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Open Access Research article

Identification of expression QTL (eQTL) of genes expressed in porcine M. longissimus dorsi and associated with meat quality traits

Siriluck Ponsuksili1, Eduard Murani2, Manfred Schwerin1, Karl Schellander3 and Klaus Wimmers2*

Author Affiliations

1 Leibniz Institute for Farm Animal Biology, Research Group Functional Genome Analysis, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany

2 Leibniz Institute for Farm Animal Biology, Research Unit Molecular Biology, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany

3 Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany

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BMC Genomics 2010, 11:572  doi:10.1186/1471-2164-11-572

Published: 16 October 2010

Abstract

Background

Genetic analysis of transcriptional profiles is a promising approach for identifying and dissecting the genetics of complex traits like meat performance. Accordingly, expression levels obtained by microarray analysis were taken as phenotypes in a linkage analysis to map eQTL. Moreover, expression levels were correlated with traits related to meat quality and principle components with high loadings of these traits. By using an up-to-date annotation and localization of the respective probe-sets, the integration of eQTL mapping data and information of trait correlated expression finally served to point to candidate genes for meat quality traits.

Results

Genome-wide transcriptional profiles of M. longissimus dorsi RNAs samples of 74 F2 animals of a pig resource population revealed 11,457 probe-sets representing genes expressed in the muscle. Linkage analysis of expression levels of these probe-sets provided 9,180 eQTL at the suggestive significance threshold of LOD > 2. We mapped 653 eQTL on the same chromosome as the corresponding gene and these were designated as 'putative cis-eQTL'. In order to link eQTL to the traits of interest, probe-sets were addressed with relative transcript abundances that showed correlation with meat quality traits at p ≤ 0.05. Out of the 653 'putative cis-eQTL', 262 transcripts were correlated with at least one meat quality trait. Furthermore, association of expression levels with composite traits with high loadings for meat quality traits generated by principle component analysis were taken into account leading to a list of 85 genes exhibiting cis-eQTL and trait dependent expression.

Conclusion

Holistic expression profiling was integrated with QTL analysis for meat quality traits. Correlations between transcript abundance and meat quality traits, combined with genetic positional information of eQTL allowed us to prioritise candidate genes for further study.