Putative epigenetic regulation mechanisms related to production, carcass and beef quality traits in Nelore cattle

Juliana Afonso^1,2Woo Jun Shim^2,3Tainã Figueiredo Cardoso¹Jennifer Bruscadin⁴Andressa Oliveira De Lima⁵Wellison J. S. Diniz⁶Ingrid Soares Garcia⁷Wei Liang Andre Tan²Priscila SN de Oliveira¹Aline Silva Mello Cesar⁸Gerson Barreto Mourao⁷Adhemar Zerlotini⁹Luiz Lehmann Coutinho¹⁰Marina Rufino Salinas Fortes²Luciana Regitano^1*

• ¹Animal Biotechnology Laboratory. Embrapa Pecuária Sudeste, São Carlos, Brazil
• ²School of Chemistry and Molecular Biosciences, Faculty of Science, The University of Queensland, Brisbane, Queensland, Australia
• ³Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
• ⁴Federal University of São Carlos, São Carlos, São Paulo, Brazil
• ⁵Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, United States
• ⁶Department of Animal Sciences, College of Agriculture, Auburn University, Auburn, Alabama, United States
• ⁷Department of Animal Science, Faculty of Animal Science and Food Engineering, University of São Paulo, São Paulo, São Paulo, Brazil
• ⁸Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Sao Paulo, Brazil
• ⁹EMBRAPA Agricultural Informatics, Campinas, São Paulo, Brazil
• ¹⁰Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Sao Paulo, Brazil

Understanding regulatory mechanisms like epigenetics can help improve beef production, carcass, and meat quality. Epigenetic states are dynamic and shaped by the environment, but due to limited studies and costly detection methods, alternative approaches are needed. Our aim was to identify candidate regulators linked to production, carcass and beef quality traits by describing genes putatively regulated by epigenetic mechanisms in the muscle of Nelore cattle. We in-silico identified discordantly regulated genes (DRGs) with the TRIAGE method and rank product analysis, using gene expression. We identified 51 DRGs across the traits and provided evidence of their regulatory status. We investigated the DRGs for being known bovine transcription factors (TFs) or co-factors (TcoFs) and tested the association of SNPs harbouring the DRGs with the traits. 26 DRGs are known bovine TFs. A SNP upstream of the PITX2 DRG was associated with conjugated linoleic acid (CLA), 35 SNPs within or around the BTNL9 DRG were associated with backfat thickness (BFT) and 13 of the DRGs showed a regulatory impact over at least one trait. Using public muscle ATAC-Seq and ChIP-Seq data, we found that the associated SNPs were harboured in open chromatin sections of the genome and/or on histone modification regions. The correlations identified among DRGs, differentially expressed genes and traits showed intricate relationships with various TFs andTcoFs, revealing the putative relationships of these elements with the traits. The LBX1 and HOXC10 genes are candidates with evidence to be regulators of the traits, while also being subjected to epigenetic regulation.