Identification of Expression Quantitative Trait Loci (eQTL) for Adipose-Specific Regulatory Mechanisms in Hanwoo (Korean Cattle)

TL;DR

This study identifies genetic variants that regulate fat accumulation in Hanwoo cattle, offering insights for improving beef quality through precision breeding.

Contribution

The study identifies key eQTLs and regulatory hotspots specific to adipose tissue in Hanwoo cattle, revealing novel molecular targets for beef quality improvement.

Findings

A total of 5362 unique top cis-eQTL pairs were identified, including genes involved in muscle development and fat accumulation.

Three major cis-regulatory hotspots and 12 trans-eQTL hotspots were identified, with SNP 21:17035557 acting as a shared cis- and trans-regulatory hub.

Functional enrichment analyses highlighted cytoskeleton- and calcium-dependent pathways in adipose regulation.

Abstract

Improving beef quality in Hanwoo cattle requires a comprehensive understanding of the genetic regulation of fat accumulation in adipose tissue. In this study, we performed expression quantitative trait loci (eQTL) analysis using RNA-Seq data from backfat tissue of Hanwoo steers to identify regulatory variants influencing gene expression. We identified 5362 significant cis-eQTLs, including key genes associated with muscle development and fat accumulation. Several genomic loci were found to act as regulatory hotspots, controlling the expression of multiple genes. Notably, a variant at chromosome 21:17035557 emerged as a major hub where both cis- and trans-regulatory signals converge. These findings provide valuable insights into the regulatory architecture of adipose tissue in Hanwoo and offer molecular targets for precision breeding strategies aimed at enhancing meat quality.

Understanding the genetic regulatory mechanisms of fat accumulation is crucial for improving beef quality. Hanwoo (Korean native cattle) is renowned for its high intramuscular fat (marbling), yet the genetic regulation of adipose gene expression remains insufficiently understood. In this study, we performed expression quantitative trait loci (eQTL) analysis using RNA-Seq data and genotype data from backfat tissue of 75 Hanwoo steers to identify regulatory variants associated with adipose deposition. A total of 25,042 significant cis-eQTL associations (FDR < 0.05) were identified, and 5362 unique top cis-eQTL pairs were retained after gene-wise filtering. Key cis-regulated genes included AGBL1, CACNG1, MYO18B, and DUSP29, which are involved in cytoskeletal organization, muscle development and calcium signaling. Three major cis-regulatory hotspots were located on BTA15 (BTA15:50354741) and BTA21 (BTA21:21526143, and BTA21:21541921). Permutation-based analysis (100,000 iterations) was conducted to control false positives, identifying 12 statistically significant trans-eQTL hotspots (FDR q < 0.05), of which SNP 6:60512276 and SNP 21:17035557 exhibited extensive trans-regulatory activity influencing 429 and 161 genes, respectively. In particular, SNP 21:17035557 acted as a shared cis- and trans-regulatory hub, indicating hierarchical control of adipose gene networks. Functional enrichment analyses revealed significant involvement of cytoskeleton- and calcium-dependent pathways, highlighting the interplay between structural remodeling and metabolic regulation in adipose tissue. These findings provide a comprehensive, system-level view of adipose gene regulation in Hanwoo cattle and highlight candidate molecular targets for genome-assisted and precision breeding. Moreover, this study offers quantitative genomic resources that can support the development of prediction models and decision-support systems for improving carcass traits in Hanwoo breeding programs.

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