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Properties of genomic relationships for estimating current genetic variances within and genetic correlations between populations

Yvonne C.J. Wientjes, Piter Bijma, Jérémie Vandenplas, Mario P.L. Calus
doi: https://doi.org/10.1101/124115
Yvonne C.J. Wientjes
*Wageningen University & Research, Animal Breeding and Genomics, 6700 AH Wageningen, The Netherlands
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Piter Bijma
*Wageningen University & Research, Animal Breeding and Genomics, 6700 AH Wageningen, The Netherlands
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Jérémie Vandenplas
*Wageningen University & Research, Animal Breeding and Genomics, 6700 AH Wageningen, The Netherlands
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Mario P.L. Calus
*Wageningen University & Research, Animal Breeding and Genomics, 6700 AH Wageningen, The Netherlands
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ABSTRACT

Different methods are available to calculate multi-population genomic relationship matrices. Since those matrices differ in base population, it is anticipated that the method used to calculate the genomic relationship matrix affect the estimate of genetic variances, covariances and correlations. The aim of this paper is to define a multi-population genomic relationship matrix to estimate current genetic variances within and genetic correlations between populations. The genomic relationship matrix containing two populations consists of four blocks, one block for population 1, one block for population 2, and two blocks for relationships between the populations. It is known, based on literature, that current genetic variances are estimated when the current population is used as base population of the relationship matrix. In this paper, we theoretically derived the properties of the genomic relationship matrix to estimate genetic correlations and validated it using simulations. When the scaling factors of the genomic relationship matrix fulfill the property Embedded Image, the genetic correlation is estimated even though estimated variance components are not necessarily related to the current population. When this property is not met, the correlation based on estimated variance components should be multiplied by Embedded Image to rescale the genetic correlation. In this study we present a genomic relationship matrix which directly results in current genetic variances as well as genetic correlations between populations.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 05, 2017.
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Properties of genomic relationships for estimating current genetic variances within and genetic correlations between populations
Yvonne C.J. Wientjes, Piter Bijma, Jérémie Vandenplas, Mario P.L. Calus
bioRxiv 124115; doi: https://doi.org/10.1101/124115
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Properties of genomic relationships for estimating current genetic variances within and genetic correlations between populations
Yvonne C.J. Wientjes, Piter Bijma, Jérémie Vandenplas, Mario P.L. Calus
bioRxiv 124115; doi: https://doi.org/10.1101/124115

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