Genome regulation and gene interaction networks inferred from muscle transcriptome underlying feed efficiency in Pigs

Feed efficiency (FE) is a key trait in pig production, as it has both high economic and environmental impact. FE is a challenging phenotype to study, as it is complex and affected by many factors, such as metabolism, growth and activity level. Furthermore, testing for FE is expensive, as it requires costly equipment to measure feed intake of individual animals, making FE biomarkers valuable. Therefore, there has been a desire to find single nucleotide polymorphisms (SNPs) as biomarkers, to assist with improved selection and improve our biological understanding of FE. We have done a cis- and trans- eQTL (expressed quantitative trait loci) analysis, in a population of Danbred Durocs (N=11) and Danbred Landrace (N=27) using both a linear and Anova model. We used bootstrapping and enrichment analysis to validate and analyze our detected eQTLs. We identified 15 eQTLs with FDR < 0.01, affecting several genes found in previous studies of commercial pig breeds. Examples include IFI6, PRPF39, TMEM222, CSRNP1,PARK7 and MFF. The bootstrapping results showed statistically significant enrichment of eQTLs with p-value < 0.01 (p-value < 2.2x0-16) in both cis and trans-eQTLs. Based on this, enrichment analysis of top trans-eQTLs revealed high enrichment for gene categories and gene ontologies associated with genomic context and expression regulation. This includes transcription factors (p-value=1.0x10-13), DNA-binding (GO:0003677, p-value=8.9x10-14), DNA-binding transcription factor activity (GO:0003700,) nucleus gene (GO:0005634, p-value<2.2x10-16), positive regulation of expression (GO:0010628), negative regulation of expression (GO:0010629, p-value<2.2x10-16). These results would be useful for future genome assisted breeding of pigs to improve FE, and in the improved understanding of the functional mechanism of trans-eQTLs. RNA-seq was performed on 41 male uncastrated pigs (13 Danbred Duroc and 28 Danbred Landace). Muscle tissue from the psoas major muscle was collected imediatly post-slaughter at 100kg. Feed intake and growth of the pigs was measured during a testing period from ~28kg to ~100kg. Based on these measurements FCR and RFI was calculated for all pigs.