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In this study lean meat water-holding capacity (WHC) of a Duroc × Pietrain (DuPi) resource populations withcorresponding genotypes and transcriptomes were investigated using the approaches of genetical genomics.WHC was characterized by drip loss measured in M. long. dorsi. Genotypes of 169 F2 DuPi animals wereidentified by the 60k Illumina SNP chips. Whole genome tanscriptomes of muscle were available for 132F2 animals using the 24k Affymetrix expression microarray. Performing genome wide associations studies(GWAS) of transcriptional profiles which are correlated with phenotypes allows elucidating cis- and trans-regulation. Expression levels of 1,228 genes were significantly correlated with drip loss and were furtheranalyzed for enrichment of functional annotation groups as defined by gene ontology and KEGG pathways.A hyper geometric gene set enrichment test was performed and revealed glycolysis/glyconeogenesis, pentosephosphate pathway and pyruvat metabolism as most promising pathways. For 267 selected transcripts eQTLanalysis was performed and revealed 78,576 significant (Paccordance of the gene underlying transcript and the eQTL location it was possible to identify 59 eQTL thatcan be assumed to be cis-regulated. Comparing the results of gene set enrichment and the eQTL detectiontests molecular networks and potential candidate genes which seem to play key roles in the expression ofwater holding capacity were detected. One gene was the glucose-6-phosphate transporter SLC37A4 whichwas assumed to be cis-regulated and involved in the glucose metabolic process. This approach supports toidentify trait-associated SNPs and to understand the biology of complex traits.