Investigation of the statistical distribution of the effects of single nucleotide polymorphic markers on the bias caused by pre-selection of animals for genotyping in genomic selection

Document Type : (original research)

Authors

1 Department of Animal Sciences, Faculty of Agriculture, Ilam university, Ilam, Iran

2 Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran

3 Department of Animal Science, Faculty of Animal and Aquatic Science, Sari Agricultural Sciences and Natural Resources University, Sari, Iran

10.22034/AEJ.2021.315863.2695

Abstract

The bias in the selection of superior animals and accurate prediction of hereditary values of animal offspring selected in future generations is one of the important topics of breeding; therefore, the study of oblique trends in successive generations can be effective in the method of unbiased selective animals in the future. The statistical distribution of the effects of single nucleotide markers can be different in different traits and occupy a range from the normal distribution to the gamma distribution; therefore, the study of the amount of bias caused by pre-selection for different traits can be different according to their genetic structure. The purpose of this study was to investigate the effect of statistical distribution of the effects of SNPs on the biased process of estimating breeding values resulting from pre-selection of animals by genomic selection method. The statistical distributions studied included two distributions of normal and gamma, the biased trend of each of which was studied during consecutive generations. The bias criterion includes the regression of actual correction values on the estimated correction values. Initial Simulation and historical population in the form of two selection scenarios in three different traits with different heritability in 10 consecutive generations by two selection scenarios of 10% and 50% and the number of three QTL species were simulated accurately to estimate genomic breeding values using QMSim software. The need for calculations was analyzed using R software. The regression of TBVs on their GEBVs in the first generation whose genotyping was random was about one and unbiased; But by making choices based on superior breeding values from the second generation onwards it created a bias. As the number of consecutive selection generations increases so does the amount of bias but the rate of change in this bias decreased dramatically after the second generation and remained almost constant in the fourth generation which could be due to a reduction in genetic and phenotypic variance as a result of continuous selection known as the Bolmer effect. The results showed that in both statistical distributions, the amount and intensity of bias and its trend are almost the same and the difference in the statistical distribution of effects will not cause a difference in the amount and trend of bias. Moreover, due to the stabilization of the amount of bias in the 4th generation onwards, it is possible to correct the amount of bias from the 4th generation onwards by using a scale corrector.

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References

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Journal of Animal Environment
Volume 14, Issue 4
February 2023
Pages 19-28

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