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

Siriluck Ponsuksili,Karl Schellander,Eduard Murani,Klaus Wimmers,Manfred Schwerin

doi:10.1186/1471-2164-11-572

Siriluck Ponsuksili, Karl Schellander + Show 3 more

Open Access

https://doi.org/10.1186/1471-2164-11-572

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Abstract

BackgroundGenetic 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.ResultsGenome-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.ConclusionHolistic 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.

Highlights

Genetic analysis of transcriptional profiles is a promising approach for identifying and dissecting the genetics of complex traits like meat performance
We have previously reported on the identification of expression QTL (eQTL) of genes showing expression levels correlated with waterholding capacity of meat measured as drip loss [5]
We focus on eQTL of genes whose expression at slaughter is significantly correlated to technological meat quality traits addressed in commercial pig breeding schemes

Summary

Introduction

Genetic analysis of transcriptional profiles is a promising approach for identifying and dissecting the genetics of complex traits like meat performance. 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 served to point to candidate genes for meat quality traits. Genetical genomics as a new approach which combines gene-expression data and marker genotypes in a segregating population, offers great perspectives to make a major contribution to the dissection of complex traits [1,2]. We expand and up-dated the analysis towards global eQTL mapping of transcripts showing variable abundance in porcine muscle and using annotation and localisation data of Affymetrix microarray probe-sets based on the current porcine sequence information [6]. We focus on eQTL of genes whose expression at slaughter is significantly correlated to technological meat quality traits addressed in commercial pig breeding schemes. Taking into account own observations on the reliability of eQTL mapping we highlight eQTL located on the same chromosome as the corresponding genes themselves [7]

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