Genetic variations (eQTLs) in muscle transcriptome and mitochondrial genes, and trans-eQTL molecular pathways in feed efficiency from Danish breeding pigs

Feed efficiency (FE) is a key trait in pig production, as improvement in FE has positive economic and environmental impact. FE is a complex phenotype and testing animals for FE is costly. Therefore, there has been a desire to find functionally relevant single nucleotide polymorphisms (SNPs) as bioma...

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Bibliographic Details
Published in:PloS one 2020-09, Vol.15 (9), p.e0239143-e0239143
Main Authors: Carmelo, Victor A. O, Kadarmideen, Haja N
Format: Article
Language:English
Subjects:
Animal husbandry
Applied mathematics
Binding
Bioinformatics
Biology and Life Sciences
Biomarkers
Breeding
Computer science
Deoxyribonucleic acid
DNA
Efficiency
Enrichment
Environmental impact
Feed conversion
Feed efficiency
Food and nutrition
Gene expression
Gene mapping
Gene regulation
Genes
Genetic aspects
Genetic diversity
Genetic variation
Genetics
Genomes
Genomics
Hogs
Identification and classification
Impact analysis
Linkage disequilibrium
Livestock breeding
Metabolism
Mitochondria
Muscles
Nucleotides
PARK7 protein
Phenotypes
Physical Sciences
Quality control
Quantitative trait loci
Research and Analysis Methods
Ribonucleic acid
RNA
Single-nucleotide polymorphism
Statistical analysis
Swine
Swine production
Transcription factors
Variance analysis
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Summary:Feed efficiency (FE) is a key trait in pig production, as improvement in FE has positive economic and environmental impact. FE is a complex phenotype and testing animals for FE is costly. Therefore, there has been a desire to find functionally relevant single nucleotide polymorphisms (SNPs) as biomarkers, to improve our biological understanding of FE as well as accuracy of genomic prediction for FE. We have performed a cis- and trans- eQTL (expression quantitative trait loci) analysis, in a population of Danbred Durocs (N = 11) and Danbred Landrace (N = 27) using both a linear and ANOVA model based on muscle tissue RNA-seq. We analyzed a total of 1425x19179 or 2.7x10.sup.7 Gene-SNP combinations in eQTL detection models for FE. The 1425 genes were from RNA-Seq based differential gene expression analyses using 25880 genes related to FE and additionally combined with mitochondrial genes. The 19179 SNPs were from applying stringent quality control and linkage disequilibrium filtering on genotype data using a GGP Porcine HD 70k SNP array. We applied 1000 fold bootstrapping and enrichment analysis to further validate and analyze our detected eQTLs. We identified 13 eQTLs with FDR < 0.1, affecting several genes found in previous studies of commercial pig breeds. Examples include MYO19, CPT1B, ACSL1, IER5L, CPT1A, SUCLA2, CSRNP1, PARK7 and MFF. The bootstrapping results showed statistically significant enrichment (p-value
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0239143