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
A comparison of partial least squares (PLS) and sparse PLS regressions in genomic selection in French dairy cattle.
C. Colombani,Pascal Croiseau,Sébastien Fritz,François Guillaume,Andres Legarra,Vincent Ducrocq,Christèle Robert-Granié +6 more
TL;DR: Both PLS and sparse PLS were more accurate than pedigree-based BLUP and generally provided lower correlations between observed and predicted phenotypes than did genomic BLUP, and required similar computing time to genomicBLUP for the study of 6 traits.
Journal ArticleDOI
Optimizing genomic selection for blight resistance in American chestnut backcross populations: A trade-off with American chestnut ancestry implies resistance is polygenic.
Jared W. Westbrook,Qian Zhang,Mihir K. Mandal,Eric V. Jenkins,Laura E. Barth,Jerry Jenkins,Jane Grimwood,Jeremy Schmutz,Jason A. Holliday +8 more
TL;DR: To accelerate selection within two backcross populations that descended from two Chinese chestnuts, genomic prediction models for five presence/absence blight phenotypes of 1,230 selection candidates and average canker severity of their BC3F3 progeny were developed and polygenic inheritance of blight resistance was found.
Journal ArticleDOI
Genomic BLUP including additive and dominant variation in purebreds and F1 crossbreds, with an application in pigs
Zulma G. Vitezica,Zulma G. Vitezica,Luis Varona,Jean-Michel Elsen,Ignacy Misztal,W. O. Herring,Andres Legarra +6 more
TL;DR: A coherent marker-based model that includes purebred and crossbred data and additive and dominant actions is presented, which can be exploited to plan assortative mating in pig, maize or other species, in order to generate superior crossbred individuals in terms of performance.
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Comparison of host genetic factors influencing pig response to infection with two North American isolates of porcine reproductive and respiratory syndrome virus
Andrew S. Hess,Zeenath U. Islam,Melanie K. Hess,Raymond R. R. Rowland,Joan K. Lunney,Andrea Doeschl-Wilson,Graham Plastow,Jack C. M. Dekkers +7 more
TL;DR: The results suggest that the KS06 PRRSV isolate is less virulent than NVSL but that genetic selection for increased resistance to either of these genetically distinct isolates is expected to increase resistance to the other isolate.
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Multi-Trait, Multi-Environment Genomic Prediction of Durum Wheat With Genomic Best Linear Unbiased Predictor and Deep Learning Methods.
Osval A. Montesinos-López,Abelardo Montesinos-López,Roberto Tuberosa,Marco Maccaferri,Giuseppe Sciara,Karim Ammar,José Crossa +6 more
TL;DR: This paper covers multi-trait prediction of grain yield, days to heading and plant height of 270 durum wheat lines that were evaluated in 43 environments across a broad range of water regimes in the Mediterranean Basin and other locations and finds that in general the best predictions were observed under the GBLUP model.
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.