Novel putative causal mutations associated with fat traits in Nellore cattle uncovered by eQTLs located in open chromatin regions
Intramuscular fat (IMF) and backfat thickness (BFT), are important economic traits, impacting meat quality. However, the molecular mechanisms underlying these traits have still not been conclusively explored in Nellore cattle. Herein, we integrated an imputed SNP panel formed by DNA and RNA-sequencing data with 553,581 variants, expression quantitative trait loci (eQTLs) mapping, genome-wide association (GWAS) and assay for transposase accessible chromatin sequencing (ATAC-Seq). We first identified eQTLs associated with the traits, and then predicted colocalization of putative causal SNPs in open chromatin regions to refine the candidates' regulatory variants. We found a total of 51,324 eQTLs, being 36,916 cis-eQTLs and 14,408 trans-eQTLs. Three eQTLs were associated with BFT and 24 with IMF. Functional enrichment analysis of genes regulated by these 27 eQTLs revealed interesting pathways, such as immune response, cytoskeleton remodeling, iron transport, and phospholipid metabolism. These pathways can play a fundamental role in lipid metabolism and fat deposition. Six eQTLs overlapped with open chromatin regions, from these, four are colocalized in regions predicted to be insulators and possible CCCTC-binding factor binding sites, and one in active enhancer. Our results provided novel insights into the regulation at a transcriptional level of IMF and BTF, unraveling putative regulatory variants.