Genomic breeding value prediction and QTL mapping of QTLMAS2011 data using Bayesian and GBLUP methods.
BACKGROUND
The goal of this study was to apply Bayesian and GBLUP methods to predict genomic breeding values (GEBV), map QTL positions and explore the genetic architecture of the trait simulated for the 15th QTL-MAS workshop.


METHODS
Three methods with models considering dominance and epistasis inheritances were used to fit the data: (i) BayesB with a proportion π = 0.995 of SNPs assumed to have no effect, (ii) BayesCπ, where π is considered as unknown, and (iii) GBLUP, which directly fits animal genetic effects using a genomic relationship matrix.


RESULTS
BayesB, BayesCπ and GBLUP with various fitted models detected 6, 5, and 4 out of 8 simulated QTL, respectively. All five additive QTL were detected by Bayesian methods. When two QTL were in either coupling or repulsion phase, GBLUP only detected one of them and missed the other. In addition, GBLUP yielded more false positives. One imprinted QTL was detected by BayesB and GBLUP despite that only additive gene action was assumed. This QTL was missed by BayesCπ. None of the methods found two simulated additive-by-additive epistatic QTL. Variance components estimation correctly detected no evidence for dominance gene-action. Bayesian methods predicted additive genetic merit more accurately than GBLUP, and similar accuracies were observed between BayesB and BayesCπ.


CONCLUSIONS
Bayesian methods and GBLUP mapped QTL to similar chromosome regions but Bayesian methods gave fewer false positives. Bayesian methods can be superior to GBLUP in GEBV prediction when genomic architecture is unknown.
Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, USA.
Jian
J
Zeng
Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poznan, Poland.|Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, Lelystad, The Netherlands.
Marcin
M
Pszczola
Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, USA.|Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poznan, Poland.
Anna
A
Wolc
Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poznan, Poland.
Tomasz
T
Strabel
Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, USA.
Rohan L
RL
Fernando
Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, USA.
Dorian J
DJ
Garrick
Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, USA.
Jack Cm
JC
Dekkers