An integrative transcriptome analysis indicates regulatory mRNA-miRNA networks for residual feed intake in Nelore cattle

Abstract

Residual Feed Intake (RFI) is an economically relevant trait in beef cattle. Among the molecular regulatory mechanisms, microRNAs (miRNAs) are an important dimension in post-transcriptional regulation and have been associated with different biological pathways. Here, we performed differential miRNAs expression and weighted gene co-expression network analyses (WGCNA) to better understand the complex interactions between miRNAs and mRNAs expressed in bovine skeletal muscle and liver. MiRNA and mRNA expression data were obtained from Nelore steers that were genetically divergent for RFI (N = 10 [low RFI or feed efficient]; N = 10 [high RFI or feed inefficient]). Differentially expressed and hub miRNAs such as bta-miR-486, bta-miR-7, bta-miR15a, bta-miR-21, bta-miR 29, bta- miR-30b, bta-miR-106b, bta-miR-199a-3p, bta-miR-204, and bta-miR 296 may have a potential role in variation of RFI. Functional enrichment analysis of differentially expressed (DE) miRNA’s target genes and miRNA–mRNA correlated modules revealed that insulin, lipid, immune system, oxidative stress and muscle development signaling pathways might potentially be involved in RFI in this population. Our study identified DE miRNAs, miRNA - mRNA regulatory networks and hub miRNAs related to RFI. These findings suggest a possible role of miRNAs in regulation of RFI, providing new insights into the potential molecular mechanisms that control feed efficiency in Nelore cattle.

Potential Biomarkers for Feed Efficiency-Related Traits in Nelore Cattle Identified by Co-expression Network and Integrative Genomics Analyses

“…In Nelore cattle, it was recently described that efficient animals seem to have a greater adaptation capacity to oxidative stress, demanding less energy expenditure than inefficient animals (Fonseca et al, 2019). Oxidative stress was previously associated with feed efficiency in our experimental population (Tizioto et al, 2015(Tizioto et al, , 2016de Oliveira et al, 2018), with genes related to oxidative stress over-represented in inefficient animals (Tizioto et al, 2016).…”

“…The role of the immune system-related biological processes in feed efficiency in Nelore cattle was previously reported by Alexandre et al (2015), who found the immune response over-represented in inefficient Nelore as an outcome of increased liver injury. Accordingly, different immune response processes were associated with feed efficiency in steers from the same population studied here (de Oliveira et al, 2018). FIGURE 6 | The integrative data network of the hub genes identified in the present study with data from previous functional studies.…”

“…Further, these studies have not evaluated the impact of gene interactions. Integrative approaches, such as systems biology methods, have been proposed to dissect complex phenotypes and overcome the limitations of single-data-type analysis (Alexandre et al, 2015;Weber et al, 2016;de Oliveira et al, 2018;Diniz et al, 2019;Fonseca et al, 2019). Among the integration approaches, grouping thousands of genes through co-expression networks analysis reduces the high-dimensionality of data and focuses on the relationship between a few modules (e.g., gene/transcript clusters) and the traits of interest (Langfelder and Horvath, 2008).…”

Differential expression of miRNAs in skeletal muscles of Indian sheep with diverse carcass and muscle traits

“…The down-regulated miR-486, in our study, is known to promote differentiation of myoblasts via PI3K/AKT signaling 41 and has been reported to show higher expression during muscle differentiation 42 . However, it was also observed to be down-regulated in cattle 43 and pig 7 . MiR-133a/b on the other hand promotes both proliferation and differentiation via MAPK1/MAPK3 signaling 44 .…”

“…It has been acknowledged as an oncomiR that represses a number of genes of the apoptotic pathway 65 . It was also identified as one of the hub miRNA related to feed efficiency in Nellore cattle 43 . The PI3K signaling regulates not only growth and proliferation but also angiogenesis, cell survival and apoptosis.…”