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 estimation of complex traits reveals ancient maize adaptation to temperate North America
Kelly Swarts,Kelly Swarts,Rafal M. Gutaker,Bruce F. Benz,Michael Blake,Robert Bukowski,James B. Holland,Melissa Kruse-Peeples,Nicholas Lepak,Lynda Prim,M. Cinta Romay,Jeffrey Ross-Ibarra,José de Jesús Sánchez-González,Chris A. Schmidt,Verena J. Schuenemann,Johannes Krause,Johannes Krause,R. G. Matson,Detlef Weigel,Edward S. Buckler,Hernán A. Burbano +20 more
TL;DR: Indirectly validated genomic models predicted that Turkey Pen maize was marginally adapted with respect to flowering, as well as short, tillering, and segregating for yellow kernel color, a characteristic of modern temperate maize.
Journal ArticleDOI
Genomic prediction in an admixed population of Atlantic salmon (Salmo salar)
TL;DR: It is hypothesized that this phenomenon may be explained by historical admixture of different founder populations, expected to reduce short-range lice density (LD) and induce long-range LD of an admixed population, while efficient utilization of relationship information may require denser markers.
Journal ArticleDOI
Genome-wide association study for 13 agronomic traits reveals distribution of superior alleles in bread wheat from the Yellow and Huai Valley of China.
Congwei Sun,Fuyan Zhang,Fuyan Zhang,Xuefang Yan,Xiangfen Zhang,Zhongdong Dong,Dangqun Cui,Feng Chen +7 more
TL;DR: New allelic variation distribution for 13 yield‐related traits in series of genome‐wide association studies (GWAS) using the wheat 90K genotyping assay, characterized in 163 bread wheat cultivars revealed that superior alleles were getting popular with time and modern cultivars had integrated many superior allele loci, especially for peduncle length‐ and plant height‐related superior allele.
Journal ArticleDOI
Genomic breeding value prediction:methods and procedures
TL;DR: At low frequencies of re-estimating marker effects, it becomes more important that the model that estimates the marker effects capitalizes on LD information that is persistent across generations to maintain the accuracy of GEBVs at an acceptable level.
BookDOI
Genome-wide association studies and genomic prediction
TL;DR: This work presents a meta-modelling framework called the Genome-Wide Association Studies (GWAS) Superparameter, which automates the very labor-intensive and therefore time-heavy and expensive and expensive process of designing and conductingGWAS studies.
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.
Journal ArticleDOI
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.