Effects of preselection of genotyped animals on reliability and bias of genomic prediction in dairy cattle.

Kenji Togashi,Toshio Watanabe,Kimihiro Moribe,Atsushi Ogino,Tsutomu Takahashi,Kouichi Tokunaka,Takanori Yasumori,Kazunori Adachi,Kazuhito Kurogi,Yoshiyuki Miyazaki

doi:10.5713/ajas.18.0161

Abstract

ObjectiveModels for genomic selection assume that the reference population is an unselected population. However, in practice, genotyped individuals, such as progeny-tested bulls, are highly selected, and the reference population is created after preselection. In dairy cattle, the intensity of selection is higher in males than in females, suggesting that cows can be added to the reference population with less bias and loss of accuracy. The objective is to develop formulas applied to any genomic prediction studies or practice with preselected animals as reference population.MethodsWe developed formulas for calculating the reliability and bias of genomically enhanced breeding values (GEBV) in the reference population where individuals are preselected on estimated breeding values. Based on the formulas presented, deterministic simulation was conducted by varying heritability, preselection percentage, and the reference population size.ResultsThe number of bulls equal to a cow regarding the reliability of GEBV was expressed through a simple formula for the reference population consisting of preselected animals. The bull population was vastly superior to the cow population regarding the reliability of GEBV for low-heritability traits. However, the superiority of reliability from the bull reference population over the cow population decreased as heritability increased. Bias was greater for bulls than cows. Bias and reduction in reliability of GEBV due to preselection was alleviated by expanding reference population.ConclusionCows are easier in expanding reference population size compared with bulls and alleviate bias and reduction in reliability of GEBV of bulls which are highly preselected than cows by expanding the cow reference population.

Highlights

Genomic prediction (GP) is used to predict the genomic breeding values of genotyped individuals [1]
The reliability of genomically enhanced breeding values (GEBV) in the bulls-only reference population was the highest among the three reference populations
The bulls-only population was superior to the cow population for low-heritability traits (h2 = 0.1), especially for the bulls-only population testing based on 100 daughters

Summary

Introduction

Genomic prediction (GP) is used to predict the genomic breeding values of genotyped individuals [1]. The GP models usually do not account for selection. The reference population which is used for estimating marker effects with GP models usually consisted of progeny test bulls which was highly selected. The prediction models are unable to incorporate past selection based on pedigree and phenotypes, perhaps leading to bias as well as decreased accuracy. A formula for approximating the reliability and bias of the genomically enhanced breeding values (GEBV) that accounted for the prior selection of genotyped test bulls from among all test bull candidates was proposed [2]. The differences between the means and standard deviations of the estimated breeding values (EBV) of all of the test bull candidates are used to estimate the proportion of selective genotyping. The selection difference or intensity of selection is calculated from quantitative genetics textbooks [3], and the authors

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Discussion

Conclusion