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Alternative single-step type genomic prediction equations
Gengler, Nicolas; Nieuwhof, G.; Konstantinov, K. et al.
2012In Book of Abstracts of the 63rd Annual Meeting of the European Federation of Animal Science
Peer reviewed
 

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Keywords :
genomic prediction; single-step; explicit genetic effects; single-step SNP BLUP; single-step GBLUP
Abstract :
[en] Current derivations of single-step equations are based on modified relationships among animals replacing for genotyped animals and on an inverted scale, pedigree based relationships, by modified ones. These relationships are obtained as linear combination of strictly genomic and pedigree based relationships, therefore implicitly 'weighting' SNP and polygenic effects. Alternative equations were recently proposed de-absorbing the genomic relationships out of the equations. This derivation did not change basic assumptions, but was derived using a matrix of relationship differences. This presentation will show a new and alternative derivation of single-step type genomic prediction equations allowing joint estimation of GEBV and SNP effects based on the partitioning of genetic (co)variances. The method was derived from a random mixed inheritance model where SNP and residual polygenic effects are jointly modeled. The derived equations were modified to allow non-genotyped animals and to estimate directly and jointly GEBV and SNP effects. Equations resemble superficially recently proposed alternative single-step equations but were derived differently and are based on completely different assumptions. They also avoid certain issues in de-absorbing derivation linked to the matrix of relationship differences by using (co)variances. Several other advantages of the new equations are that weighting of SNP and polygenic effects becomes explicitly and that SNP effects are also estimated. This method makes better use of High-Density SNP panels and can be easily modified to accommodate other genetic effects as major gene effects or copy-number variant based effects. Finally these alternative equations combine advantages of single-step and of explicit SNP effect estimation based methods. Additional research is required to test and validate further the proposed method.
Disciplines :
Genetics & genetic processes
Animal production & animal husbandry
Author, co-author :
Gengler, Nicolas  ;  Université de Liège - ULiège > Agronomie, Bio-ingénierie et Chimie (AgroBioChem) > Ingénierie des productions animales et nutrition
Nieuwhof, G.
Konstantinov, K.
Goddard, M.
Language :
English
Title :
Alternative single-step type genomic prediction equations
Publication date :
August 2012
Event name :
63rd Annual Meeting of the European Federation of Animal Science
Event organizer :
EAAP - European Federation of Animal Science
Event place :
Bratislava, Slovakia
Event date :
27-31 August 2012
Audience :
International
Main work title :
Book of Abstracts of the 63rd Annual Meeting of the European Federation of Animal Science
Publisher :
Wageningen Academic Publishers, Wageningen, Netherlands
Edition :
Bratislava 2012
ISBN/EAN :
978-90-8686-206-1
Collection name :
Nº. 18
Pages :
131
Peer reviewed :
Peer reviewed
European Projects :
FP7 - 211708 - ROBUSTMILK - Innovative and Practical Breeding Tools for Improved Dairy Products from More Robust Dairy Cattle
Funders :
CE - Commission Européenne [BE]
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since 25 March 2019

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