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.

肌内脂肪（Intramuscular Fat, IMF）与背膘厚度（Backfat Thickness, BFT）是影响肉质的重要经济性状。然而，内洛尔牛（Nellore cattle）上述性状背后的分子机制仍未得到明确阐释。本研究将包含DNA与RNA测序数据的填充型单核苷酸多态性（Single Nucleotide Polymorphism, SNP）芯片（共包含553,581个变异位点）、表达数量性状位点（expression quantitative trait loci, eQTL）定位、全基因组关联分析（genome-wide association study, GWAS）以及转座酶可及性染色质测序（assay for transposase accessible chromatin sequencing, ATAC-Seq）进行整合分析。我们首先鉴定出与目标性状相关的eQTL，随后预测潜在致因SNP在开放染色质区域的共定位情况，以筛选候选调控变异。本研究共鉴定得到51,324个eQTL，其中顺式eQTL（cis-eQTL）36,916个，反式eQTL（trans-eQTL）14,408个。其中3个eQTL与BFT相关，24个eQTL与IMF相关。对这27个eQTL所调控的基因进行功能富集分析，发现了免疫应答、细胞骨架重塑、铁转运以及磷脂代谢等关键通路。这些通路在脂质代谢与脂肪沉积过程中发挥基础性作用。其中6个eQTL与开放染色质区域重叠，进一步分析显示，4个eQTL共定位于预测的绝缘子及潜在CCCTC结合因子（CCCTC-binding factor）结合位点，1个eQTL定位于活性增强子区域。本研究结果为肌内脂肪与背膘厚度的转录调控机制提供了全新见解，揭示了潜在的调控变异位点。