A simple algorithm to estimate genetic variance in an animal threshold model using Bayesian inference.

Genetics, Selection, Evolution : GSE
J ØdegårdPer Madsen

Abstract

In the genetic analysis of binary traits with one observation per animal, animal threshold models frequently give biased heritability estimates. In some cases, this problem can be circumvented by fitting sire- or sire-dam models. However, these models are not appropriate in cases where individual records exist on parents. Therefore, the aim of our study was to develop a new Gibbs sampling algorithm for a proper estimation of genetic (co)variance components within an animal threshold model framework. In the proposed algorithm, individuals are classified as either "informative" or "non-informative" with respect to genetic (co)variance components. The "non-informative" individuals are characterized by their Mendelian sampling deviations (deviance from the mid-parent mean) being completely confounded with a single residual on the underlying liability scale. For threshold models, residual variance on the underlying scale is not identifiable. Hence, variance of fully confounded Mendelian sampling deviations cannot be identified either, but can be inferred from the between-family variation. In the new algorithm, breeding values are sampled as in a standard animal model using the full relationship matrix, but genetic (co)variance compo...Continue Reading

References

Mar 5, 2003·Journal of Dairy Science·B HeringstadK A Welgel
Feb 20, 2007·Genetics, Selection, Evolution : GSE·Kathrin Friederike StockIna Hoeschele

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Citations

Mar 23, 2011·Genetics, Selection, Evolution : GSE·Jørgen ØdegårdMorten Rye
May 10, 2012·Genetics, Selection, Evolution : GSE·Jørgen Ødegård, Theo H E Meuwissen
Oct 19, 2013·Genetics, Selection, Evolution : GSE·Anna K SonessonLars Rönnegård
Nov 19, 2015·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·T H LeE Norberg
Sep 18, 2014·European Journal of Human Genetics : EJHG·Hauke ThomsenKari Hemminki
Nov 22, 2018·Animal : an International Journal of Animal Bioscience·R E CrumpL E Green
Oct 12, 2019·Heredity·Winati NurhayuMichel Raymond
Jan 16, 2016·Genetics, Selection, Evolution : GSE·Rodrigo R MotaFernando F Cardoso
Jul 12, 2011·Journal of Animal Science·B VillanuevaM A Toro
Dec 15, 2010·Journal of Animal Science·J ØdegårdT H E Meuwissen

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Software Mentioned

DMU
AnimB
AnimA
MATLAB
DMU software package for

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