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

Publikation: KonferencebidragPosterForskning

Standard

Integrated GWAS and Pathway profiling for feed efficiency traits in pigs leads to novel genes and their molecular pathways. / Do, Duy Ngoc; Ostersen, Tage; Strathe, Anders Bjerring; Jensen, Just; Mark, Thomas; Kadarmideen, Haja.

2013. Poster session præsenteret ved 14th International Conference on Systems Biology , Copenhagen, Danmark.

Publikation: KonferencebidragPosterForskning

Harvard

Do, DN, Ostersen, T, Strathe, AB, Jensen, J, Mark, T & Kadarmideen, H 2013, 'Integrated GWAS and Pathway profiling for feed efficiency traits in pigs leads to novel genes and their molecular pathways', 14th International Conference on Systems Biology , Copenhagen, Danmark, 30/08/2013 - 03/09/2013.

APA

Do, D. N., Ostersen, T., Strathe, A. B., Jensen, J., Mark, T., & Kadarmideen, H. (2013). Integrated GWAS and Pathway profiling for feed efficiency traits in pigs leads to novel genes and their molecular pathways. Poster session præsenteret ved 14th International Conference on Systems Biology , Copenhagen, Danmark.

CBE

Do DN, Ostersen T, Strathe AB, Jensen J, Mark T, Kadarmideen H. 2013. Integrated GWAS and Pathway profiling for feed efficiency traits in pigs leads to novel genes and their molecular pathways. Poster session præsenteret ved 14th International Conference on Systems Biology , Copenhagen, Danmark.

MLA

Do, Duy Ngoc o.a.. Integrated GWAS and Pathway profiling for feed efficiency traits in pigs leads to novel genes and their molecular pathways. 14th International Conference on Systems Biology , 30 aug. 2013, Copenhagen, Danmark, Poster, 2013. 1 s.

Vancouver

Do DN, Ostersen T, Strathe AB, Jensen J, Mark T, Kadarmideen H. Integrated GWAS and Pathway profiling for feed efficiency traits in pigs leads to novel genes and their molecular pathways. 2013. Poster session præsenteret ved 14th International Conference on Systems Biology , Copenhagen, Danmark.

Author

Do, Duy Ngoc ; Ostersen, Tage ; Strathe, Anders Bjerring ; Jensen, Just ; Mark, Thomas ; Kadarmideen, Haja. / Integrated GWAS and Pathway profiling for feed efficiency traits in pigs leads to novel genes and their molecular pathways. Poster session præsenteret ved 14th International Conference on Systems Biology , Copenhagen, Danmark.1 s.

Bibtex

@conference{2765e88ee7b644869a746e33556b20eb,
title = "Integrated GWAS and Pathway profiling for feed efficiency traits in pigs leads to novel genes and their molecular pathways",
abstract = "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.",
author = "Do, {Duy Ngoc} and Tage Ostersen and Strathe, {Anders Bjerring} and Just Jensen and Thomas Mark and Haja Kadarmideen",
note = "Poster Session 1, Poster no. 42; 14th International Conference on Systems Biology , ICBS ; Conference date: 30-08-2013 Through 03-09-2013",
year = "2013",
month = "8",
day = "30",
language = "English",

}

RIS

TY - CONF

T1 - Integrated GWAS and Pathway profiling for feed efficiency traits in pigs leads to novel genes and their molecular pathways

AU - Do, Duy Ngoc

AU - Ostersen, Tage

AU - Strathe, Anders Bjerring

AU - Jensen, Just

AU - Mark, Thomas

AU - Kadarmideen, Haja

N1 - Poster Session 1, Poster no. 42

PY - 2013/8/30

Y1 - 2013/8/30

N2 - 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.

AB - 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.

M3 - Poster

ER -