Genomic prediction using subsampling.
BACKGROUND
Genome-wide assisted selection is a critical tool for the genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each round of a Markov Chain Monte Carlo. We evaluated the effect of subsampling bootstrap on prediction and computational parameters.


RESULTS
Across datasets, we observed an optimal subsampling proportion of observations around 50% with replacement, and around 33% without replacement. Subsampling provided a substantial decrease in computation time, reducing the time to fit the model by half. On average, losses on predictive properties imposed by subsampling were negligible, usually below 1%. For each dataset, an optimal subsampling point that improves prediction properties was observed, but the improvements were also negligible.


CONCLUSIONS
Combining subsampling with Gibbs sampling is an interesting ensemble algorithm. The investigation indicates that the subsampling bootstrap Markov chain algorithm substantially reduces computational burden associated with model fitting, and it may slightly enhance prediction properties.
Department of Agronomy, Purdue University, 915 W. State St., Lilly Hall, West Lafayette, IN, 47907, USA.
Alencar
A
Xavier
Department of Plant Science, University of California, 3134 Batchelor Hall, Riverside, CA, 92521, USA.
Shizhong
S
Xu
Department of Animal Science, Purdue University, 915 W. State St., Lilly Hall, West Lafayette, IN, 47907, USA.
William
W
Muir
Department of Agronomy, Purdue University, 915 W. State St., Lilly Hall, West Lafayette, IN, 47907, USA. krainey@purdue.edu.
Katy Martin
KM
Rainey
D000818:Animals; D001499:Bayes Theorem; D055106:Genome-Wide Association Study / Q000379:methods*; D023281:Genomics / Q000379:methods*; D006801:Humans; D012494:Sampling Studies
Bayesian analysis; Bootstrapping; Genome-wide selection