Trait correlated expression combined with expression QTL analysis reveals biological pathways and candidate genes affecting water holding capacity of muscle

BACKGROUND: Leakage of water and ions and soluble pr oteins from muscle cells occurs during prolonged exercise due to ischemia causing muscle damage. Also post mortem anoxia during conversion of muscle to meat is marked by loss of water and soluble components from the muscle cell. There is considerable variation in the water holding capacity of meat affecting economy of meat production. Water holding capa city depends on numerous geneti c and environmental factors relevant to structural and biochemical muscle fibre properties a well as ante and post slaughter metabolic processes. RESULTS: Expression microarray analysis of M. longissimus dorsi RNAs of 74 F2 animals of a resource population showed 1,279 transcripts with trait co rrelated expression to water holding capacity. Negatively correlated transcript s were enriched in functional categories an d pathways like extracellular matrix receptor interaction an d calcium signalling. Transcripts with positive correlation dominantly represented biochemical processes including oxid ative phosphorylation, mitochondrial pathways, as well as transporter a ctivity. A linkage analysis of abundance of trait correlated transcripts revealed 897 expression QTL (eQTL) with 104 eQTL coinciding with QTL regions for water holding capacity; 96 transcripts had trans acting and 8 had cis acting regulation. CONCLUSION: The complex relationships betw een biological processes taking place in live skeletal muscle and meat quality are driven on the one hand by the energy reserves and their utilisation in the muscle and on the other hand by the muscle structure itself and calcium signalling. Holistic expression profiling was integrated with QTL an alysis for the trait of interest and for gene expression levels for crea tion of a priority list of genes out of the orchestra of genes of biological networks relevant to the liability to develo p elevated drip loss