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

Abstract

Background: Leakage of water and ions and soluble proteins 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 capacity depends on numerous genetic 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 correlated expression to water holding capacity. Negatively correlated transcripts were enriched in functional categories and pathways like extracellular matrix receptor interaction and calcium signalling. Transcripts with positive correlation dominantly represented biochemical processes including oxidative phosphorylation, mitochondrial pathways, as well as transporter activity. 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 between 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 analysis for the trait of interest and for gene expression levels for creation of a priority list of genes out of the orchestra of genes of biological networks relevant to the liability to develop elevated drip loss.

Figure 1

Strategy of identification of candidate genes for WHC. Genes rated present after normalization were included in the statistical analysis. Both expression and phenotype data were adjusted using the general linear model before performing Pearson correlation analysis. Genes with trait correlated expression were included in the eQTL analysis. Genes with significant eQTL were assigned cis regulated if the genes' position matches the position of its eQTL, others were considered trans regulated. Also the position of the genes relative to QTL for drip was taken into account.

Figure 2

Histogram of the distribution of pair wise correlation coefficients of expression value and drip loss.

Figure 3

F-statistic of a total of 897 eQTL on all 18 porcine chromosomes. The horizontal lines represent the respective significance thresholds.

Figure 4

Histogram of the distribution of drip loss phenotypes among a subset of 74 animals of the DuPi population selected for chip hybridization.