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
Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping
Laercio R. Porto-Neto,Laercio R. Porto-Neto,Laercio R. Porto-Neto,Tad S. Sonstegard,George E. Liu,Derek M. Bickhart,Marcos V.B. da Silva,Marco Antonio Machado,Yuri Tani Utsunomiya,José Fernando Garcia,Cedric Gondro,Curtis P. Van Tassell +11 more
TL;DR: Genomic regions that are potentially linked to purifying or balancing selection processes in domestic cattle were identified and are of particular interest to understand the natural and human selective pressures to which these subspecies were exposed to and how the genetic background of these populations evolved in response to environmental challenges and human manipulation.
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Genomic Prediction of Genotype × Environment Interaction Kernel Regression Models
Jaime Cuevas,José Crossa,Víctor Soberanis,Sergio Pérez-Elizalde,Paulino Pérez-Rodríguez,Gustavo de los Campos,Osval A. Montesinos-López,Juan Burgueño +7 more
TL;DR: This study proposes using two nonlinear Gaussian kernels: the reproducing kernel Hilbert space with kernel averaging (RKHS KA) and the Gaussian kernel with the bandwidth estimated through an empirical Bayesian method ( RKHS EB).
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Enhancing Genetic Gain through Genomic Selection: From Livestock to Plants.
Yunbi Xu,Yunbi Xu,Xiaogang Liu,Junjie Fu,Hongwu Wang,Jiankang Wang,Changling Huang,Boddupalli M. Prasanna,Michael Olsen,Guoying Wang,Aimin Zhang +10 more
TL;DR: Large-scale application of genomic selection in plants can be achieved by refining field management to improve heritability estimation and prediction accuracy and developing optimum GS models with the consideration of genotype-by-environment interaction and non-additive effects, along with significant cost reduction.
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Impacts of both reference population size and inclusion of a residual polygenic effect on the accuracy of genomic prediction
TL;DR: Fitting a residual polygenic effect in the model resulted in less biased genome-enhanced breeding values and decreased the correlation between direct genomic values and estimated breeding values of sires in the reference population, finding genetic evaluation of dairy cattle enhanced with genomic information is highly effective in increasing reliability, as well as using large genomic reference populations.
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Genome-wide association study for intramuscular fat deposition and composition in Nellore cattle
Aline Silva Mello Cesar,Luciana Correia de Almeida Regitano,Gerson Barreto Mourão,Rymer Ramiz Tullio,Dante Pazzanese Duarte Lanna,Renata Tieko Nassu,Mauricio A. Mudado,Priscila S. N. de Oliveira,M. L. Nascimento,Amália Saturnino Chaves,Maurício Mello de Alencar,Tad S. Sonstegard,Dorian J. Garrick,James M. Reecy,Luiz Lehmann Coutinho +14 more
TL;DR: The genomic regions and genes identified contribute to a better understanding of the genetic control of fatty acid deposition and can lead to DNA-based selection strategies to improve meat quality for human consumption.
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.