Effects of different weaning protocols on the differential gene expression profile of the skeletal muscle of Nelore cattle in semi-intensive finishing

• Grant number: 24/11117-0
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• Start date: September 01, 2024
• End date: December 31, 2025
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Principal Investigator: Guilherme Luis Pereira
• Grantee: Nicole da Silva Tucci
• Host Institution: Faculdade de Medicina Veterinária e Zootecnia (FMVZ). Universidade Estadual Paulista (UNESP). Campus de Botucatu. Botucatu , SP, Brazil
• Associated scholarship(s): 24/21522-0 - Characterization of the abundance of metabolic profiles in skeletal intramuscular fat related to dietary changes in early weaned Nellore calves., BE.EP.IC

Abstract

One of the largest producers and exporters of beef, Brazil has the world's largest commercial herd of beef cattle. Predominantly, its herd is composed of Nelore cattle, which, although well adapted to tropical climates, must compete with taurine cattle in certain international market niches. Additionally, the industry faces economic challenges related to land costs and competition with agriculture. In this context, to increase production efficiency, various nutritional management practices have been adopted by ranchers, such as supplementation during dry periods and finishing in intensive systems. Moreover, more specialized nutritional management practices aimed at improving herd reproductive indicators have also been adopted on some farms, particularly calf supplementation to reduce energy demands on cows, allowing them to regain good body condition and enter new estrous and pregnancy cycles. One example is early weaning, which aims to separate the calf from the cow at less than 150 days old, improving metrics related to pregnancy rates and calving intervals, especially in first-calf heifers. However, when weaning such young calves, it is necessary to ensure an adequate diet to meet their nutritional needs to prevent growth losses. Some studies have shown that depending on the type of supplementation and the amount administered during this period, there can be significant modulations in the calves' energy metabolism, resulting in faster growth and better carcass finish, as well as improved meat quality. Therefore, the objective of this study is to identify genes with differential expression in muscle tissue between groups of Nelore cattle in the finishing phase that were subjected to conventional and early weaning protocols. To achieve this, samples of the Longissimus thoracis muscle from 40 contemporary cow calves were obtained by biopsy 48 hours before slaughter, with eight muscle aliquots randomly selected from each group (early weaning and conventional weaning). Total RNA was extracted from these samples, and mRNA genomic libraries were constructed using the Illumina Stranded mRNA Prep kit, then sequenced with Illumina's NextSeq 550. To obtain transcriptome data, programs such as FastQC v.26, MultiQC v.1.13, STAR v.2.7.20, and featureCounts v.2.0.3 will be used for quality assessment of raw reads, mapping sequences to the reference genome (Bos taurus - ARS-UCD1.2), and obtaining the count matrix, respectively. Differentially expressed genes (DEGs) will be identified using the edgeR package in R. Functional enrichment of metabolic pathways and biological processes will be performed through over-representation analysis using R packages (clusterProfiler, enrichR, and enrichPlot). From the results of this project, we expect to gain a better understanding of how supplemented early weaning can affect gene expression levels in skeletal muscle and modulate metabolic pathways throughout the animal's life. Considering the Nelore breed, these results will be unprecedented in the international literature. Furthermore, the results can be associated with metabolome data in a partnership being established between FMVZ-Unesp and Purdue University, enhancing the findings and providing international experience opportunities for the student.