Analysis of merged transcriptomic and genomic datasets to identify genes and pathways underlying residual feed intake in growing pigs
Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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Analysis of merged transcriptomic and genomic datasets to identify genes and pathways underlying residual feed intake in growing pigs. / Ibragimov, Emil; Pedersen, Anni Øyan; Xiao, Liang; Cirera, Susanna; Fredholm, Merete; Karlskov-Mortensen, Peter.
I: Scientific Reports, Bind 12, 21946, 2022.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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TY - JOUR
T1 - Analysis of merged transcriptomic and genomic datasets to identify genes and pathways underlying residual feed intake in growing pigs
AU - Ibragimov, Emil
AU - Pedersen, Anni Øyan
AU - Xiao, Liang
AU - Cirera, Susanna
AU - Fredholm, Merete
AU - Karlskov-Mortensen, Peter
N1 - Publisher Copyright: © 2022, The Author(s).
PY - 2022
Y1 - 2022
N2 - Improvement of feed efficiency (FE) in pigs is an important milestone in order to reduce the economic and environmental impact of pig production. The goal of finding biomarkers for FE has persisted for decades. However, due to the complexity of the FE trait, these goals have still not been met. Here, we search for quantitative trait loci (QTL), candidate genes, and biological pathways associated with FE using both genotype and RNA-seq data. We obtained genotype and colon epithelium RNA-seq data for 375 and 96 pigs, respectively. In total, a genome-wide association study (GWAS) and differential expression (DE) analysis led to detection of three QTL on SSC9 and 17 DE-genes associated with FE. Possible intersection points between genes located in QTL and DE-genes were found on levels of transcription factor-target interaction. Moreover, cis-eQTL analysis revealed associations between genotype and expression levels of three DE-genes and three genes located in the GWAS QTLs, which may establish the connection between genotype and phenotype through DE. Finally, single nucleotide polymorphism calling using RNA-seq data for genes located in GWAS QTLs revealed 53 polymorphisms of which eleven were missense variants.
AB - Improvement of feed efficiency (FE) in pigs is an important milestone in order to reduce the economic and environmental impact of pig production. The goal of finding biomarkers for FE has persisted for decades. However, due to the complexity of the FE trait, these goals have still not been met. Here, we search for quantitative trait loci (QTL), candidate genes, and biological pathways associated with FE using both genotype and RNA-seq data. We obtained genotype and colon epithelium RNA-seq data for 375 and 96 pigs, respectively. In total, a genome-wide association study (GWAS) and differential expression (DE) analysis led to detection of three QTL on SSC9 and 17 DE-genes associated with FE. Possible intersection points between genes located in QTL and DE-genes were found on levels of transcription factor-target interaction. Moreover, cis-eQTL analysis revealed associations between genotype and expression levels of three DE-genes and three genes located in the GWAS QTLs, which may establish the connection between genotype and phenotype through DE. Finally, single nucleotide polymorphism calling using RNA-seq data for genes located in GWAS QTLs revealed 53 polymorphisms of which eleven were missense variants.
U2 - 10.1038/s41598-022-26496-1
DO - 10.1038/s41598-022-26496-1
M3 - Journal article
C2 - 36536008
AN - SCOPUS:85144327269
VL - 12
JO - Scientific Reports
JF - Scientific Reports
SN - 2045-2322
M1 - 21946
ER -
ID: 330900972