First large-scale genomic prediction in the honey bee

TL;DR

This study demonstrates the potential of genomic selection in honey bees by analyzing predictive abilities and biases of pedigree-based and genomic breeding values for various traits, showing promising results especially for traits with high heritability.

Contribution

First large-scale genomic prediction study in honey bees, evaluating the effectiveness of genomic selection for multiple traits using a honey bee-specific model.

Findings

Genomic data improved predictive ability for honey yield and workability traits.

Genomic selection showed no improvement for disease resistance traits.

Bias levels were similar between genomic and pedigree-based methods.

Abstract

Genomic selection has increased genetic gain in several livestock species, but due to the complicated genetics and reproduction biology not yet in honey bees. Recently, 2 970 queens were genotyped to gather a reference population. For the application of genomic selection in honey bees, this study analyses the predictive ability and bias of pedigree-based and genomic breeding values for honey yield, three workability traits and two traits for resistance against the parasite Varroa destructor. For breeding value estimation, we use a honey bee-specific model with maternal and direct effects, to account for the contributions of the workers and the queen of a colony to the phenotypes. We conducted a validation for the last generation and a five-fold cross-validation. In the validation for the last generation, the predictive ability of pedigree-based estimated breeding values was 0.06 for honey yield, and ranged from 0.2 to 0.41 for the workability traits. The inclusion of genomic marker data improved these predictive abilities to 0.11 for honey yield, and a range from 0.22 to 0.44 for the workability traits. The inclusion of genomic data did not improve the predictive ability for the disease related traits. Traits with high heritability for maternal effects compared to the heritability for direct effects showed the most promising results. Across all traits, the bias with genomic methods was close to the bias with pedigree-based BLUP. The results show that genomic selection can successfully be applied to honey bees.