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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #422567
Research Project: Accelerating Genetic Improvement of Ruminants Through Enhanced Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: Comprehensive multi-omics analysis of regulatory variants for body weight in cattle

Author
item NIU, QUNHAO - Chinese Academy Of Agricultural Sciences
item WU, JIAYUAN - Chinese Academy Of Agricultural Sciences
item WU, TIANYI - Chinese Academy Of Agricultural Sciences
item ZHANG, TIANLIU - Chinese Academy Of Agricultural Sciences
item WANG, TIANZHE - Chinese Academy Of Agricultural Sciences
item XU, ZHENG - Chinese Academy Of Agricultural Sciences
item ZHAO, ZHIDA - Chinese Academy Of Agricultural Sciences
item XU, LING - University Of Hong Kong
item WANG, ZEZHAO - Chinese Academy Of Agricultural Sciences
item ZHU, BO - Chinese Academy Of Agricultural Sciences
item ZHANG, LUPEI - Chinese Academy Of Agricultural Sciences
item GAO, HUIJIANG - Chinese Academy Of Agricultural Sciences
item Liu, Ge
item LI, JUNYA - Chinese Academy Of Agricultural Sciences
item XU, LINGYANG - Chinese Academy Of Agricultural Sciences

Submitted to: Genomics, Proteomics and Bioinformatics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/4/2025
Publication Date: 8/18/2025
Citation: Niu, Q., Wu, J., Wu, T., Zhang, T., Wang, T., Xu, Z., Zhao, Z., Xu, L., Wang, Z., Zhu, B., Zhang, L., Gao, H., Liu, G., Li, J., Xu, L. 2025. Comprehensive multi-omics analysis of regulatory variants for body weight in cattle. Genomics, Proteomics and Bioinformatics. https://doi.org/10.1093/gpbjnl/qzaf067.
DOI: https://doi.org/10.1093/gpbjnl/qzaf067

Interpretive Summary: Progress in functional genome annotation has helped us understand how genes and regulatory elements affect traits in different species. This study examined tissue-specific epigenetic patterns in cattle, identifying regulatory elements linked to beef traits and selection. It highlights a genetic variant near ARPP19 that may help explain trait differences. This study will be valuable for farmers, scientists, and policymakers focused on enhancing animal health and production through genome-enabled selection.

Technical Abstract: Functional annotation of genomes has been extensively improved across farm animals, while elucidation of the organism-specific regulatory information is critical to understanding the phenotypes of interest in the authentic biological context. Here, we generated comprehensive epigenetic changes across major tissues and characterized the tissue specificity of DNA methylation, chromatin accessibility, and gene expression across five tissues in cattle. We found that tissue-specific epigenomic regulation plays a key role in the intricate regulation of gene expression, which may contribute to shaping unique biological functions. Moreover, we also identify several tissue-specific regulatory elements involving with selection sweeps between dairy and beef cattle. Our enrichment analysis exhibits the significant enrichment of genomic signals related to beef yield traits (e.g. GWAS, and eQTL) in tissue-specific regulatory elements such as open chromatin region (OCR) and hypomethylated region (HMR). Finally, we detect one eVariant (rs42286228) on BTA10 proximity to muscle-specific open chromatin region (OCR) may regulate ARPP19 expression by influencing the binding site of TFs (MEF2 family). Our study provides a valuable resource to improve the functional annotation across the bovine genome and lay a foundation for interpreting the potential regulatory mechanism of complex traits during the breed formation.