title: Genome-wide linkage analysis of global gene expression in loin muscle tissue identifies candidate genes in pigs.
abstract: BACKGROUND
  Nearly 6,000 QTL have been reported for 588 different traits in pigs, more than in any other livestock species. However, this effort has translated into only a few confirmed causative variants. A powerful strategy for revealing candidate genes involves expression QTL (eQTL) mapping, where the mRNA abundance of a set of transcripts is used as the response variable for a QTL scan.
  
  
  RESULTS
  We utilized a whole genome expression microarray and an F(2) pig resource population to conduct a global eQTL analysis in loin muscle tissue, and compared results to previously inferred phenotypic QTL (pQTL) from the same experimental cross. We found 62 unique eQTL (FDR <10%) and identified 3 gene networks enriched with genes subject to genetic control involved in lipid metabolism, DNA replication, and cell cycle regulation. We observed strong evidence of local regulation (40 out of 59 eQTL with known genomic position) and compared these eQTL to pQTL to help identify potential candidate genes. Among the interesting associations, we found aldo-keto reductase 7A2 (AKR7A2) and thioredoxin domain containing 12 (TXNDC12) eQTL that are part of a network associated with lipid metabolism and in turn overlap with pQTL regions for marbling, % intramuscular fat (% fat) and loin muscle area on Sus scrofa (SSC) chromosome 6. Additionally, we report 13 genomic regions with overlapping eQTL and pQTL involving 14 local eQTL.
  
  
  CONCLUSIONS
  Results of this analysis provide novel candidate genes for important complex pig phenotypes.
authors.affiliation: Department of Animal Science, Michigan State University, East Lansing, Michigan, United States of America.
authors.forename: Juan Pedro
authors.initials: JP
authors.lastname: Steibel
authors.forename: Ronald O
authors.initials: RO
authors.lastname: Bates
authors.forename: Guilherme J M
authors.initials: GJ
authors.lastname: Rosa
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Tempelman
authors.forename: Valencia D
authors.initials: VD
authors.lastname: Rilington
authors.forename: Ashok
authors.initials: A
authors.lastname: Ragavendran
authors.forename: Nancy E
authors.initials: NE
authors.lastname: Raney
authors.forename: Antonio Marcos
authors.initials: AM
authors.lastname: Ramos
authors.forename: Fernando F
authors.initials: FF
authors.lastname: Cardoso
authors.forename: David B
authors.initials: DB
authors.lastname: Edwards
authors.forename: Catherine W
authors.initials: CW
authors.lastname: Ernst
mesh_terms: D000818:Animals; D005260:Female; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks / Q000235:genetics; D008040:Genetic Linkage / Q000235:genetics*; D023281:Genomics; D006824:Hybridization, Genetic; D008297:Male; D009132:Muscles / Q000033:anatomy & histology* / Q000166:cytology / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D009841:Oligonucleotides / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D013552:Swine / Q000033:anatomy & histology* / Q000235:genetics*
chemical_list: D009841:Oligonucleotides; D012333:RNA, Messenger