Accuracy of the unified approach in maternally influenced traits - illustrated by a simulation study in the honey bee (Apis mellifera)

Pooja Gupta,Tim Conrad,Andreas Spötter,Norbert Reinsch,Kaspar Bienefeld

doi:10.1186/1471-2156-14-36

Abstract

BackgroundThe honey bee is an economically important species. With a rapid decline of the honey bee population, it is necessary to implement an improved genetic evaluation methodology. In this study, we investigated the applicability of the unified approach and its impact on the accuracy of estimation of breeding values for maternally influenced traits on a simulated dataset for the honey bee. Due to the limitation to the number of individuals that can be genotyped in a honey bee population, the unified approach can be an efficient strategy to increase the genetic gain and to provide a more accurate estimation of breeding values. We calculated the accuracy of estimated breeding values for two evaluation approaches, the unified approach and the traditional pedigree based approach. We analyzed the effects of different heritabilities as well as genetic correlation between direct and maternal effects on the accuracy of estimation of direct, maternal and overall breeding values (sum of maternal and direct breeding values). The genetic and reproductive biology of the honey bee was accounted for by taking into consideration characteristics such as colony structure, uncertain paternity, overlapping generations and polyandry. In addition, we used a modified numerator relationship matrix and a realistic genome for the honey bee.ResultsFor all values of heritability and correlation, the accuracy of overall estimated breeding values increased significantly with the unified approach. The increase in accuracy was always higher for the case when there was no correlation as compared to the case where a negative correlation existed between maternal and direct effects.ConclusionsOur study shows that the unified approach is a useful methodology for genetic evaluation in honey bees, and can contribute immensely to the improvement of traits of apicultural interest such as resistance to Varroa or production and behavioural traits. In particular, the study is of great interest for cases where negative correlation between maternal and direct effects and uncertain paternity exist, thus, is of relevance for other species as well. The study also provides an important framework for simulating genomic and pedigree datasets that will prove to be helpful for future studies.

Highlights

The honey bee is an economically important species
The study provided comparative insight into genetic evaluation performed using: (1) the traditional Best Linear Unbiased Prediction (BLUP) approach based on pedigree data and (2) the unified approach based on both pedigree and marker data
We propose that the extra gain from genomic selection is larger, when the correlations between direct and maternal effects are negative, compared to scenarios with positive correlations

Summary

Introduction

The honey bee is an economically important species. With a rapid decline of the honey bee population, it is necessary to implement an improved genetic evaluation methodology. Due to the limitation to the number of individuals that can be genotyped in a honey bee population, the unified approach can be an efficient strategy to increase the genetic gain and to provide a more accurate estimation of breeding values. The unified approach was proposed by Legarra et al [5] and Christensen and Lund [6], and it combines full pedigree and genomic information from both genotyped and ungenotyped individuals The advantage of this procedure over the multi-step approach is that it gives a more accurate estimate of breeding values for ungenotyped animals [6,7] and is resistant to selection bias [8]. It is simpler to implement as compared to the multi-step approach and provides an easy extension to a multi-trait model [9] with maternal effects in honey bees

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Results

Discussion

Conclusion