Imputation of single nucleotide polymorphism genotypes in ungenotyped sport horses from the genotypes of their progeny.
Abstract: Many sport horse studbooks worldwide use microsatellite markers for parentage verification. However, many have expressed a desire to introduce genomic selection using genome-wide dense single nucleotide polymorphism (SNP) genotypes to complement their current breeding programmes. Hence, it does not make sense to genotype the same animal for both microsatellite markers and SNP markers. Transitioning to SNP-based parentage verification is an obvious solution but one barrier to this transition is the lack of SNP data on parents from which to verify parentage against. Therefore, the objective of this study was to assess the ability to impute the SNP genotype of a stallion from the genotypes of its progeny, with or without the consideration of the genotype of the progeny's dam. Genotype information from 55 935 SNPs was available on 13 327 horses. A total of 98 stallions had genotype data on 10 progeny and the genotypes of these stallions were used as a test population. Genome-wide genotype imputation was undertaken by combining a family- and population-based imputation approach. Several different scenarios were assessed to quantify the ability to accurately impute the genotype of a stallion based on genotype data of incrementally more half-sibling progeny. Using genomic information from four progeny the average genotype concordance of the imputed sire genotype compared to the actual sire's genotype was 0.932. The average genotype concordance rate increased to 0.960 when the genotypes of 10 progeny were included in the imputation process. The inclusion of the genotypes of the dams of the progeny improved the concordance rate from 0.932 to 0.977 when based on the genotype of just four progeny and their dams and from 0.960 to 0.996 when based on the genotype of 10 progeny and their dams. These results suggest it is possible to impute the genotype of a non-genotyped horse from the genotypes of its progeny and that the inclusion of the genotypes of the dams of the progeny improves this imputation accuracy further.
Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.
Publication Date: 2024-07-31 PubMed ID: 39213910DOI: 10.1016/j.animal.2024.101278Google Scholar: Lookup
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- Journal Article
Summary
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The study investigates the utility of using genotypes of horse progeny to predict the genotypes of ungenotyped stallions. The results indicate that this method is highly effective, with improved accuracy when considering the genotypes of the progeny’s dam.
Objective and Context
- The research was guided by an ongoing shift in horse studbooks from using microsatellite markers for parentage verification to genome-wide dense single nucleotide polymorphism (SNP) genotypes. This modern method promises a more detailed overview of a horse’s genetic makeup.
- However, moving to a new method necessitates genotyping the same horse for both types of genetic markers, which isn’t practical. A particular problem is that SNP data on parent horses, which is needed for verification, is often not available.
- To address this drawback, the researchers set out to investigate whether it’s possible to predict the SNP genotype of a stallion using the genotypes of its progeny. This process, called genotype imputation, could help make the transition to SNP-based parentage verification smoother.
Methods
- The researchers had access to genotype information from 55,935 SNPs on 13,327 horses. Of these, 98 stallions (male horses) had genotype information on 10 of their progeny, and were thus used as a test population.
- A combination of family- and population-based imputation methods was used for genome-wide genotype imputation. Multiple scenarios were tested to check the accuracy of stallion genotype prediction based on the genotypes of progressively more half-sibling progeny.
Results
- The genotype concordance (agreement between predicted and actual genotypes) was generally high, reaching 0.932 when genotypes from four progeny were used. This rate increased to 0.960 when genotypes from 10 progeny were included.
- Including the genotypes of the dams (female parents) of the progeny improved concordance further, reaching 0.977 with genotypes from four progeny and their dams, and 0.996 with genotypes from 10 progeny and their dams.
Conclusion
- These findings imply that it is feasible to predict the genotype of an ungenotyped stallion based on its progeny’s genotypes. This method’s accuracy only becomes better when the mother’s genotypes are also included. The research could ease the transition to SNP-based parentage verification in horse breeding.
Cite This Article
APA
Doyle JL, Egan S, Berry DP.
(2024).
Imputation of single nucleotide polymorphism genotypes in ungenotyped sport horses from the genotypes of their progeny.
Animal, 18(9), 101278.
https://doi.org/10.1016/j.animal.2024.101278 Publication
Researcher Affiliations
- Horse Sport Ireland, Beech House, Millennium Park, Naas, Co. Kildare W91TK7N, Ireland. Electronic address: jdoyle@horsesportireland.ie.
- Horse Sport Ireland, Beech House, Millennium Park, Naas, Co. Kildare W91TK7N, Ireland.
- Animal & Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Co. Cork P61 C996, Ireland.
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