Mendelian sampling covariability of marker effects and genetic values.

Sarah Bonk,Dierck Segelke,Friedrich Teuscher,Manuela Reichelt,Norbert Reinsch

doi:10.1186/s12711-016-0214-0

Sarah Bonk, Dierck Segelke + Show 3 more

Open Access

https://doi.org/10.1186/s12711-016-0214-0

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Abstract

BackgroundMeasures of the expected genetic variability among full-sibs are of practical relevance, such as in the context of mating decisions. An important application field in animal and plant breeding is the selection and allocation of mates when large or small amounts of genetic variability among offspring are desired, depending on user-specific goals. Estimates of the Mendelian sampling variance can be obtained by simulating gametes from parents with known diplotypes. Knowledge of recombination rates and additive marker effects is also required. In this study, we aimed at developing an exact method that can account for both additive and dominance effects.ResultsWe derived parent-specific covariance matrices that exactly quantify the within-family (co-)variability of additive and dominance marker effects. These matrices incorporate prior knowledge of the parental diplotypes and recombination rates. When combined with additive marker effects, they allow the exact derivation of the Mendelian sampling (co-)variances of (estimated) breeding values for several traits, as well for the aggregate genotype. A comparative analysis demonstrated good average agreement between the exact values and the simulation results for a practical dataset (74,353 German Holstein cattle).ConclusionsThe newly derived method is suitable for calculating the exact amount of intra-family variation of the estimated breeding values and genetic values (comprising additive and dominance effects).

Highlights

Measures of the expected genetic variability among full-sibs are of practical relevance, such as in the context of mating decisions
It is assumed that the genetic distances between all markers are known in terms of their recombination rates, which are summarized in a comprehensive genetic map for all Single nucleotide polymorphism (SNP)
The Mendelian correlation between FKG and PKG was an exception because most of the values were positive and the distribution was bimodal. This bimodality is a consequence of the DGAT1 gene, for which heterozygous animals led to the smaller peak at correlations below 0.5 and homozygotes were responsible for the larger peak with correlations above 0.5

Summary

Introduction

Measures of the expected genetic variability among full-sibs are of practical relevance, such as in the context of mating decisions. Estimates of the Mendelian sampling variance can be obtained by simulating gametes from parents with known diplotypes. The degree of genetic variability among full-sibs is known as Mendelian sampling variance. This variability is due to the inheritance of random samples of alleles from both parents. Under additivity and with unlinked loci, the Mendelian sampling variance is the sum of two parental contributions, σa (1 − F♂) + σa2(1. F♀), where σa is the additive genetic variance [1] The latter expression is of general importance in quantitative genetics, especially in the context of estimating genetic parameters and in genetic evaluations. In certain models (e.g. [2, 3]), it is used explicitly for the relative weighting of observations

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