Impact of genotypic errors with equal and unequal family contribution on accuracy of genomic prediction in aquaculture using simulation

Khalilisamani, N., Thomson, P.C., Raadsma, H., and Khatkar, M. (2021) Impact of genotypic errors with equal and unequal family contribution on accuracy of genomic prediction in aquaculture using simulation. Scientific Reports, 11 (1). 18318.

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Abstract

Genotypic errors, conflict between recorded genotype and the true genotype, can lead to false or biased population genetic parameters. Here, the effect of genotypic errors on accuracy of genomic predictions and genomic relationship matrix are investigated using a simulation study based on population and genomic structure comparable to black tiger prawn, Penaeus monodon. Fifty full-sib families across five generations with phenotypic and genotypic information on 53 K SNPs were simulated. Ten replicates of different scenarios with three heritability estimates, equal and unequal family contributions were generated. Within each scenario, four SNP densities and three genotypic error rates in each SNP density were implemented. Results showed that family contribution did not have a substantial impact on accuracy of predictions across different datasets. In the absence of genotypic errors, 3 K SNP density was found to be efficient in estimating the accuracy, whilst increasing the SNP density from 3 to 20 K resulted in a marginal increase in accuracy of genomic predictions using the current population and genomic parameters. In addition, results showed that the presence of even 10% errors in a 10 and 20 K SNP panel might not have a severe impact on accuracy of predictions. However, below 10 K marker density, even a 5% error can result in lower accuracy of predictions.

Item ID: 69931
Item Type: Article (Research - C1)
ISSN: 2045-2322
Copyright Information: This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
Date Deposited: 27 Apr 2022 03:33
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