Multi-omics approach to the effects of creep-feeding on chromatin accessibility and epigenetic regulation in the Longissimus thoracis muscle of Nelore cattle

• Grant number: 25/07716-9
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: September 01, 2025
• End date: July 31, 2027
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Animal Nutrition and Feeding
• Principal Investigator: Guilherme Luis Pereira
• Grantee: Gustavo Henrique Russo
• Host Institution: Faculdade de Medicina Veterinária e Zootecnia (FMVZ). Universidade Estadual Paulista (UNESP). Campus de Botucatu. Botucatu , SP, Brazil
• Associated research grant: 23/10842-0 - Effect of concentrate diet on epigenetic marks of Longissimus thoracis muscle tissue of Nellore cattle and their relationships with carcass aspects and meat quality, AP.R

Abstract

Brazil is the largest beef exporter in the world, with the Nelore cattle breed forming the backbone of its national herd due to its adaptation to tropical climates. However, the meat quality and growth rates of this breed remain below its genetic potential, primarily due to suboptimal nutritional practices. Studies indicate that Nelore beef has lower tenderness and marbling compared to taurine breeds, with these differences largely attributed to feeding management. Early nutritional interventions, such as creep-feeding (exclusive supplementation for nursing calves), have shown positive effects on muscle and adipose development, as well as modulation of epigenetic processes that may permanently impact meat quality. The main objective of this study is to evaluate the effects of creep-feeding on chromatin accessibility, DNA methylation, and gene expression in the Longissimus thoracis muscle of Nelore cattle, integrating multi-omics data to unravel the underlying epigenetic mechanisms. Specifically, we aim to identify differentially accessible chromatin regions (DACRs) between supplemented and non-supplemented animals, correlating them with methylation patterns and gene expression. Furthermore, we will prospect transcription factors and metabolic pathways associated with these changes, employing functional and integrative analyses to elucidate how early nutrition influences muscle development and meat quality. The experiment involved 40 Nelore calves divided into two groups: one receiving creep-feeding (CF) and the other only mineral salt (SCF) during the lactation phase. Post-weaning, all animals underwent intensive supplementation until slaughter. Muscle samples were collected at weaning and slaughter for ATAC-Seq (chromatin accessibility), RNA-Seq (gene expression), and RRBS (DNA methylation) analyses. ATAC-Seq libraries will be prepared using the Omni-ATAC protocol, sequenced on an Illumina platform, and analyzed with bioinformatic tools (e.g., MACS2, DiffBind) to identify DACRs. Data will be integrated via multi-omics analysis (DIABLO/sPLS-DA) to correlate chromatin accessibility, methylation, and gene expression, while functional enrichment analyses (GO, KEGG) will reveal impacted metabolic pathways. This approach will clarify how creep-feeding modulates epigenetic regulation throughout the animal's life, providing insights for nutritional strategies to enhance beef productivity and quality.