Replacement of microsatellite markers by imputed medium-density SNP arrays for parentage control in German warmblood horses.
Abstract: In horses, parentage control is currently performed based on an internationally standardized panel of 17 microsatellite (MS) markers comprising 12 mandatory and five optional markers. Unlike MS, single nucleotide polymorphism (SNP) profiles support a wider portfolio of genomic applications, including parentage control. A transition to SNP-based parentage control is favorable, but requires additional efforts for ensuring generation-overlapping availability of marker genotypes of the same type. To avoid double genotyping of either parents or offspring for changing to SNP technology and enable efficient transition, we tested whether MS genotypes used for parentage control could be reliably imputed from a medium-density SNP panel in German warmblood horses. Imputation accuracy was tested in a tenfold cross-validation with two approaches: within breed (option A) and across breeds (option B). Average imputation accuracies of 97.98% (A) and 96.17% (B) were achieved, respectively. Due to interbreed differences in genotyping rates, five MS markers of low genotyping rate (GTR; < 90%) could be imputed with higher accuracy within breed (98.18%) than across breeds (90.73%). MS markers with high GTR performed homogeneously well in option B (98.44%) and showed slightly lower accuracy in option A (97.90%). Among these markers, AHT5 proved to be problematic for imputation regardless of the approach, revealing accuracies of 86.40% (A) and 88.70% (B). Better results for MS markers with high GTR and savings in computational processing justified the choice of option B for routine implementation. To date, more than 9500 horses have undergone the new parentage control based on imputed MS genotypes.
© 2022. The Author(s).
Publication Date: 2022-09-29 PubMed ID: 36173533PubMed Central: PMC9637052DOI: 10.1007/s13353-022-00725-9Google Scholar: Lookup
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- Journal Article
Summary
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This research explored the idea of replacing microsatellite markers with imputed medium-density single nucleotide polymorphism (SNP) profiles for parentage control in German warmblood horses, with results showing a high level of accuracy and offering an efficient way to transition to SNP technology.
Objective and Methodology
- Research aimed to evaluate the feasibility and accuracy of replacing the traditionally used microsatellite (MS) markers with SNP profiles for parentage control in German Warmblood horses.
- To ensure a smooth transition without the need for double-genotyping of either parents or offspring, the researchers examined the possibility of reliable imputation of MS genotypes from a medium-density SNP panel.
- This was done using a tenfold cross-validation method applied in two different approaches: within breed (option A) and across breeds (option B).
Results and Findings
- The process yielded high average imputation accuracies for both options, with 97.98% for option A and 96.17% for option B.
- The study further found that five MS markers with a low genotyping rate (less than 90%) could be imputed more accurately within breed (98.18%) as compared to across breeds (90.73%); owing to distinct differences between breeds’ genotyping rates.
- MS markers with high genotyping rate performed pretty well in both options, however, they were slightly more successful in option B (98.44%) as compared to option A (97.90%).
- One microsatellite marker AHT5, however, was observed to present challenges for imputation, regardless of the approach used. It exhibited relatively low imputation accuracies of 86.40% (option A) and 88.70% (option B).
- Option B was chosen for routine implementation because it produced better results for MS markers with high genotyping rates and also required lesser computational processing resources.
- Till the time the research was conducted, about 9500 horses had successfully undergone new parentage control based on imputed MS genotypes.
Conclusions
- The application of SNP arrays for parentage control in German warmblood horses demonstrated a smooth and efficient transition from traditional microsatellite markers.
- The imputation method allowed for better processing and higher accuracy, thus making an effective case for its regular implementation.
Cite This Article
APA
Nolte W, Alkhoder H, Wobbe M, Stock KF, Kalm E, Vosgerau S, Krattenmacher N, Thaller G, Tetens J, Kühn C.
(2022).
Replacement of microsatellite markers by imputed medium-density SNP arrays for parentage control in German warmblood horses.
J Appl Genet, 63(4), 783-792.
https://doi.org/10.1007/s13353-022-00725-9 Publication
Researcher Affiliations
- Research Institute for Farm Animal Biology, Institute of Genome Biology, 18196, Dummerstorf, Germany.
- Saxon State Office for Environment, Agriculture and Geology, 01468, Moritzburg, Germany.
- IT Solutions for Animal Production, 27283, Verden, Germany.
- IT Solutions for Animal Production, 27283, Verden, Germany.
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), 30559, Hanover, Germany.
- IT Solutions for Animal Production, 27283, Verden, Germany.
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), 30559, Hanover, Germany.
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, 24118, Kiel, Germany.
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, 24118, Kiel, Germany.
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, 24118, Kiel, Germany.
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, 24118, Kiel, Germany.
- Department of Animal Sciences, Georg-August-University, 37077, Göttingen, Germany.
- Research Institute for Farm Animal Biology, Institute of Genome Biology, 18196, Dummerstorf, Germany. kuehn@fbn-dummerstorf.de.
- Faculty of Agricultural and Environmental Sciences, University Rostock, 18059, Rostock, Germany. kuehn@fbn-dummerstorf.de.
MeSH Terms
- Horses / genetics
- Animals
- Polymorphism, Single Nucleotide
- Genotype
- Genome
- Genomics
- Microsatellite Repeats
Conflict of Interest Statement
The authors declare no competing interests.
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