Document Type : Research Paper
Authors
Department of Animal Science, Faculty of Agriculture, University of Shahid Bahonar, Kerman, Iran
Abstract
Keywords
Main Subjects
Extended Abstract
Introduction
Livestock production represents one of the most crucial economic sectors globally, with beef cattle farming holding particular importance for food security and rural development. Marbling, defined as the intramuscular fat distribution pattern in beef, has emerged as a critical quality indicator that determines both the economic value and consumer acceptance of beef products. This complex polygenic trait directly influences meat tenderness, juiciness, and flavor profile, making it a primary target for genetic improvement programs. Understanding the molecular mechanisms controlling marbling quality is essential for developing targeted breeding strategies that can enhance meat quality and improve the competitiveness of the beef industry.
Materials and Methods
Literature Search and Study Selection
The study employed a systematic meta-analytical approach to identify genomic regions significantly associated with marbling traits in beef cattle. A comprehensive literature search was conducted across major scientific databases including Web of Science, Scopus, and PubMed, focusing on publications from 2010 to 2025 that examined relationships between single nucleotide polymorphisms (SNPs) and marbling-related traits. Inclusion criteria encompassed original research articles reporting associations between SNPs and marbling traits with precise statistical data.
Genomic Interval Analysis and Meta-Analysis
The methodological framework involved systematic data extraction and standardization procedures to ensure compatibility across different studies. Key parameters including trait descriptions, SNP identifiers, chromosome numbers, genomic positions, sample sizes, candidate genes, and p-values were systematically extracted and standardized using Microsoft Excel. For studies presenting graphical data without direct numerical values, WebPlotDigitizer software (version 4.6) was employed for precise data extraction. Genomic positions were standardized to the UMD3.1 bovine reference genome assembly, trait nomenclatures were harmonized to prevent inconsistencies, and p-values were recalculated where necessary when reported as -log10(p-value) formats. Incomplete or non-standardizable data (such as cases with insufficient information about genomic positions or sample sizes) were excluded from analyses to maintain input data quality.
Standardization of Genomic Coordinates and Meta-Analysis Procedures
Genomic positions were standardized to the UMD3.1 bovine reference genome assembly, and SNPs located within 5000 kilobase distances were grouped into unified intervals. Meta-analytical procedures employed both Fisher’s method and Stouffer’s method to combine p-values within each interval. Gene network analysis was performed using the STRING database (version 12.0) with a focus on Bos taurus species, examining gene interactions with medium confidence thresholds. Manhattan plots were generated using R software to visualize the distribution of significant genomic regions.
Results
The meta-analytical approach demonstrated substantial advantages over individual studies in identifying genomic regions associated with marbling traits. Through integration of multiple datasets, the effective sample size increased significantly, resulting in enhanced statistical power and improved precision in quantitative trait loci (QTL) detection. The combined analysis successfully identified 17 significant genomic regions across 14 different chromosomes, with combined-log10(p-value) values (Stouffer’s method) ranging from 8.39 to 29.24.
The most prominent finding was the CADM1 gene on chromosome 15 with the highest significance level (-log10(p) = 29.24). Additionally, large clusters of immune system-related genes were identified on chromosomes 5 and 19, playing important roles in marbling regulation. Manhattan plot analysis revealed that the combined analysis showed dramatic differences compared to individual studies, with stronger peaks observed, particularly on chromosome 15. Chromosomes 2, 12, 17, 19, and 24 also presented significant peaks in the range of -log10(p) = 20-27.
Gene co-expression network analysis revealed sophisticated molecular mechanisms underlying marbling control. CLEC12A emerged as the primary hub gene of the network, with extensive direct interactions with numerous other genes. This gene, belonging to the C-type lectin family, functions as a central regulator in multiple biological pathways. CD69 was also identified as a secondary hub gene interacting with genes such as BCL6 and KLRG1. The network analysis demonstrated that genes are organized into three main functional clusters: lipid metabolism, cellular regulation, and transcriptional control.
Discussion
The identification of key candidate genes, particularly CADM1 on chromosome 15 with the highest significance level, represents a prime candidate for targeted breeding programs due to its role in cellular adhesion and metabolic processes. The identification of the CLEC gene family clusters provides concrete targets for genomic selection programs aimed at improving meat quality. The comprehensive gene network analysis provided fundamental insights into the biological pathways controlling intramuscular fat deposition, revealing mechanisms including adipogenesis pathways, inflammatory regulation, and metabolic coordination.
The practical implications of these findings extend to the development of molecular markers for targeted genomic selection, potentially enhancing meat quality while maintaining production efficiency. The identified genetic variants can be incorporated into breeding value estimation systems, enabling more accurate prediction of marbling potential in breeding animals. These results provide a set of candidate genes for use in breeding programs to improve marbling traits, offering possibilities for developing molecular markers that can improve meat quality and increase competitiveness of the meat industry.
Conclusions
This comprehensive meta-analysis successfully identified 17 significant genomic intervals associated with marbling traits in beef cattle, providing valuable insights into the genetic architecture underlying this economically important trait. The integration of multiple studies through meta-analytical approaches significantly enhanced the detection power for genomic regions that remained undetectable in individual studies due to statistical limitations.
The study’s limitations include the focus on specific cattle breeds and the reliance on available published data, which may introduce publication bias. Future research directions should incorporate whole-genome sequencing data and multi-omics approaches to provide more comprehensive understanding of the molecular mechanisms underlying marbling traits. Validation studies in diverse cattle populations and environments will be essential to confirm the universal applicability of these findings across different production systems.
Author Contributions
Ehsan Moazami: Data collection, Writing original draft of the manuscript, Data curation and organization, Data analysis, Investigation, and Methodology.
Ali Esmailizadeh: Conceptualization, Project administration, Supervision of all phases of the scientific work, Validation, and Review and Editing the manuscript.
Mohammad Reza Mohammadabadi: Supervision, Review and Editing the manuscript, Validation, and Contributing to better presentation of the scientific work.
Iman Moazemi: Data analysis assistance, Data acquisition and collection, Investigation, and Methodology support.
Data Availability Statement
Not applicable. This study used data published online and published articles, all of which are publicly available.
Ethical considerations
Not applicable. The study used data published online and in printed articles and did not involve any living organisms.
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