Comparison between Bayesc and GBLUP in Estimating Genomic Breeding Values under Different QTL Variance Distributions

Shirali, Masoud; Miraei-Ashtiani, Seyed Reza; Pakdel, Abbas; Haley, Chris; Pong-Wong, Ricardo

doi:10.22059/ijas.2012.28534

Comparison between Bayesc and GBLUP in Estimating Genomic Breeding Values under Different QTL Variance Distributions

Authors

Masoud Shirali

Seyed Reza Miraei-Ashtiani

Abbas Pakdel

Chris Haley

Ricardo Pong-Wong

10.22059/ijas.2012.28534

Abstract

A genome consisted of 1000 biallelic single nucleotide polymorphisems (SNPs) on one chromosome with 100 CM length was simulated and different QTL variance distributions (Uniform, Normal and Gamma) and various numbers of QTL (5, 10 and 20) were considered as simulation assumptions and consecutively 9 various traits were generated. The comparison between GEBVs obtained from BayesC and GBLUP showed that GEBVs and true breeding values were largely correlated (r > 0.80) in training population for all traits. Comparing accuracies of GEBVs showed that both BayesC and GBLUP methods performed similarly, except in traits with 5 QTLs BayesC performed significantly better (P < 0.05). The accuracies of estimations using BayesC indicated that this method performed better under scenarios with low number of QTL and gamma variance distribution in trait of interest. However, GBLUP presented accurate estimations in all traits; and number of QTL and QTL variance distributions had no impact on accuracies of GBLUP estimations. These results can be due to assumed genetics model in trait of interest in each method.

Keywords

BayesC

Breeding value

GBLUP

Number of QTL

QTL variance distribution