuracy from purebred, crossbred and combined purebred and crossbred reference populations in sheep
Nasir Moghaddar,Nasir Moghaddar,Andrew Swan,Andrew Swan,Julius H. J. van der Werf,Julius H. J. van der Werf +5 more
TL;DR: This study demonstrates that crossbred animals can be used for genomic prediction of purebred animals using 50 k SNP marker density and GBLUP, but crossbred data provided lower accuracy than purebred data.
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Characterization and genome-wide association mapping of resistance to leaf rust, stem rust and stripe rust in a geographically diverse collection of spring wheat landraces
Peace Kankwatsa,Davinder Singh,Peter C. Thomson,Ebrahiem M. Babiker,J. M. Bonman,Maria Newcomb,Robert F. Park +6 more
TL;DR: The presence of a range of possibly unidentified effective seedling and APRs among the landraces is revealed, which might represent new sources of rust resistance for the ongoing effort to develop improved wheat cultivars.
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Impact of reference population on accuracy of imputation from 6K to 50K single nucleotide polymorphism chips in purebred and crossbreed beef cattle.
Ricardo Vieira Ventura,Duc Lu,Flavio S Schenkel,Zhiqiang Wang,Changxi Li,Changxi Li,Stephen P. Miller,Stephen P. Miller +7 more
TL;DR: In this paper, population imputation, using linkage dis- equilibrium among markers, was implemented using the software BEAGLE, FIMPUTE 2.2, and IMPUTE2 in a multibreed, crossbred taurine beef cattle popula- tion genotyped with the Illumina SNP50.
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Predictive ability of genome-assisted statistical models under various forms of gene action
Mehdi Momen,Ahmad Ayatollahi Mehrgardi,Ayyub Sheikhi,Andreas Kranis,Llibertat Tusell,Gota Morota,Guilherme J. M. Rosa,Daniel Gianola +7 more
TL;DR: The results corroborate the view that there is no universally best prediction models, and that the development of robust prediction models is an important research objective, and suggest that prediction models must be selected according to the most probably underlying architecture of traits.
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.