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Open Access Highly Accessed Methodology article

Multi-population genomic prediction using a multi-task Bayesian learning model

Liuhong Chen1*, Changxi Li13, Stephen Miller2 and Flavio Schenkel2

Author Affiliations

1 Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada

2 Department of Animal and Poultry Science, University of Guelph, Guelph, ON N1G 2W1, Canada

3 Agriculture and Agri-Food Canada, Lacombe Research Centre, 6000 C&E Trail, Lacombe, AB T4L 1W1, Canada

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BMC Genetics 2014, 15:53  doi:10.1186/1471-2156-15-53

Published: 3 May 2014

Abstract

Background

Genomic prediction in multiple populations can be viewed as a multi-task learning problem where tasks are to derive prediction equations for each population and multi-task learning property can be improved by sharing information across populations. The goal of this study was to develop a multi-task Bayesian learning model for multi-population genomic prediction with a strategy to effectively share information across populations. Simulation studies and real data from Holstein and Ayrshire dairy breeds with phenotypes on five milk production traits were used to evaluate the proposed multi-task Bayesian learning model and compare with a single-task model and a simple data pooling method.

Results

A multi-task Bayesian learning model was proposed for multi-population genomic prediction. Information was shared across populations through a common set of latent indicator variables while SNP effects were allowed to vary in different populations. Both simulation studies and real data analysis showed the effectiveness of the multi-task model in improving genomic prediction accuracy for the smaller Ayshire breed. Simulation studies suggested that the multi-task model was most effective when the number of QTL was small (n = 20), with an increase of accuracy by up to 0.09 when QTL effects were lowly correlated between two populations (ρ = 0.2), and up to 0.16 when QTL effects were highly correlated (ρ = 0.8). When QTL genotypes were included for training and validation, the improvements were 0.16 and 0.22, respectively, for scenarios of the low and high correlation of QTL effects between two populations. When the number of QTL was large (n = 200), improvement was small with a maximum of 0.02 when QTL genotypes were not included for genomic prediction. Reduction in accuracy was observed for the simple pooling method when the number of QTL was small and correlation of QTL effects between the two populations was low. For the real data, the multi-task model achieved an increase of accuracy between 0 and 0.07 in the Ayrshire validation set when 28,206 SNPs were used, while the simple data pooling method resulted in a reduction of accuracy for all traits except for protein percentage. When 246,668 SNPs were used, the accuracy achieved from the multi-task model increased by 0 to 0.03, while using the pooling method resulted in a reduction of accuracy by 0.01 to 0.09. In the Holstein population, the three methods had similar performance.

Conclusions

Results in this study suggest that the proposed multi-task Bayesian learning model for multi-population genomic prediction is effective and has the potential to improve the accuracy of genomic prediction.

Keywords:
Multi-task learning; Bayesian model; Multi-population; Genomic prediction; Stochastic search variable selection