Exploring genome, transcriptome, and microbiome interactions related to feed efficiency and methane emissions in Bos indicus through multi-omics network analysis.

The minor effects of many SNP interactions often determine complex traits. This interaction, known as epistasis, represents a non-additive genetic effect in which the influence of one variant depends on the presence of others. In this study, we tested for epistatic effects on the residual feed intake (RFI) and residual methane emission (RME) traits of Nelore cattle. Additionally, we evaluated the impact of these interactions in other omics layers (i.e., microorganism profiles in the rumen content and feces and mRNA and miRNA expression in the rumen wall). The genomic interaction modules identified 14 and 10 significant SNP-SNP modules associated with RME and RFI traits, respectively. The majority of these SNPs were located in intronic and intergenic regions. The top pathways and processes associated with the SNP-SNP modules were identified, with several pathways related to the immune system and actin cytoskeleton organization. Furthermore, many other omics data were correlated with these SNP-SNP modules. Our findings suggest that the immune response and cilium organization may play important roles in feed efficiency. These insights not only provide novel candidates for enhancing these traits through microbiota composition and transcriptional regulation but also underscore the power of network analysis in uncovering new functional interactions. This research provides new insights and highlights candidate features for improving cattle feed efficiency and methane emissions.