By J.L. Doyle, S. Egan, D.P. Berry
Graphics: Horse Sport Ireland

Full article title: Imputation of single nucleotide polymorphism genotypes in ungenotyped sport horses from the genotypes of their progeny

Many sport horse studbooks are still using microsatellite markers for parentage verification. Transitioning to single nucleotide polymorphism-based parentage verification would support the implementation of genomic evaluations, but the lack of availability of single nucleotide polymorphism genotypes from older horses to verify their progeny hinders this transition. Based on the fact that an animal receives half its DNA from its sire and half from its dam, the hypothesis was that the genotype of a non-genotyped sire could be predicted from the genotypes of its progeny. Results confirmed this hypothesis, thus, the necessity and cost associated with genotyping older animals could be reduced.

Introduction

Whole genome-enabled selection (Meuwissen et al., 2001) using genome-wide single nucleotide polymorphism (SNP) data is now an integral part of genetic evaluation systems for many animal and plant species (Van Raden and Sullivan, 2010, Meuwissen et al., 2016). Such a paradigm shift has been enabled by the commercial availability of relatively low-cost genotyping platforms that can generate genotypes for tens or hundreds of thousands of SNPs on individual animals. Such data have extensive uses, complementary to genomic evaluations (Berry and Spangler, 2023); one such use, is the ability of the dense genotypes to not only verify parentage (and deeper ancestry; Werner et al., 2004) but also discover parentage (Nani et al., 2020). Achieving this, however, is conditional on the candidate parents also having SNP genotype information available for comparative purposes.
Parentage testing in many species was, however, traditionally based on microsatellite technology which was not directly compatible with SNP technology for parentage verification or assignment. Approaches were developed in a multitude of species including horses (Nolte et al., 2022) and other domesticated animals (McClure et al. 2012) to predict the microsatellite (MS) genotype at a certain location based on the flanking SNP genotype. This approach could be used to impute the microsatellite parentage panel of animals with SNP genotypes which could then be compared with the microsatellite genotypes of candidate parents.
Another approach could be to impute the SNP genotype of individuals with many offspring. This approach is simply based on the fact that each progeny receives a relatively random sample of half the DNA of each parent; simply probability theory implies that, under these conditions, the accuracy of predicting the genotype of a parent should increase as the number of genotyped progeny increases.
Imputation of parental SNP genotypes from the SNP genotypes of their progeny has been proven to be effective in beef and dairy cattle (Van Raden et al., 2013, Berry et al., 2014, Boison et al., 2014, Piccoli et al., 2014), as well as in sheep (Berry et al., 2018) and swine (See et al., 2022). The average genotype concordance rate between the imputed and actual genotypes of an animal was estimated to be 0.986 when SNP genotype information from 12 progeny were available (on either a medium− or high-density genotyping platform) in beef and dairy cattle (Berry et al., 2014).
In sheep, a genotype concordance rate between imputed and actual genotypes (11 129 SNPs) of 0.988 was achieved when the genotypes of 7 progeny, and their dams, were available (Berry et al., 2018). No study to date has attempted to impute genotypes of non-genotyped horses even though many stallions could have many progeny.
In all sport horse studbooks in Ireland, every foal registered with recorded parentage must be parentage tested against both the sire and dam. Since 2023, the majority of the Irish studbooks have been SNP genotyping all foals, but there has been a lack of genotype information available on parents to use these genotypes for parentage verification. The objective therefore of the present study was to quantify the ability to impute the SNP genotype of a horse based on the SNP genotypes of its progeny, with or without the availability of the SNP genotypes of the progeny’s other parent. Preliminary results have been published previously in abstract form (Doyle et al., 2024)...

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