title: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Research Institute for the Biology of Farm Animals (FBN), Research Group Functional Genomics, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany. s.wimmers@fbn-dummerstorf.de
authors.forename: Siriluck
authors.initials: S
authors.lastname: Ponsuksili
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Jonas
authors.forename: Eduard
authors.initials: E
authors.lastname: Murani
authors.forename: Chirawath
authors.initials: C
authors.lastname: Phatsara
authors.forename: Tiranun
authors.initials: T
authors.lastname: Srikanchai
authors.forename: Christina
authors.initials: C
authors.lastname: Walz
authors.forename: Manfred
authors.initials: M
authors.lastname: Schwerin
authors.forename: Karl
authors.initials: K
authors.lastname: Schellander
authors.forename: Klaus
authors.initials: K
authors.lastname: Wimmers
mesh_terms: D000818:Animals; D001834:Body Water / Q000502:physiology*; D005260:Female; D020869:Gene Expression Profiling; D008040:Genetic Linkage; D008297:Male; D008460:Meat; D018482:Muscle, Skeletal / Q000502:physiology*; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013552:Swine / Q000235:genetics