Integrated GWAS and Pathway profiling for feed efficiency traits in pigs leads to novel genes and their molecular pathways

Publikation: Bidrag til bog/antologi/rapport/proceedingKonferenceabstrakt i proceedingsForskning

  • Duy Ngoc Do, Animal Genetics, Bioinformatics and Breeding, Danmark
  • Tage Ostersen, 2Danish Agriculture & Food Council, Pig Research Centre, Danmark
  • Anders Bjerring Strathe, Animal Genetics, Bioinformatics and Breeding, Danmark
  • Just Jensen
  • Thomas Mark, Animal Genetics, Bioinformatics and Breeding, Danmark
  • Haja Kadarmideen, 2012 Genetik og Bioinformatik, Danmark
Genome wide association studies (GWAS) are being extensively used in revealing genetic architecture of complex traits. However, GWAS offer limited understanding of the biological role of significant single nucleotide polymorphisms (SNPs) affecting complex traits. Pathway analysis using GWAS results is an important step where we firstly detect genes located near GWAS-detected SNPs and subsequently we detect enrichment of these genes in various biological processes and pathways. The objective of this study was to apply these steps to identify relevant pathways involved in residual feed intake (RFI) in pigs. Residual feed intake is a feed efficiency measure and is highly economically important in animal production. In our study, a total of 596 Yorkshire boars had phenotypic and genotypic records. After quality control, 37,915 SNPs were available for GWAS which was implemented in the DMU software package. Genome wide association analysis detected 3,450 SNPs (P < 0.05) significantly associated with this trait. Using the R-NCBI2R package, 7,169 nearby genes were found in 0.5 Mb flanking the SNP positions for all 3,450 SNPs. Among them, 2,934 genes were functionally recognized in pigs and were used as input in Database for Annotation, Visualization and Integrated Discovery (DAVID). Neuroactive ligand-receptor interaction, SNARE interactions in vesicular transport, pyruvate metabolism and Wnt signaling pathway were detected by using KEGG tools, growth hormone and phospholipase C signaling pathway were detected by using BioCarta pathway analysis tools and asynaptic_vesicle_trafficking and thyrotropin-releasing hormone receptor signaling pathways were identified by using Panther-pathway profiling tools. Several of these pathways such as Wnt, growth hormone and thyrotropin-releasing hormone receptor signaling pathway are known to be involved in biological processes closely related to regulation of feed intake or residual feed intake. These results provide insights into the genetic architecture as well as the systems biological mechanisms of this complex trait in pigs.
OriginalsprogEngelsk
TitelAbstract Book
Antal sider1
Udgivelsesår30 aug. 2013
Sider157
StatusUdgivet - 30 aug. 2013
Begivenhed14th International Conference on Systems Biology - Tivoli Congress Center, Copenhagen, Danmark
Varighed: 30 aug. 20133 sep. 2013
Konferencens nummer: 14

Konference

Konference14th International Conference on Systems Biology
Nummer14
LokationTivoli Congress Center
LandDanmark
ByCopenhagen
Periode30/08/201303/09/2013

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