title: A genetical genomics approach reveals new candidates and confirms known candidate genes for drip loss in a porcine resource population.
abstract: In this study lean meat water-holding capacity (WHC) of a Duroc × Pietrain (DuPi) resource population with corresponding genotypes and transcriptomes was investigated using genetical genomics. WHC was characterized by drip loss measured in M. longissimus dorsi. The 60K Illumina SNP chips identified genotypes of 169 F2 DuPi animals. Whole-genome transcriptomes of muscle samples were available for 132 F2 animals using the Affymetrix 24K GeneChip® Porcine Genome Array. Performing genome-wide association studies of transcriptional profiles, which are correlated with phenotypes, allows elucidation of cis- and trans-regulation. Expression levels of 1,228 genes were significantly correlated with drip loss and were further analyzed for enrichment of functional annotation groups as defined by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways. A hypergeometric gene set enrichment test was performed and revealed glycolysis/glyconeogenesis, pentose phosphate pathway, and pyruvate metabolism as the most promising pathways. For 267 selected transcripts, expression quantitative trait loci (eQTL) analysis was performed and revealed a total of 1,541 significant associations. Because of positional accordance of the gene underlying transcript and the eQTL location, it was possible to identify eight eQTL that can be assumed to be cis-regulated. Comparing the results of gene set enrichment and the eQTL detection tests, molecular networks and potential candidate genes, which seemed to play key roles in the expression of WHC, were detected. The α-1-microglobulin/bikunin precursor (AMBP) gene was assumed to be cis-regulated and was part of the glycolysis pathway. This approach supports the identification of trait-associated SNPs and the further biological understanding of complex traits.
authors.affiliation: Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany.
authors.forename: Hanna
authors.initials: H
authors.lastname: Heidt
authors.forename: Mehmet Ulas
authors.initials: MU
authors.lastname: Cinar
authors.forename: Muhammad Jasim
authors.initials: MJ
authors.lastname: Uddin
authors.forename: Christian
authors.initials: C
authors.lastname: Looft
authors.forename: Heinz
authors.initials: H
authors.lastname: Jüngst
authors.forename: Dawit
authors.initials: D
authors.lastname: Tesfaye
authors.forename: Astrid
authors.initials: A
authors.lastname: Becker
authors.forename: Andreas
authors.initials: A
authors.lastname: Zimmer
authors.forename: Siriluck
authors.initials: S
authors.lastname: Ponsuksili
authors.forename: Klaus
authors.initials: K
authors.lastname: Wimmers
authors.forename: Ernst
authors.initials: E
authors.lastname: Tholen
authors.forename: Karl
authors.initials: K
authors.lastname: Schellander
authors.forename: Christine
authors.initials: C
authors.lastname: Große-Brinkhaus
mesh_terms: D000510:Alpha-Globulins / Q000235:genetics / Q000378:metabolism; D000818:Animals; D003890:Desiccation; D063427:Food Quality; D055106:Genome-Wide Association Study; D008460:Meat; D053858:Metabolic Networks and Pathways; D018482:Muscle, Skeletal / Q000378:metabolism*; D010641:Phenotype; D040641:Quantitative Trait Loci; D034421:Sus scrofa / Q000235:genetics; D059467:Transcriptome; D014867:Water / Q000378:metabolism*
chemical_list: D000510:Alpha-Globulins; D014867:Water
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