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Integrative Genomic and Metabolomic Analysis Identifies mQTLs Associated with Genetic Selection for Tenderness in Nellore Cattle

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Valim, Joao Marcos Bovetto de Campos ; Herreira, Vinicius Laerte Silva ; Gongora, Ana Laura dos Santos Munhoz ; Beltrao, Lauro Cesar Ferreira ; dos Santos, Eduardo Solano Pina ; de Oliveira, Brenda Santos ; Pugliesi, Guilherme ; Santana, Miguel Henrique de Almeida ; Polizel, Guilherme Henrique Gebim ; Colnago, Luiz Alberto ; Ocampos, Fernanda Maria Marins ; Ramirez-Zamudio, German Dario ; Silva, Saulo Luz ; Consolo, Nara Regina Brandao
Número total de Autores: 14
Tipo de documento: Artigo Científico
Fonte: METABOLITES; v. 15, n. 12, p. 16-pg., 2025-11-25.
Resumo

Background: Beef tenderness is a key quality attribute that significantly influences consumer satisfaction; however, it exhibits considerable variability due to both genetic and environmental factors. While genomic selection based on Expected Progeny Differences (EPDs) has improved the accuracy of predictions, a substantial portion of tenderness variability remains unexplained. Metabolomics has emerged as a valuable approach to address this gap, as metabolites reflect gene-environment interactions and may serve as biomarkers for complex traits such as meat tenderness. Objectives: This study aimed to integrate genomic and metabolomic data to identify genetic loci associated with serum metabolites in Nellore calves, offspring of sires with contrasting EPDs for meat tenderness. Methods: Ninety-five male calves were evaluated and divided into two groups according to the sires' genetic merit: FA-T (favorable EPD for tenderness, n = 45) and UN-T (unfavorable EPD for tenderness, n = 46). Blood serum samples were analyzed by 1H NMR spectroscopy to quantify 40 metabolites, and genotyping was performed using a medium-density SNP panel. Metabolite quantitative trait loci (mQTL) were identified using the MatrixEQTL package, and metabolic enrichment analysis was performed in MetaboAnalyst 6.0. Results: In the FA-T group, SNPs were associated with metabolites such as phenylalanine, tyrosine, and succinate, suggesting enhanced oxidative metabolism and preservation of proteolysis. In the UN-T group, associations of pyruvate, creatinine, and glutamine with distinct SNPs indicated greater reliance on anaerobic glycolysis and early ATP consumption, potentially impairing phosphorylation and postmortem proteolytic activity. Conclusions: These findings suggest that genetic selection for tenderness may induce early divergent metabolic profiles, likely leading to persistent differences in postmortem biochemical pathways, with important implications for meat tenderness. (AU)

Processo FAPESP: 25/00509-8 - Desenvolvimento e aplicações das espectroscopias de rmn e infravermelho na análise de insumos e produtos agrícolas
Beneficiário:Luiz Alberto Colnago
Modalidade de apoio: Auxílio à Pesquisa - Regular
Processo FAPESP: 22/16074-2 - Caracterização do metabótipo de bezerros Nelore ao nascimento e desmame progênie de touros com variação genética para maciez da carne
Beneficiário:Vinicius Laerte Silva Herreira
Modalidade de apoio: Bolsas no Brasil - Mestrado
Processo FAPESP: 20/08845-3 - Abordagem metabolômica para melhora da maciez da carne de bovinos Nelore: o conceito de metabotype e biomarcadores
Beneficiário:Nara Regina Brandão Cônsolo
Modalidade de apoio: Auxílio à Pesquisa - Jovens Pesquisadores
Processo FAPESP: 23/00661-9 - Abordagem integrômica de dados ômicos de machos Nelore progênie de touros com variação genética para maciez da carne.
Beneficiário:João Marcos Bovetto de Campos Valim
Modalidade de apoio: Bolsas no Brasil - Mestrado
Processo FAPESP: 23/11605-2 - Otimização de métodos de aquisição espectral de ressonância magnética nuclear para análise metabolômica de soro bovino: validação de processos
Beneficiário:Fernanda Maria Marins Ocampos
Modalidade de apoio: Bolsas no Brasil - Programa Fixação de Jovens Doutores