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Genome-wide linkage analysis of global gene expression in loin muscle tissue identifies candidate genes in pigs

Steibel, Juan Pedro ; Bates, Ronald O ; Rosa, Guilherme J M ; Tempelman, Robert J ; Rilington, Valencia D ; Ragavendran, Ashok ; Raney, Nancy E ; Ramos, Antonio Marcos ; Cardoso, Fernando F ; Edwards, David B ; Ernst, Catherine W Roberts, Roland

PloS one, 2011-02, Vol.6 (2), p.e16766-e16766 [Periódico revisado por pares]

United States: Public Library of Science

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Título:
Genome-wide linkage analysis of global gene expression in loin muscle tissue identifies candidate genes in pigs
Autor: Steibel, Juan Pedro ; Bates, Ronald O ; Rosa, Guilherme J M ; Tempelman, Robert J ; Rilington, Valencia D ; Ragavendran, Ashok ; Raney, Nancy E ; Ramos, Antonio Marcos ; Cardoso, Fernando F ; Edwards, David B ; Ernst, Catherine W
Roberts, Roland
Assuntos: Aldo-keto reductase ; Animal sciences ; Animals ; Biology ; Cell cycle ; Chromosome 6 ; Chromosomes ; Deoxyribonucleic acid ; DNA ; DNA biosynthesis ; DNA microarrays ; DNA repair ; DNA replication ; Endoplasmic reticulum ; Female ; Gene expression ; Gene Expression Profiling ; Gene mapping ; Gene Regulatory Networks - genetics ; Genes ; Genetic aspects ; Genetic control ; Genetic Linkage - genetics ; Genomes ; Genomics ; Hogs ; Hybridization, Genetic ; Linkage analysis ; Lipid metabolism ; Livestock ; Male ; Metabolism ; Muscles - anatomy & histology ; Muscles - cytology ; Muscles - metabolism ; Oligonucleotide Array Sequence Analysis ; Oligonucleotides - genetics ; Pigs ; Proteins ; Quantitative genetics ; Quantitative trait loci ; Quantitative Trait Loci - genetics ; RNA ; RNA, Messenger - genetics ; Swine ; Swine - anatomy & histology ; Swine - genetics ; Thioredoxin ; Thioredoxins ; Zoology
É parte de: PloS one, 2011-02, Vol.6 (2), p.e16766-e16766
Notas: ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
Conceived and designed the experiments: CWE JPS ROB GJMR RJT FFC. Performed the experiments: VDR NER AMR DBE. Analyzed the data: JPS CWE AR. Wrote the paper: JPS CWE.
Descrição: Nearly 6,000 QTL have been reported for 588 different traits in pigs, more than in any other livestock species. However, this effort has translated into only a few confirmed causative variants. A powerful strategy for revealing candidate genes involves expression QTL (eQTL) mapping, where the mRNA abundance of a set of transcripts is used as the response variable for a QTL scan. We utilized a whole genome expression microarray and an F(2) pig resource population to conduct a global eQTL analysis in loin muscle tissue, and compared results to previously inferred phenotypic QTL (pQTL) from the same experimental cross. We found 62 unique eQTL (FDR <10%) and identified 3 gene networks enriched with genes subject to genetic control involved in lipid metabolism, DNA replication, and cell cycle regulation. We observed strong evidence of local regulation (40 out of 59 eQTL with known genomic position) and compared these eQTL to pQTL to help identify potential candidate genes. Among the interesting associations, we found aldo-keto reductase 7A2 (AKR7A2) and thioredoxin domain containing 12 (TXNDC12) eQTL that are part of a network associated with lipid metabolism and in turn overlap with pQTL regions for marbling, % intramuscular fat (% fat) and loin muscle area on Sus scrofa (SSC) chromosome 6. Additionally, we report 13 genomic regions with overlapping eQTL and pQTL involving 14 local eQTL. Results of this analysis provide novel candidate genes for important complex pig phenotypes.
Editor: United States: Public Library of Science
Idioma: Inglês

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Genome-wide linkage analysis of global gene expression in loin muscle tissue identifies candidate genes in pigs

Steibel, Juan Pedro ; Bates, Ronald O ; Rosa, Guilherme J M ; Tempelman, Robert J ; Rilington, Valencia D ; Ragavendran, Ashok ; Raney, Nancy E ; Ramos, Antonio Marcos ; Cardoso, Fernando F ; Edwards, David B ; Ernst, Catherine W Roberts, Roland

United States: Public Library of Science

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