Open Access Open Badges Methodology article

Rapid screening for phenotype-genotype associations by linear transformations of genomic evaluations

Jose L Gualdrón Duarte1, Rodolfo JC Cantet1, Ronald O Bates2, Catherine W Ernst2, Nancy E Raney2 and Juan P Steibel23*

Author Affiliations

1 Departamento de Producción Animal, Facultad de Agronomía, UBA-CONICET, Buenos Aires, Argentina

2 Department of Animal Science, Michigan State University, East Lansing, MI, USA

3 Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA

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BMC Bioinformatics 2014, 15:246  doi:10.1186/1471-2105-15-246

Published: 19 July 2014



Currently, association studies are analysed using statistical mixed models, with marker effects estimated by a linear transformation of genomic breeding values. The variances of marker effects are needed when performing the tests of association. However, approaches used to estimate the parameters rely on a prior variance or on a constant estimate of the additive variance. Alternatively, we propose a standardized test of association using the variance of each marker effect, which generally differ among each other. Random breeding values from a mixed model including fixed effects and a genomic covariance matrix are linearly transformed to estimate the marker effects.


The standardized test was neither conservative nor liberal with respect to type I error rate (false-positives), compared to a similar test using Predictor Error Variance, a method that was too conservative. Furthermore, genomic predictions are solved efficiently by the procedure, and the p-values are virtually identical to those calculated from tests for one marker effect at a time. Moreover, the standardized test reduces computing time and memory requirements.

The following steps are used to locate genome segments displaying strong association. The marker with the highest − log(p-value) in each chromosome is selected, and the segment is expanded one Mb upstream and one Mb downstream of the marker. A genomic matrix is calculated using the information from those markers only, which is used as the variance-covariance of the segment effects in a model that also includes fixed effects and random genomic breeding values. The likelihood ratio is then calculated to test for the effect in every chromosome against a reduced model with fixed effects and genomic breeding values. In a case study with pigs, a significant segment from chromosome 6 explained 11% of total genetic variance.


The standardized test of marker effects using their own variance helps in detecting specific genomic regions involved in the additive variance, and in reducing false positives. Moreover, genome scanning of candidate segments can be used in meta-analyses of genome-wide association studies, as it enables the detection of specific genome regions that affect an economically relevant trait when using multiple populations.

Genome wide association; Marker variance; Pig genotype