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
Genome-Wide Association and Regional Heritability Mapping of Plant Architecture, Lodging and Productivity in Phaseolus vulgaris.
Rafael Tassinari Resende,Marcos Deon Vilela de Resende,Marcos Deon Vilela de Resende,Camila Ferreira Azevedo,Fabyano Fonseca e Silva,Leonardo Cunha Melo,Helton Santos Pereira,Thiago Lívio Pessoa Oliveira de Souza,P. A. M. R. Valdisser,Claudio Brondani,Rosana Pereira Vianello +10 more
TL;DR: RHM in autogamous species had the potential to identify larger-effect QTL combining allelic variants that could be effectively incorporated into whole-genome prediction models and tracked through breeding generations using marker-assisted selection.
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Updating the reference population to achieve constant genomic prediction reliability across generations
TL;DR: The results showed that, approximately, 600 animals were needed every generation to maintain the DGV reliability at a constant level across generations, and theSum of squared relationships between RP and EVA and the sum of off-diagonal coefficients of the inverse of the genomic relationship matrix for RP, separately explained 53% of the variation in the reliability across generations.
Journal ArticleDOI
Evolutionary Quantitative Genomics of Populus trichocarpa.
Ilga Porth,Ilga Porth,Jaroslav Klápště,Jaroslav Klápště,Athena D. McKown,Jonathan La Mantia,Jonathan La Mantia,Robert D. Guy,Pär K. Ingvarsson,Richard C. Hamelin,Shawn D. Mansfield,Jürgen Ehlting,Carl J. Douglas,Yousry A. El-Kassaby +13 more
TL;DR: The molecular basis of climate adaptation in Populus trichocarpa genotypes originating across western North America is studied by employing an integrative quantitative genetics and landscape genomics approach and it is highlighted that important loci underlying adaptive trait variation also show relationship to climate of origin.
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Structural equation models to disentangle the biological relationship between microbiota and complex traits: Methane production in dairy cattle as a case of study
Alejandro Saborio-Montero,Mónica Gutiérrez-Rivas,A. García-Rodríguez,Raquel Atxaerandio,Idoia Goiri,Evangelina López de Maturana,José Antonio Jiménez-Montero,R. Alenda,Oscar González-Recio +8 more
TL;DR: It is suggested that rumen's whole metagenome recursively regulates methane emissions in dairy cows and that both CH4 and the microbiota compositions are partially controlled by the host genotype.
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.