Potential candidate genes influencing meat production phenotypic traits in sheep: a review

Abstract

This review examines the genetic basis of meat production phenotypic traits in sheep, addressing the challenge of enhancing carcass and meat quality to meet global demand. The article identifies key potential genes associated with vertebral traits, body size, muscle development, and fat deposition across diverse sheep breeds worldwide. Through comprehensive analysis of recent literature (2018–2025), the study synthesizes findings from genome-wide association studies, candidate gene approaches, and transcriptomic analyses. Specific potential genes like VRTN, NR6A1, MSTN, ADIPOQ, LCORL, MEF2B, FASN, FABP4, SCD, DGAT1, BMP and HOX family genes demonstrate significant associations with economically valuable traits. The potential genes influencing meat production phenotypic traits (intramuscular fat contents, growth, vertebral traits and body size traits) have been highlighted in this review. This comprehensive genetic marker catalog serves as a critical resource repository for implementing marker-assisted selection programs, providing breeders and researchers with validated genetic targets to accelerate breeding efficiency and enhance meat production in sheep worldwide.

1 Introduction

Sheep farming plays a critical role in global agricultural production, serving as a significant source of meat, wool, and other essential products (1). Global food consumption is projected to witness a substantial rise by 2050, particularly in the demand for animal protein products. This demand, however, will not only be driven by quantity but also by the quality of animal protein products desired by consumers. Notably, tenderness stands out as a paramount sensory attribute for consumers when it comes to meat consumption (2, 3). As global food demand continues to rise, there is an increasing imperative to enhance livestock productivity through advanced genetic approaches. The genetic improvement of meat production traits in sheep represents a crucial strategy for addressing these challenges, offering the potential to develop more efficient, high-quality meat-producing breeds that can contribute to global food security.

The complex nature of meat production traits in sheep involves multiple genetic and environmental factors that influence characteristics such as muscle growth, carcass quality, fat deposition, and overall meat quantity and quality (4, 5). Recent advances in molecular genetics and genomic technologies have opened unprecedented opportunities for understanding the genetic mechanisms underlying these important phenotypic traits (6–10). Genome-wide association studies (GWAS), transcriptome and candidate gene approaches have increasingly revealed the intricate genetic architecture that controls meat production characteristics, providing researchers and animal breeders with valuable insights into potential genetic markers and selection strategies (11).

This review article aims to comprehensively explore the current landscape of genetic research related to meat production traits in sheep. By systematically examining recent scientific literature, we will synthesize the most significant candidate genes associated with critical meat production phenotypes across various sheep breeds worldwide. Our analysis will not only highlight the genetic diversity and potential for genetic improvement but also provide a roadmap for future marker-assisted selection (MAS) programs. Through this comprehensive review, we seek to contribute to the ongoing efforts to optimize sheep breeding strategies, ultimately supporting more sustainable and productive livestock farming practices.

2 Literature search and selection criteria

This review article was designed to overview the potential candidate genes linked to various meat production traits in sheep. For this purpose, we selected articles published within the last 5 years (2018–2025), reflecting the contemporary landscape of research in the field. However, for the introductory section of this review, we extended our purview to include articles dating back to the year 2015. This comprehensive approach allowed us to establish a robust historical context for the subject matter.

The keywords employed in our search strategy were thoughtfully chosen to capture the multifaceted dimensions of the topic. These keywords included “carcass weight,” “muscle pH,” “muscle tenderness,” “meat quality and quantity,” “vertebrae,” “body size,” “body weight,” “Sheep “molecular breeding,” and “genetic markers, potential genes.” The selection of genes reported by any article for inclusion in this review was underpinned by their recognition as significant (p < 0.05) potential candidate genes associated with meat quality and quality-related traits. This recognition was based on the declarations made by authors in their respective published articles, signifying the genes’ significance in the field. To perform functional enrichment analysis and identify biological pathways associated with the genes examined in this review, we used ShinyGO online software (12).

In order to maintain a rigorous standard, we excluded articles published in non-science citation index–(SCI) journals and those not published in the English language. This deliberate choice was made to ensure that the articles included in our review were subjected to peer-review processes and accessible to a wider academic audience. Furthermore, it is important to note that book chapters and unpublished data were excluded from our discussion. However, we did consider the foundational insights from previously published review articles pertaining to specific genes associated with meat production traits in small ruminants. The summary of articles used in the current review is provided in Figure 1.

Figure 1

3 Overview of potential genes associated with meat production phenotypic traits in sheep

The study of genes associated with meat production phenotypic traits in sheep has significant agricultural and economic importance, as identifying these genetic markers enables more efficient selective breeding programs that can improve meat quality, yield, and production efficiency. Consistently, the association of genes associated with meat production traits have already been documented in previous studies (13, 14). By understanding the genetic basis of traits like muscle growth, fat deposition, tenderness, and flavor profile, researchers can develop genomic-based selection tools that allow producers to make breeding decisions earlier in an animal’s life, reducing costs while increasing genetic gains. Additionally, this genetic knowledge helps address consumer demands for consistent, high-quality meat products while potentially improving animal welfare through selecting for traits that enhance health and reduce stress susceptibility. Such research also contributes to broader food security goals by helping develop more efficient and sustainable sheep production systems that can adapt to changing environmental conditions and market demands.

3.1 Potential genes associated with number of vertebral traits in sheep

During the course of livestock evolution, there has been significant variation in the body size of domestic animals, both between and within species or breeds. Among the traits of economic importance, the number of vertebrae is noteworthy due to its association with body length and carcass characteristics. Notably, the association of variations in the number of thoracic and lumbar vertebrae thoracolumbar vertebrae with carcass length have been observed across different breeds of pigs (15), donkey (16–20), sheep (21) and cattle (22). It is worth mentioning that variations in the number of thoracolumbar vertebrae have been considered a selection trait in commercial animal breeding due to its correlations with growth and meat production.

In a general context, the arrangement of vertebrae in sheep typically includes 7 cervical vertebrae (C), 13 thoracic vertebrae (T), 6 lumbar vertebrae (L), and 4 sacral vertebrae (S), resulting in a total of 30 vertebrae. Among these, mutations in the thoracolumbar region, such as T14L6 or T13L7, have been reported as the most common (23). Multi-vertebrae sheep, exhibiting such mutations, demonstrate advantages in terms of adaptability and meat production performance (23). In the case of Kazakh sheep, which are indigenous to west Xinjiang of China, it is observed that there is variation in the number of lumbar vertebrae. Typically, for most sheep, the count includes 13 thoracic vertebrae and 6 lumbar vertebrae, often labeled as T13L6. However, in the case of Kazakh sheep, variations have been found, specifically T13L7 and T14L6, which, respectively, result in increased carcass length by 2.22 cm and 2.93 cm compared to normal T13L6 Kazakh sheep. Additionally, carcass weight is raised by 1.68 kg and 1.90 kg, respectively (23–26). Given the significant economic and productive advantages associated with vertebral variations in sheep, particularly the increased carcass length and weight observed in T13L7 and T14L6 configurations, understanding the underlying genetic mechanisms controlling these traits has become a priority in livestock genomics research. Recent advances in genomic technologies, have enabled researchers to identify candidate genes associated (SYNDIG1L, VRTN, NR6A1, LTBP2, BMP4) with vertebral development and segmentation (23, 26–30). Table 1 presents a comprehensive overview of genes associated with vertebral development and bone formation in various sheep breeds. This research area is particularly significant for the sheep industry as the number and structure of vertebrae directly influence carcass length, meat yield, and overall productivity.

3.2 Screening potential genes associated with growth, carcass and body size traits using RNA sequencing (RNA-seq) and GWAS in sheep

The integration of RNA-seq and GWAS represents a powerful approach for identifying genes and genetic variants associated with economically important meat production traits in sheep. This comprehensive strategy combines transcriptomic profiling to reveal differentially expressed genes in relevant tissues with population-based association analyses to pinpoint significant genetic variants. By correlating expression pat-terns with phenotypic data and genetic polymorphisms, researchers can identify candidate genes influencing key traits such as muscle growth, fat deposition, meat quality, and carcass composition. Understanding the genetic basis of growth and carcass-related traits in sheep plays a pivotal role in enhancing muscle growth, hypertrophy, and, ultimately, meat production (31, 32). Recently, several meat production associated genetic markers have been identified in various meat sheep breeds (Uruguayan Merino sheep, Romney, Karachaevsky Sheep, Hu, Dorper, Awassi, Afghani, Bandur, Baluch etc.) (Table 2). Consistently, a study has highlighted several genes (LHX3, LHX4, CAPN, MEF2B, TRHDE, MEF2A, MEF2C, MEF2D, FTO, APOBR, TP53, DRB1 2001, MSTN, GH, GRM1, MBD5, UBR2, RPL7, SMC2, and SHISA9) associated with various meat quality traits, including body weight, growth, and chest girth in sheep (33). Additionally, this study identified genes (CAST, LEP, MSTN, RFXANK, RIPK2, DGAT1, UCP1, and MCPs) linked to carcass and fat traits in sheep. The genetic analysis of sheep from Table 2 reveals a comprehensive landscape of genes controlling economically valuable production traits. The myostatin gene (MSTN) emerges as a critical regulator of muscle development, while LCORL and NCAPG appear repeatedly as major determinants of growth and body size traits. Fat metabolism and deposition are primarily influenced by DGAT2, FABP4, and SCD, which regulate lipid biosynthesis and transport. The bone morphogenetic protein (BMP) family, particularly BMP2, plays a significant role in both skeletal development and fat deposition in tail regions. Growth hormone pathways involving GHR and IGF1 control overall growth performance, while muscle-specific genes like MYL2 and TNNC2 influence meat quality characteristics. Notably, these candidate genes have been validated across multiple sheep populations worldwide using both GWAS and RNA-seq approaches, providing robust genetic markers that could be incorporated into breeding programs aimed at enhancing meat production efficiency and quality in commercial sheep operations. The summary of potential genes affecting meat production phenotypic traits in sheep is provided in Table 2.

3.3 Candidate gene approach to screen potential genetic markers associated with meat production phenotypic traits in sheep

The candidate gene approach represents a targeted strategy in sheep genetics research that focuses on identifying and analyzing specific genes with potential influence on economically important meat production traits. This method selectively examines genes with known biological functions related to muscle development, growth, fat deposition, and meat quality characteristics based on prior physiological knowledge or findings from other livestock species. For example, researchers typically analyze polymorphisms within these candidate genes—such as myostatin (MSTN), calpain (CAPN), calpastatin (CAST), leptin (LEP), DGAT1 and growth hormone (GH)—to establish associations with phenotypic traits including carcass weight, muscle mass, intramuscular fat content, tenderness, and meat flavor profile (Table 3). Consistently, our previously published research extensively examined the role of DGAT1 K232A polymorphism in enhancing sheep meat quality traits (34). Fatty acid-binding protein 4 (FABP4) is involved in fatty acid transportation, and variations in this gene have been reported to influence fat deposition in mammals. Several studies have consistently demonstrated the involvement of FABP4 in regulating meat quality traits in sheep (35). Additionally, Alwan et al. (35) observed a detrimental effect of p.61Thr > Asp on FABP4, resulting in reduced fatty acid binding efficiency and increased carcass traits in Karakul and Awassi Sheep. Furthermore, other studies have documented associations between FABP4 variations and various economic traits in sheep, such as carcass and growth traits in New Zealand Romney lambs (36), morphometric traits in Albanian sheep (37), body weight, final weight, and average daily gain in three Egyptian sheep breeds (38), as well as intramuscular and internal fat weight in two Russian sheep breeds (39). The approach has proven valuable for marker-assisted selection programs in sheep breeding, allowing producers to make informed breeding decisions that enhance meat production efficiency and quality while reducing the time and resources required compared to genome-wide studies. Despite limitations in detecting novel genes, the candidate gene approach continues to provide practical applications in sheep breeding programs focused on improving commercially relevant meat production traits. The summary of determinant genes associated with meat production phenotypic traits in sheep is provided in Table 3.

4 Discussion

The genetic architecture underlying meat production traits in sheep represents a sophisticated biological system wherein multiple interconnected pathways coordinate growth, muscle development, fat deposition, and skeletal formation. Brief information about the genes documented in this review and their related pathways is provided in Supplementary Files 1, 2. This complex network involves numerous candidate genes that have been consistently reported across diverse sheep populations (Figure 2; Tables 1–3) and breeding programs worldwide, each contributing specific functional roles while participating in broader regulatory circuits that determine economically valuable traits.

Figure 2

Central to this genetic framework, myogenesis pathways control the fundamental processes of muscle development and ultimately determine muscle mass and composition that defines meat yield. The MSTN gene operates as a negative regulator within the transforming growth factor-beta signaling network, where its expression limits muscle growth through inhibition of satellite cell activation and myoblast proliferation. Consequently, when MSTN signaling is reduced through genetic variants, normal growth constraints are released, resulting in increased muscle fiber number and size, which translates directly to enhanced muscle mass and improved carcass composition. Furthermore, muscle-specific transcription factors MEF2B, MYOD1, and MYF5 coordinate myogenic differentiation programs, controlling the expression of muscle-specific genes that determine fiber type characteristics and contractile properties. These regulatory networks interact synergistically with calcium-dependent signaling pathways involving troponin components such as TNNC2 and myosin light chains including MYL2, which collectively determine muscle fiber contractility and ultimately influence meat texture and quality attributes. Complementing the myostatin pathway, the growth hormone regulatory network represents another critical system controlling overall growth performance and carcass development. This integrated pathway encompasses insulin-like growth factor 1 and its receptor, along with growth hormone and its corresponding receptor, functioning as a master regulator of somatic growth and metabolic processes through a sophisticated feedback system that regulates traits ranging from birth weight to final carcass characteristics. The signaling mechanism initiates with growth hormone binding to its receptor, triggering downstream activation of IGF1 synthesis in the liver and peripheral tissues. Subsequently, IGF1 binds to its receptor, initiating intracellular signaling cascades that promote protein synthesis, muscle fiber development, and overall growth performance. This pathway directly influences carcass weight and yield by regulating cell proliferation, differentiation, and metabolism throughout the animal’s development, demonstrating dual influence on both muscle development and fat metabolism through intricate feedback mechanisms that ensure balanced growth processes responsive to physiological demands. In parallel, lipid metabolism pathways represent equally critical regulatory systems determining fat deposition patterns and meat quality characteristics. The triglyceride synthesis pathway, culminating in DGAT1 and DGAT2 enzymatic activity, controls the final steps of fat formation and storage. Notably, the diacylglycerol O-acyltransferase 1 gene catalyzes the final enzymatic step in triglyceride synthesis, demonstrating remarkable consistency in its associations with meat quality traits across sheep populations. Specific polymorphisms, particularly the K232A variant, have been extensively validated for their positive effects on loin meat yield and intramuscular fat content, directly influencing consumer-perceived meat quality. Concurrently, fatty acid-binding protein 4 plays a crucial role in fatty acid transport and cellular uptake, with genetic variations affecting both fat deposition patterns and meat quality characteristics. The fatty acid synthesis pathway, regulated by FASN, controls the production of fatty acids from acetyl-CoA precursors, while stearoyl-CoA desaturase introduces unsaturation into fatty acid chains, influencing membrane fluidity and meat quality attributes. Additionally, the bone morphogenetic protein family introduces an intriguing dimension to meat production genetics through its dual functionality in both skeletal development and adipogenesis. Specifically, BMP2 and BMP4 operate through specialized signaling pathways that simultaneously regulate fat tail development in certain sheep breeds while affecting bone formation and overall body size determination. This dual role becomes particularly relevant for breeds adapted to harsh environmental conditions, where fat reserves serve as critical survival mechanisms during periods of feed scarcity, thus representing an evolutionary adaptation that balances immediate production goals with long-term survival capacity. Moreover, skeletal development pathways contribute significantly to carcass characteristics through their control of bone formation and vertebral segmentation. The vertebral development genes VRTN and NR6A1 regulate axial skeleton segmentation during embryogenesis, with genetic variants affecting the number of thoracic and lumbar vertebrae. Increased vertebral number directly correlates with longer carcass length and greater total carcass weight, providing measurable economic benefits. The HOX gene family provides positional information during development, ensuring proper spatial organization of skeletal structures that determine final body conformation and carcass geometry. Transcending individual pathway effects, master regulatory genes emerge as overarching controllers of multiple production traits through their influence on chromatin remodeling and transcriptional regulation. The LCORL and NCAPG genes appear consistently across genome-wide association studies investigating body size and growth traits, suggesting fundamental roles in determining mature body size and growth rate. These genes operate through epigenetic modifications and transcriptional control mechanisms, influencing the expression of numerous downstream targets involved in muscle development, bone growth, and overall body size determination. Similarly, HMGA2 and PLAG1 contribute additional layers of transcriptional control, particularly influencing growth-related gene expression patterns that determine mature body size and growth trajectory. The calpain-calpastatin proteolytic system represents a specialized post-mortem pathway that significantly influences meat quality and consumer acceptance. The calpain proteases, regulated by the calpastatin inhibitor encoded by the CAST gene, control protein degradation processes that occur after slaughter, determining the extent of myofibrillar protein breakdown that directly affects meat tenderness development during aging. Genetic variants affecting calpastatin expression influence the balance between protease activity and inhibition, ultimately determining the rate and extent of tenderization during post-mortem storage.

Furthermore, metabolic regulation pathways connect nutritional status with growth performance and carcass composition through genes such as adiponectin and leptin. These genes regulate energy homeostasis, fat distribution, appetite control, and energy expenditure, creating essential links between metabolic efficiency and production outcomes. The adiponectin pathway influences energy balance and fat distribution patterns, while leptin regulates appetite and energy expenditure, ensuring that growth processes remain aligned with nutritional resources and metabolic capacity.

Environmental interactions add considerable complexity to these genetic systems, wherein genes like the fat mass and obesity-associated gene respond to nutritional status and environmental stressors, modulating their effects on growth and fat deposition based on external conditions. This environmental responsiveness indicates that gene expression can be influenced by factors including nutrition quality, health issues, temperature stress, and management practices, suggesting that optimal genetic selection programs must account for genotype-by-environment interactions to achieve consistent performance across diverse production systems (Figure 3).

Figure 3

The integration of these multiple pathways reveals that successful meat production genetics requires a systems-level approach rather than optimization of individual genes. Growth hormone signaling pathways interact extensively with muscle development regulators, while fat metabolism genes simultaneously influence meat quality characteristics and adaptive capacity. Bone morphogenetic proteins affect both skeletal development and fat deposition patterns, demonstrating the interconnected nature of physiological systems underlying meat production traits. Consequently, modern genomic selection approaches increasingly recognize these pathway interactions, moving beyond single-gene effects toward polygenic selection strategies that capture cumulative effects across multiple biological systems. This systems-level understanding provides the foundation for developing comprehensive genetic evaluation programs that can enhance meat production efficiency while maintaining genetic diversity and adaptive capacity essential for sustainable sheep production worldwide.

Based on published data, we concluded that current genetic research faces several significant limitations. Primarily, most genetic associations are discovered within specific breeds but lack validation across diverse populations. This creates limited applicability due to varying genetic backgrounds, distinct linkage disequilibrium patterns, and divergent population histories that cause population stratification effects. Furthermore, the field suffers from insufficient attention to epigenetic factors. DNA methylation patterns are largely ignored despite their significant influence on gene expression. Similarly, environmental interactions remain poorly understood, particularly how nutrition, climate, and management practices interact with genetic variants through complex epigenetic mechanisms. Moreover, the inheritance and influence of epigenetic marks across generations through transgenerational effects remains inadequately investigated. Consequently, the lack of comprehensive epigenome mapping across relevant tissues such as muscle, fat, and liver creates substantial knowledge gaps. This subsequently limits our understanding of tissue-specific regulatory mechanisms. Another critical limitation involves functional validation, where many identified single nucleotide polymorphisms may merely be in linkage disequilibrium with actual causal variants rather than being functionally relevant themselves. Additionally, insufficient experimental validation of how genetic variants actually affect gene function and protein activity perpetuates an oversimplified understanding of gene interactions within complex biological pathways.

To address these multifaceted challenges, future research must embrace multi-omics integration approaches. This includes combining epigenomics data such as DNA methylation, histone modifications, and chromatin accessibility with transcriptomics through expression quantitative trait loci mapping. Furthermore, incorporating proteomics and metabolomics will effectively link genetic variants to protein abundance and metabolite levels. Finally, investigating host-microbiome interactions that significantly affect production traits represents a critical research priority for advancing the field.

5 Conclusion and future research directions

This review has cataloged an extensive array of potential genes associated with meat production traits in sheep breeds globally. The identified genes—particularly those affecting vertebral development, muscle growth, and fat deposition—provide valuable targets for marker-assisted selection strategies to enhance sheep meat production efficiency. Future research should focus on validating these genetic associations across diverse populations and production environments to ensure broader applicability. Integration of advanced genomic technologies, including whole-genome sequencing and multi-omics approaches, will be crucial to understand the functional mechanisms underlying these genetic markers. Additionally, research examining gene–environment interactions and the role of epigenetic modifications on meat production traits deserves attention. Development of cost-effective genotyping platforms suitable for implementing these findings in resource-limited settings would further extend their practical value. Finally, the integration of consumer preferences with genetic selection represents a critical pathway for sustainable sheep breeding programs, where market demands increasingly favor specific meat quality attributes that should directly inform trait selection priorities. Consumer preference for leaner cuts drives selection for enhanced muscle development while reducing excessive fat deposition, while market premiums for higher carcass yield support prioritizing traits that increase carcass length and overall meat yield through improved skeletal development. Premium markets increasingly value optimal marbling for tenderness and flavor, requiring breeding programs to focus not just on fat deposition, but on achieving consumer-preferred intramuscular fat distribution that enhances both meat yield and quality characteristics. Growing consumer awareness of health benefits drives demand for favorable omega-3 to omega-6 fatty acid ratios, necessitating selection for optimized fatty acid synthesis and desaturation pathways to improve nutritional profiles, while market differentiation through functional meat products requires targeted selection of lipid metabolism traits. Post-mortem tenderization processes directly affect meat tenderness, a primary consumer concern, requiring selection programs to balance rapid growth with meat quality attributes that determine consumer satisfaction and repeat purchases. Future strategies should develop market-responsive breeding indices that weight genetic markers based on current consumer preferences and price premiums, establish feedback loops between consumer testing, market analysis, and breeding decisions, and consider regional market variations in trait preferences when implementing marker-assisted selection programs, ensuring that genetic improvements translate into economic value throughout the supply chain while meeting evolving consumer expectations for meat quality, nutrition, and eating experience.

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