Accuracy of Imputation of Microsatellite Markers from a 50K SNP Chip in Spanish Assaf Sheep
1
Department of Animal Production, Faculty of Veterinary Medicine, University of León, Campus de Vegazana s/n, 24071 León, Spain
2
CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia, Brisbane, QLD 4067, Australia
*
Author to whom correspondence should be addressed.
Animals 2021, 11(1), 86; https://doi.org/10.3390/ani11010086
Received: 24 November 2020
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Revised: 30 December 2020
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Accepted: 31 December 2020
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Published: 5 January 2021
(This article belongs to the Special Issue New Technologies to Improve Efficiency and Profitability and Reduce Environmental Impacts on Small Ruminant Farms)
Simple Summary
Parentage misassignments directly affect genetic gain in traditional breeding programs. The use of genetic markers facilitates parentage verification. In sheep, microsatellite markers and single nucleotide polymorphism (SNP) markers have been proposed by the International Society of Animal Sciences (ISAG) for parentage testing. Since the implementation of genomic selection, the microsatellite information used for parental testing in previous generations is gradually being replaced by SNPs. However, parentage verifications should all be performed using the same technology. A strategy for transitioning from microsatellites to SNP markers, while avoiding extra genotyping costs, is the imputation of microsatellite alleles from SNP haplotypes. This study aims to identify the optimum approach, using a minimum number of SNPs to accurately impute microsatellite markers and developing a low-density SNP chip for parentage verification in the Assaf sheep breed. The imputation approach described here reached high accuracies using a low number of SNP markers, which supports the development of a low-density SNP chip that could avoid the problems of genotyping with both technologies, being a cost-effective method for parentage testing. This study will help sheep breeders to perform parentage verification when different genotyping platforms have been used across generations.
Transitioning from traditional to new genotyping technologies requires the development of bridging methodologies to avoid extra genotyping costs. This study aims to identify the optimum number of single nucleotide polymorphisms (SNPs) necessary to accurately impute microsatellite markers to develop a low-density SNP chip for parentage verification in the Assaf sheep breed. The accuracy of microsatellite marker imputation was assessed with three metrics: genotype concordance (C), genotype dosage (length r2), and allelic dosage (allelic r2), for all imputation scenarios tested (0.5–10 Mb microsatellite flanking SNP windows). The imputation accuracy for the three metrics analyzed for all haplotype lengths tested was higher than 0.90 (C), 0.80 (length r2), and 0.75 (allelic r2), indicating strong genotype concordance. The window with 2 Mb length provides the best accuracy for the imputation procedure and the design of an affordable low-density SNP chip for parentage testing. We additionally evaluated imputation performance under two null models, naive (imputing the most common allele) and random (imputing by randomly selecting the allele), which in comparison showed weak genotype concordances (0.41 and 0.15, respectively). Therefore, we describe a precise methodology in the present article to impute multiallelic microsatellite genotypes from a low-density SNP chip in sheep and solve the problem of parentage verification when different genotyping platforms have been used across generations.
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Keywords:
pedigree verification; sheep; microsatellites; SNPs; marker imputation
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MDPI and ACS Style
Marina, H.; Suarez-Vega, A.; Pelayo, R.; Gutiérrez-Gil, B.; Reverter, A.; Esteban-Blanco, C.; Arranz, J.J. Accuracy of Imputation of Microsatellite Markers from a 50K SNP Chip in Spanish Assaf Sheep. Animals 2021, 11, 86. https://doi.org/10.3390/ani11010086
AMA Style
Marina H, Suarez-Vega A, Pelayo R, Gutiérrez-Gil B, Reverter A, Esteban-Blanco C, Arranz JJ. Accuracy of Imputation of Microsatellite Markers from a 50K SNP Chip in Spanish Assaf Sheep. Animals. 2021; 11(1):86. https://doi.org/10.3390/ani11010086
Chicago/Turabian StyleMarina, Héctor, Aroa Suarez-Vega, Rocío Pelayo, Beatriz Gutiérrez-Gil, Antonio Reverter, Cristina Esteban-Blanco, and Juan J. Arranz. 2021. "Accuracy of Imputation of Microsatellite Markers from a 50K SNP Chip in Spanish Assaf Sheep" Animals 11, no. 1: 86. https://doi.org/10.3390/ani11010086
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