Marker genotyping error effects on genomic predictions under different genetic architectures
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ORIGINAL ARTICLE
Marker genotyping error effects on genomic predictions under different genetic architectures Tahere Akbarpour1 · Navid Ghavi Hossein‑Zadeh1 · Abdol Ahad Shadparvar1 Received: 20 May 2020 / Accepted: 19 September 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract This study aimed to determine the effect of different rates of marker genotyping error on the accuracy of genomic prediction that was examined under distinct marker and quantitative trait loci (QTL) densities and different heritability estimates using a stochastic simulation approach. For each scenario of simulation, a reference population with phenotypic and genotypic records and a validation population with only genotypic records were considered. Marker effects were estimated in the ref‑ erence population, and then their genotypic records were used to predict genomic breeding values in the validation popula‑ tion. The prediction accuracy was calculated as the correlation between estimated and true breeding values. The prediction bias was examined by computing the regression of true genomic breeding value on estimated genomic breeding value. The accuracy of the genomic evaluation was the highest in a scenario with no marker genotyping error and varied from 0.731 to 0.934. The accuracy of the genomic evaluation was the lowest in a scenario with marker genotyping error equal to 20% and changed from 0.517 to 0.762. The unbiased regression coefficients of true genomic breeding value on estimated genomic breeding value were obtained in the reference and validation populations when the rate of marker genotyping error was equal to zero. The results showed that marker genotyping error can reduce the accuracy of genomic evaluations. Moreover, marker genotyping error can provide biased estimates of genomic breeding values. Therefore, for obtaining accurate results it is recommended to minimize the marker genotyping errors to zero in genomic evaluation programs. Keyword Accuracy · Genomic evaluation · Genotyping error · Linkage disequilibrium · Marker and quantitative trait loci (QTL)
Introduction The genomic selection was introduced in 1998 (Visscher and Haley 1998), and then its methods and principles were presented by Meuwissen et al. (2001). Genomic selection is a new tool for the selection of animals based on marker information besides traditional information (Meuwissen et al. 2001). Implementing genomic selection takes place in two steps. First, the effects of genetic markers, typically single nucleotide polymorphism (SNP), are estimated in a reference population (animals with both marker and phe‑ notypic information). Second, the estimated effects of the genetic markers are used to predict genomic breeding values for individuals of the validation population (animals with * Navid Ghavi Hossein‑Zadeh [email protected] 1
Department of Animal Science, Faculty of Agricultural Sciences, University of Guilan, 41635‑1314 Rasht, Iran
marker information and without phenotypic information). Genomic selection pr
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