Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Research article

Extension of the bayesian alphabet for genomic selection

David Habier1*, Rohan L Fernando1, Kadir Kizilkaya12 and Dorian J Garrick23

Author Affiliations

1 Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, IA 50011, USA

2 Department of Animal Science, Adnan Menderes University, Aydin 09100, Turkey

3 Institute of Veterinary, Animal & Biomedical Science, Massey University, Palmerston North, New Zealand

For all author emails, please log on.

BMC Bioinformatics 2011, 12:186  doi:10.1186/1471-2105-12-186

Published: 23 May 2011

Abstract

Background

Two Bayesian methods, BayesCπ and BayesDπ, were developed for genomic prediction to address the drawback of BayesA and BayesB regarding the impact of prior hyperparameters and treat the prior probability π that a SNP has zero effect as unknown. The methods were compared in terms of inference of the number of QTL and accuracy of genomic estimated breeding values (GEBVs), using simulated scenarios and real data from North American Holstein bulls.

Results

Estimates of π from BayesCπ, in contrast to BayesDπ, were sensitive to the number of simulated QTL and training data size, and provide information about genetic architecture. Milk yield and fat yield have QTL with larger effects than protein yield and somatic cell score. The drawback of BayesA and BayesB did not impair the accuracy of GEBVs. Accuracies of alternative Bayesian methods were similar. BayesA was a good choice for GEBV with the real data. Computing time was shorter for BayesCπ than for BayesDπ, and longest for our implementation of BayesA.

Conclusions

Collectively, accounting for computing effort, uncertainty as to the number of QTL (which affects the GEBV accuracy of alternative methods), and fundamental interest in the number of QTL underlying quantitative traits, we believe that BayesCπ has merit for routine applications.