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A genetical genomics approach reveals new candidates and confirms known candidate genes for drip loss in a porcine resource population

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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.

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Acknowledgments

Authors are grateful to Prof. Dr. med. Markus M. Nöthen from the Institute of Human Genetics, University of Bonn, for genotyping the samples with an Illumina 60K Porcine SNP Chip. This work was part of the DRIP phase II (Genetic-functional background of the water-holding capacity in pork) project and supported by the German Research Foundation (DFG), Germany (Grant No. SCHE562/13-1).

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Authors and Affiliations

  1. Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany

    Hanna Heidt, Mehmet Ulas Cinar, Muhammad Jasim Uddin, Christian Looft, Heinz Jüngst, Dawit Tesfaye, Ernst Tholen, Karl Schellander & Christine Große-Brinkhaus

  2. Department of Animal Science, Faculty of Agriculture, Erciyes University, 38039, Kayseri, Turkey

    Mehmet Ulas Cinar

  3. Institute of Molecular Psychiatry, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany

    Astrid Becker & Andreas Zimmer

  4. Research Group Functional Genomics, Research Institute for the Biology of Farm Animals (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany

    Siriluck Ponsuksili

  5. Research Unit Molecular Biology, Research Institute for the Biology of Farm Animals (FBN), Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany

    Klaus Wimmers

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  1. Hanna Heidt
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Correspondence to Christine Große-Brinkhaus.

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Heidt, H., Cinar, M.U., Uddin, M.J. et al. A genetical genomics approach reveals new candidates and confirms known candidate genes for drip loss in a porcine resource population. Mamm Genome 24, 416–426 (2013). https://doi.org/10.1007/s00335-013-9473-z

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