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

Heidt, Hanna, Cinar, Mehmet Ulas, Uddin, Muhammad Jasim, Looft, Christian, Juengst, Heinz, Tesfaye, Dawit, Becker, Astrid, Zimmer, Andreas, Ponsuksili, Siriluck, Wimmers, Klaus, Tholen, Ernst, Schellander, Karl and Grosse-Brinkhaus, Christine (2013) A genetical genomics approach reveals new candidates and confirms known candidate genes for drip loss in a porcine resource population. Mammalian Genome, 24 9-10: 416-426. doi:10.1007/s00335-013-9473-z


Author Heidt, Hanna
Cinar, Mehmet Ulas
Uddin, Muhammad Jasim
Looft, Christian
Juengst, Heinz
Tesfaye, Dawit
Becker, Astrid
Zimmer, Andreas
Ponsuksili, Siriluck
Wimmers, Klaus
Tholen, Ernst
Schellander, Karl
Grosse-Brinkhaus, Christine
Title A genetical genomics approach reveals new candidates and confirms known candidate genes for drip loss in a porcine resource population
Journal name Mammalian Genome   Check publisher's open access policy
ISSN 0938-8990
1432-1777
Publication date 2013-10-01
Year available 2001
Sub-type Article (original research)
DOI 10.1007/s00335-013-9473-z
Volume 24
Issue 9-10
Start page 416
End page 426
Total pages 11
Place of publication New York, NY, United States
Publisher Springer
Language eng
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.
Keyword Water-Holding Capacity
Meat Quality Traits
Quantitative Trait
Glucose-6-Phosphate Transport
Pietrain Population
Postmortem Muscle
Skeletal-Muscle
Qtl Analysis
Igf2 Locus
Expression
Q-Index Code C1
Q-Index Status Provisional Code
Grant ID SCHE562/13-1
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
School of Veterinary Science Publications
 
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