Identification of eQTLs and differential gene expression associated with fetal programming in beef cattle

Abstract

This study assessed differential gene expression and identified expression quantitative trait loci (eQTLs) from samples of Longissimus lumborum muscle from bulls at 15 months of age submitted to different prenatal nutrition. Upon confirmation of pregnancy, 126 dams were separated into three diet treatments varying the period of inclusion of energy protein supplementation (NP, PP, and FP). At calving, 63 males were genotyped with GGP LD BeadChip. The skeletal muscle of 15 bulls was sequenced (RNA-seq) at 15 months of age. The EdgeR package was used for differential gene expression and principal component analysis (PCA), and the Matrix eQTL package was used for the eQTLs analysis (R statistical). The functional enrichment analysis was performed using the MetaCore® software. No genes differentially expressed were found between treatments (FDR > 0.05); nevertheless, we found 179 cis-tag-eQTLs and 20,762 trans-tag-eQTLs (FDR < 0.05) after linkage disequilibrium analysis. The functional enrichment analysis identified terms from gene ontology related to genes associated to trans-eQTLs (FDR < 0.05) as well as metabolic pathways (> gScore). Most biological pathways and genes found had been previously associated to fetal programming. The different prenatal supplementation strategies did not impact on muscle transcriptome of bulls. Additionally, there is a link between genotype and gene expression levels related to developmental traits in Nellore cattle.

Keywords: Nellore; Prenatal nutrition; SNPs; Trans-eQTLs; Transcriptome; WNT family genes.