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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Impact of QTL minor allele frequency on genomic evaluation using real genotype data and simulated phenotypes in Japanese Black cattle
TL;DR: The MAF of QTL had an impact on heritability estimation and prediction accuracy and in population size, a large sample size is needed to increase the accuracy of GEBV under all QTL MAF categories.
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Evaluation of the utility of diagonal elements of the genomic relationship matrix as a diagnostic tool to detect mislabelled genotyped animals in a broiler chicken population
TL;DR: Distribution of diagonal elements of genomic relationship matrix (G) may be a useful tool to help identify mislabelled animals or secondary populations and the utility of G as a diagnostic tool to detect mislabelling animals in a genomic dataset is evaluated.
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Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: II: carcass merit traits
Yining Wang,Yining Wang,Feng Zhang,Robert Mukiibi,Liuhong Chen,Liuhong Chen,M. Vinsky,Graham Plastow,John A. Basarab,Paul Stothard,Changxi Li,Changxi Li +11 more
TL;DR: The GWAS results have shown that the carcass merit traits are controlled by a few DNA variants with large effects and manyDNA variants with small effects, which will improve the understanding on genetic controls of carcASS merit traits in beef cattle.
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Utility of Climatic Information via Combining Ability Models to Improve Genomic Prediction for Yield Within the Genomes to Fields Maize Project.
Diego Jarquin,Natalia de Leon,Cinta Romay,Martin O. Bohn,Edward S. Buckler,Ignacio A. Ciampitti,Jode W. Edwards,David S. Ertl,Sherry Flint-Garcia,Michael A. Gore,Christopher Graham,Candice N. Hirsch,James B. Holland,David C. Hooker,Shawn M. Kaeppler,Joseph E. Knoll,Elizabeth C. Lee,Carolyn J. Lawrence-Dill,Jonathan P. Lynch,Stephen P. Moose,Seth C. Murray,Rebecca Nelson,Torbert Rocheford,James C. Schnable,Patrick S. Schnable,Margaret E. Smith,Nathan M. Springer,Peter R. Thomison,Mitch Tuinstra,Randall J. Wisser,Wenwei Xu,Jianming Yu,Aaron J. Lorenz +32 more
TL;DR: In this paper, the authors assessed the usefulness of including weather data variables in genomic prediction models using a naive environmental kinship model across 30 environments comprising the Genomes to Fields (G2F) initiative.
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Genome-wide association study reveals that different pathways contribute to grain quality variation in sorghum ( Sorghum bicolor )
TL;DR: This study aimed to dissect the natural variation of sorghum grain quality traits and identify the underpinning genetic loci by genome-wide association study, and reconstructed the biosynthetic pathways for aspartate and branched-chain amino acids based on 15 candidate genes identified in this study.
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.