Study identifies molecular markers related to meat quality in Nelore cattle

By combining different techniques, researchers at São Paulo State University in Brazil have revealed biological pathways related to tenderness, fat deposition, and other relevant characteristics of the meat of the predominant cattle breed in Brazil. The results could optimize strategies to enhance product quality and bolster the competitiveness of Brazilian livestock farming.

By André Julião  |  Agência FAPESP – Researchers at São Paulo State University (UNESP) in Brazil have identified a robust set of genetic markers associated with meat quality in the Nelore cattle breed (Bos taurus indicus) genome. The results pave the way for substantial progress in the genetic enhancement of the Zebu breed, which accounts for about 80% of the Brazilian beef herd. The research has direct implications for the productivity and quality of Brazilian beef, reinforcing the country’s standing as a major beef exporter. The results were published in the journal Scientific Reports.

In previous studies, the group had identified genes and proteins by studying meat and carcass characteristics separately using different techniques. For the current study, however, the researchers integrated these techniques and examined multiple characteristics using data from 6,910 young Nelore bulls from four commercial genetic improvement programs.

Because the biological material was collected immediately after slaughter, a comprehensive and detailed assessment of characteristics directly influencing meat quality was possible.

“The group had already made significant progress using different ‘omics’ [genomics, transcriptomics, and proteomics] approaches, but it became increasingly clear that no single technique is sufficient to understand the complexity of the biological systems that control variation in meat and carcass quality,” says Gabriela Frezarim, first author of the study. She conducted the study during her PhD at the Faculty of Agricultural and Veterinary Sciences (FCAV) at UNESP in Jaboticabal.

“By integrating these omics techniques, we were able to elucidate not only the isolated genes but also the biological networks involved in the variation of certain animal phenotypes,” adds the researcher, who was supervised by Lucia Galvão de Albuquerque, a professor at FCAV-UNESP. 

Albuquerque is coordinating the project “Genetic aspects of quality, efficiency, and sustainability of meat production in Nelore cattle”, which is supported by FAPESP. Some of the work was conducted during a previous project, which was also funded by the Foundation (read more at: agencia.fapesp.br/28157).

Largest exporter in the world

The results of the current study provide researchers with a series of accurate molecular data that can be used by the productive sector in the future to select animals that produce higher-quality meat and carcasses with a higher commercial yield.

Brazil leads the world in meat exports with 2.89 million tons in 2024. However, the Nelore zebu is known for having meat that is less tender than that of taurine breeds, such as the European Angus (Bos taurus taurus).

In recent years, other research groups have made progress in developing chips that can identify genetic variations associated with characteristics that are of interest for selecting Nelore cattle (read more at: revistapesquisa.fapesp.br/en/cattle-genes/). 

The present study goes further by investigating not only isolated genes, but also complex molecular networks related to extreme performance (high and low) in meat quality traits. The study emphasizes genes and metabolic pathways that explain the differences between individuals. These findings expand the possibilities for genetic selection.

“When working at the DNA level, there’s no guarantee that a particular variation in the genome will necessarily result in the production of a specific RNA or protein because there are complex biological processes involved in these stages that aren’t yet fully understood. Our study seeks to understand these pathways and identify the molecular basis of meat and carcass characteristic expression,” explains Larissa Fonseca, co-supervisor of the study. She is a postdoctoral researcher at FCAV-UNESP and a FAPESP scholarship recipient.

From muscle to meat

“Understanding the molecular mechanisms that influence meat and carcass quality is essential to explaining the phenotypic variability observed in Nelore cattle. The study offers an integrated view of the biological pathways involved in these characteristics and identifies genes and proteins that directly affect tenderness, marbling, and subcutaneous fat thickness,” says Lúcio Mota, another co-author of the study who is conducting postdoctoral research at FCAV-UNESP with a scholarship from FAPESP.

The researcher explains that this approach provides clear molecular bases for the phenotypic differences observed between animals, allowing for more precise selection strategies in genetic improvement.

For example, the researchers found that genes associated with growth, cell cycle regulation, and heat shock proteins are directly linked to meat tenderness.

These proteins maintain muscle structure and control fiber degradation after slaughter, which directly impacts meat tenderness. The expression levels of these genes and proteins differ between cattle, which helps explain why some Nelore cattle have more tender meat, as they favor a more efficient breakdown of muscle fibers after slaughter.

Another conclusion was that genes, transcripts, and proteins involved in organizing the cytoskeleton (the structure that maintains cell shape) and in programmed cell death (apoptosis) directly influence muscle development and consequently the loin eye area (LEA). LEA is an international measure that indicates muscle mass and carcass yield.

Regarding marbling, the intramuscular fat responsible for the flavor and juiciness of meat, proteins related to fatty acid synthesis and composition were identified, along with proteins involved in actin binding and microtubule formation, which are essential for various cellular functions. These findings suggest that the regulation of these proteins may directly impact intramuscular fat deposition, thereby influencing the sensory quality of meat.

Finally, genes associated with the regulation of energy metabolism and muscle tissue remodeling were identified as important for subcutaneous fat thickness, which is a relevant measure of carcass quality.

“This is an initial study, but it provides important guidelines for genetic improvement programs and the development of more effective selection strategies in Nelore cattle for meat and carcass traits,” says Albuquerque.

The researchers now plan to expand their analyses to achieve an even higher level of accuracy. This could allow them to more accurately select animals that will directly improve the quality of Brazilian beef.

The article “Multi-omics integration identifies molecular markers and biological pathways for carcass and meat quality traits in Nellore cattle” can be read at: www.nature.com/articles/s41598-025-93714-x.

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