PSVII-7 Putative epigenetic regulating fatty acids content in muscle of Nelore cattle

• Published in: Journal of animal science 2024-09, Vol.102 (Supplement_3), p.446-447
• Main Authors: Afonso, Juliana, Cardoso, Tainã Figueiredo, Bruscadin, Jennifer Jéssica, de Lima, Andressa Oliveira, Da Diniz, Wellison Jarles Silva, Mourao, Gerson Barreto, Cesar, Aline Silve Mello, Zerlotini, Adhemar, Coutinho, Luiz Lehmann, Fortes, Marina R S, de Regitano, Luciana Correia Almeida
• Format: Article
• Language: English
• ISSN: 0021-8812; 1525-3163
• DOI: 10.1093/jas/skae234.505

Fatty acid (FA) content has a significant role in the quality and nutritional composition of beef. However, genetic and epigenetic mechanisms governing FA content in beef are not fully understood. Therefore, we identified putative regulatory genes potentially modulating FA content in Nelore cattle muscle that are also being epigenetically repressed. These genes are called discordantly regulated genes (DRGs). We used genome-wide expression data from muscle samples of Nelore steers, which were selected based on contrasting levels of five specific fatty acids. Our study cohort comprised 15 muscle samples per contrasting group, sourced from an experimental breeding herd, born between 2009 and 2011 and assayed on feedlot at the Brazilian Agricultural Research Corporation (EMBRAPA/Brazil). These animals were sired by 34 unrelated bulls representing prominent genealogies prevalent in Brazil during that period. We identified 48 unique DRGs associated with the content of at least one FA. There were 24 DRGs for conjugated linoleic acid (CLA), 32 for oleic acid (OA), 26 for palmitic acid (PA), 22 for eicosapentaenoic acid (EPA) and 22 for docosahexaenoic acid (DHA). These DRGs have crucial roles in developmental and differentiation processes, aligning with expectations for genes under epigenetic regulation. Notably, 10 DRGs were identified as common regulators across all five FAs (COMP, HOXC10, LBX1, PAX7, PITX2, SIM2, SOX17, TBX15, TBX3 and ZIC4); five DRGs were previously published differentially expressed genes for CLA, 25 were annotated as known bovine transcription factors and one as a known bovine transcription cofactor, further supporting their regulatory potential. To investigate genetic variants associated with epigenetically regulated genomic regions linked to FA traits, we conducted association tests with SNPs proximal to the transcription start sites (TSS) of DRGs. For that we considered a window of 10 kb for each side, and the previously published genetic estimated breeding value for the fatty acids in the study. We identified a significant SNP, rs110498194, associated with CLA (FDR < 0.05). This SNP is within an intron of the PITX2 gene, located 7,537 bp downstream of its TSS. PITX2 is a DRG for all five FA and is a known bovine transcription factor. To validate the presence of epigenetic elements within the genomic region associated with CLA, we examined two bovine muscle samples from the FAANG project using the UCSC Genome Browser. We identified ATAC-