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

Victor Adriano Okstoft Carmelo, Haja N Kadarmideen

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Abstract

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 2.7x107 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
Original languageEnglish
Article numbere0239143
JournalPLOS ONE
Volume15
Issue number9
Number of pages18
ISSN1932-6203
DOIs
Publication statusPublished - 2020

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