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This article is part of the supplement: Proceedings of the 14th European workshop on QTL mapping and marker assisted selection (QTL-MAS)

Open Access Proceedings

Comparison of analyses of the QTLMAS XIV common dataset. I: genomic selection

Marcin Pszczola123, Tomasz Strabel1, Anna Wolc14, Sebastian Mucha1 and Maciej Szydlowski1*

Author Affiliations

1 Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland

2 Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, 8200 AB Lelystad, The Netherlands

3 Animal Breeding and Genomics Centre, Wageningen Institute of Animal Sciences Wageningen University, 6700 AH Wageningen, The Netherlands

4 Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, IA 50011-3150, USA

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BMC Proceedings 2011, 5(Suppl 3):S1  doi:10.1186/1753-6561-5-S3-S1

Published: 27 May 2011

Abstract

Background

For the XIV QTLMAS workshop, a dataset for traits with complex genetic architecture has been simulated and released for analyses by participants. One of the tasks was to estimate direct genomic values for individuals without phenotypes. The aim of this paper was to compare results of different approaches used by the participants to calculate direct genomic values for quantitative trait (QT) and binary trait (BT).

Results

Participants applied 26 approaches for QT and 15 approaches for BT. Accuracy for QT was between 0.26 and 0.89 for males and between 0.31 and 0.89 for females, and for BT ranged from 0.27 to 0.85. For QT, percentage of lost response to selection varied from 8% to 83%, whereas for BT the loss was between 15% and 71%.

Conclusions

Bayesian model averaging methods predicted breeding values slightly better than GBLUP in a simulated data set. The methods utilizing genomic information performed better than traditional pedigree based BLUP analyses. Bivariate analyses was slightly advantageous over single trait for the same method. None of the methods estimated the non-additivity of QTL affecting the QT, which may be one of the constrains in accuracy observed in real data.