Different genomic relationship matrices for single-step analysis using phenotypic, pedigree and genomic information

Selma Forni,Ignacy Misztal,Ignacio Aguilar

doi:10.1186/1297-9686-43-1

Selma Forni, Ignacy Misztal + Show 1 more

Open Access

https://doi.org/10.1186/1297-9686-43-1

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Abstract

BackgroundThe incorporation of genomic coefficients into the numerator relationship matrix allows estimation of breeding values using all phenotypic, pedigree and genomic information simultaneously. In such a single-step procedure, genomic and pedigree-based relationships have to be compatible. As there are many options to create genomic relationships, there is a question of which is optimal and what the effects of deviations from optimality are.MethodsData of litter size (total number born per litter) for 338,346 sows were analyzed. Illumina PorcineSNP60 BeadChip genotypes were available for 1,989. Analyses were carried out with the complete data set and with a subset of genotyped animals and three generations pedigree (5,090 animals). A single-trait animal model was used to estimate variance components and breeding values. Genomic relationship matrices were constructed using allele frequencies equal to 0.5 (G05), equal to the average minor allele frequency (GMF), or equal to observed frequencies (GOF). A genomic matrix considering random ascertainment of allele frequencies was also used (GOF*). A normalized matrix (GN) was obtained to have average diagonal coefficients equal to 1. The genomic matrices were combined with the numerator relationship matrix creating H matrices.ResultsIn G05 and GMF, both diagonal and off-diagonal elements were on average greater than the pedigree-based coefficients. In GOF and GOF*, the average diagonal elements were smaller than pedigree-based coefficients. The mean of off-diagonal coefficients was zero in GOF and GOF*. Choices of G with average diagonal coefficients different from 1 led to greater estimates of additive variance in the smaller data set. The correlation between EBV and genomic EBV (n = 1,989) were: 0.79 using G05, 0.79 using GMF, 0.78 using GOF, 0.79 using GOF*, and 0.78 using GN. Accuracies calculated by inversion increased with all genomic matrices. The accuracies of genomic-assisted EBV were inflated in all cases except when GN was used.ConclusionsParameter estimates may be biased if the genomic relationship coefficients are in a different scale than pedigree-based coefficients. A reasonable scaling may be obtained by using observed allele frequencies and re-scaling the genomic relationship matrix to obtain average diagonal elements of 1.

Highlights

The incorporation of genomic coefficients into the numerator relationship matrix allows estimation of breeding values using all phenotypic, pedigree and genomic information simultaneously
As an entire population is unlikely to be genotyped in livestock species, Legarra et al [3] and Misztal et al [4] have proposed the integration of the numerator relationship matrix (A) and G into a single matrix (H)
For GOF and GOF*, the average diagonal coefficients were smaller than the pedigreebased coefficients

Summary

Introduction

The incorporation of genomic coefficients into the numerator relationship matrix allows estimation of breeding values using all phenotypic, pedigree and genomic information simultaneously. In such a single-step procedure, genomic and pedigree-based relationships have to be compatible. Traditional genetic evaluation of livestock combines only phenotypic data and probabilities that genes are identical by descent using the pedigree information. Various G used in a genetic evaluation by Aguilar et al [5] have resulted in different scaling and accuracies of EBV. Different G can lead to different accuracies of EBV [5] These differences could be due to an incorrect scaling of G relative to A

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