Associations between gene polymorphisms and selected meat traits in cattle - A review

Genotype-Dependent Variations in Oxidative Stress Markers and Bioactive Proteins in Hereford Bulls: Associations with DGAT1, LEP, and SCD1 Genes

The objective of this study is to assess the influence of genetic polymorphisms in DGAT1, LEP, and SCD1 on the oxidative stress biomarkers and bioactive protein levels in Hereford bulls. A total of sixty-eight bulls were analyzed at 22 months of age to assess growth metrics and carcass quality, with a focus on polymorphisms in these genes. The key markers of oxidative stress, including malondialdehyde (MDA), and the activities of antioxidant enzymes such as glutathione reductase (GluRed), glutathione peroxidase (GPx), and superoxide dismutase (SOD) were measured, alongside bioactive compounds like taurine, carnosine, and anserine. The results show that the TT genotype of DGAT1 is linked to significantly higher MDA levels, reflecting increased lipid peroxidation, but is also associated with higher GluRed and GPx activities and elevated levels of taurine, carnosine, and anserine, suggesting an adaptive response to oxidative stress. The LEP gene analysis revealed that the CC genotype had the highest MDA levels but also exhibited increased GPx and SOD activities, with the CT genotype showing the highest SOD activity and the TT genotype the highest total antioxidant status (TAS). The SCD1 AA genotype displayed the highest activities of GluRed, GPx, and SOD, indicating a more effective antioxidant defence, while the VA genotype had the highest MDA levels and the VV genotype showed lower MDA levels, suggesting protective effects against oxidative damage. These findings highlight genotype specific variations in the oxidative stress markers and bioactive compound levels, providing insights into the genetic regulation of oxidative stress and antioxidant defences, which could inform breeding strategies for improving oxidative stress resistance in livestock and managing related conditions.

Long non-coding RNA (LncRNA) and epigenetic factors: their role in regulating the adipocytes in bovine

Investigating the involvement of long non-coding RNAs (lncRNAs) and epigenetic processes in bovine adipocytes can provide valuable new insights into controlling adipogenesis in livestock. Long non-coding RNAs have been associated with forming chromatin loops that facilitate enhancer-promoter interactions during adipogenesis, as well as regulating important adipogenic transcription factors like C/EBPα and PPARγ. They significantly influence gene expression regulation at the post-transcriptional level and are extensively researched for their diverse roles in cellular functions. Epigenetic modifications such as chromatin reorganization, histone alterations, and DNA methylation subsequently affect the activation of genes related to adipogenesis and the progression of adipocyte differentiation. By investigating how fat deposition is epigenetically regulated in beef cattle, scientists aim to unravel molecular mechanisms, identify key regulatory genes and pathways, and develop targeted strategies for modifying fat deposition to enhance desirable traits such as marbling and meat tenderness. This review paper delves into lncRNAs and epigenetic factors and their role in regulating bovine adipocytes while focusing on their potential as targets for genetic improvement to increase production efficiency. Recent genomics advancements, including molecular markers and genetic variations, can boost animal productivity, meeting global demands for high-quality meat products. This review establishes a foundation for future research on understanding regulatory networks linked to lncRNAs and epigenetic changes, contributing to both scholarly knowledge advancement and practical applications within animal agriculture.

Effects of GH L127V and TG5 C422T polymorphisms on the hormonal profile, slaughter traits, and meat quality of Hereford bulls

Background and Aim

The creation of objective methods for the evaluation and improvement of quantitative and qualitative indicators of meat productivity in farm animals should be based on a comprehensive analysis of the genetic, physiological, and biochemical parameters of the animal. This study aimed to investigate the effects of growth hormone (GH) and thyroglobulin (TG5) gene polymorphisms on the hormonal status, slaughter traits, and chemical, amino acid, and fatty acid composition of meat in Hereford bulls.

Materials and Methods

Hereford bulls (n = 9) were reared under the same feeding and housing conditions until the age of 21 months, after which they were slaughtered. Polymerase chain reaction-restriction fragment length polymorphism was performed for genotyping GH L127V and TG5 C422T polymorphisms. The experimental animals were evaluated to determine slaughter traits (including pre-slaughter weight, carcass, and internal fat weight and yield), chemical, fatty acid, and amino acid composition of ground beef, and hormonal status using serum concentrations of GH, triiodothyronine, and thyroxine.

Results

Animals with the valine homozygous (VV) genotype of GH had the maximum serum GH level of 9.33 mIU/mL (p = 0.10) higher than leucine homozygous (LL) genotype carriers. Individuals with the LL genotype outperformed V-allele carriers in serum thyroxine (T4) concentration by 21.3-30.5 nmol/L (16.15%-24.86%; p < 0.01-0.05). Genetic differentiation induced by TG5 C422T polymorphism was determined to a lesser extent by the hormonal status of the Hereford animals. The V-allele was associated with increased carcass weight, with VV homozygotes significantly outperforming LL individuals by 45.0 kg (13.61%; p < 0.05). The T allele at the TG5 gene polymorphism was associated with more intense lipogenesis and less protein synthesis in muscle tissue and these effects were enhanced in the homozygous state. Young animals with the TT variant of the TG5 gene exhibited a significantly superior polyunsaturated fatty acid/saturated fatty acid ratio of 0.012 units (p < 0.01). Carriers of the LL genotype were characterized by minimum amino acid content in muscle tissue. Heterozygous bulls exceeded LL homozygotes in the sum of essential amino acids by 3.09% (p = 0.10) and non-essential amino acids by 1.9% (p < 0.05).

Conclusion

The development of breeding programs for the Hereford breed should be carried out considering genetic features that determine the formation of economic traits in animals. Analysis of polymorphisms in the TG5 gene is a promising method for the early diagnosis of the fatty acid composition of beef. Identification of polymorphisms in the GH gene allows the prediction of higher productivity potential and amino acid composition of meat. The different effects of the GH and TG5 genes on the development of various economic traits allowed us to determine further vectors for scientific research on their complex associations in Hereford cattle, which will be useful for planning effective breeding schemes.

Relationship between Selected SNPs (g.16024A/G, g.16039T/C and g.16060A/C) of the FASN Gene and the Fat Content and Fatty Acid Profile in the Milk of Three Breeds of Cows

Fat is an important energy and nutritional component of milk and consists of fatty acids. FASN (fatty acid synthase) is an enzyme that regulates the synthesis of fatty acids in the milk and meat of cattle. It was hypothesized that knowing the relationships between the genotypes of the tested single nucleotide polymorphisms (SNPs) and the content of fat and specific fatty acids would make it possible to improve milk quality in the selection process during cattle breeding. This study aimed to analyze the relationships of SNPs (g.16024A/G, g.16039T/C) of the FASN gene and their genotypes with the fat and fatty acid content of the milk of the following breeds: Polish Red-White (ZR), Polish Red (RP), and Polish Holstein-Friesian Red-White (RW). The SNP g.16060A/C was included in the study, although its effect on the fat composition of cow's milk has not yet been widely studied. Milk was obtained during test milkings. SNP genotyping was performed using the real-time PCR (HRM) method. The milk from ZR and RP cows was more often characterized by a more favorable fatty acid profile than the milk from RW cows. This information can be used by cattle breeders and consumers of so-called functional food.

Genetic Markers Related to Meat Quality Properties in Fattened HF and HF x Charolaise Steers

This study involved 45 Holstein and 60 Holstein-Charolaise steers, tailored with specific diets according to breed and rearing systems. DNA genotyping was conducted for DGAT1, LEP, SCD1, SREBF1, and TG genes to investigate their impact on carcass conformation traits, beef quality traits, and sensory quality traits. The results showed associations between the genetic variants and the analyzed traits. Specifically, DGAT1 was found to affect drip loss, meat brightness, and color saturation. The TG gene was associated with marbling and meat color. LEP influenced trim fat and pH levels, while SCD1 was linked to metabolic energy live weight gains, and pH levels. SREBF1 was related to fatness.

Effect of IGF-1 C472T, GH C2141G, and GHR T914A polymorphisms on growth performance and feed efficiency in young Kazakh white-headed cattle

Background and Aim

Improving the feed efficiency of beef cattle is necessary to increase the profitability of meat production. Implementing marker-assisted selection breeding systems can improve the genetic potential of beef cattle for increased productivity. This research aimed to study the effects of insulin-like growth factor (IGF)-1 C472T, growth hormone (GH) C2141G, and GH receptor (GHR) T914A polymorphisms on growth performance and feed efficiency in young Kazakh white-headed cattle.

Materials and Methods

Young Kazakh white-headed cattle (n = 50) were grouped after weaning according to sex (28 bulls and 22 heifers) and they were genotyped according to the IGF-1 C472T, GH C2141G, and GHR T914A polymorphisms. The test period was conducted from 8 to 15 months of age. The experimental animals were evaluated for live weight (LW) at the beginning and end of the test period. They were also assessed for average daily gain, hip height, metabolic mid-weight (MMWT), actual dry matter intake (DMI), and residual feed intake (RFI).

Results

Significant differences in MMWT were found between the bulls with the IGF-1TT and IGF-1CT genotypes, which was a 2.2 kg increase in heterozygous cattle (p < 0.05). Heterozygous IGF-1CT bulls differed with a higher DMI of 0.087 kg/day (p < 0.05) compared to IGF-1TT homozygotes. Carriers of the IGF-1TT genotype had the greatest feed efficiency at 0.068 kg/day (p < 0.05). Heifers with the GHCC genotype differed in their maximum DMI with an increase of 1.17%-1.57% (p < 0.05) relative to the other genotypes. The G allele in the GH C2141G polymorphism was associated with better (p < 0.05) feed efficiency in the Kazakh white-headed breed. The minimum DMI and RFI in GHR T914A heterozygous heifers were significantly inferior (p < 0.05) to the other genotypes.

Conclusion

Association studies of the IGF-1 C472T, GH C2141G, and GHR T914A polymorphisms indicate a relationship between growth, development, and feed efficiency with the genetic characteristics of young Kazakh white-headed cattle. A significant (p < 0.05) dominant effect was found in the IGF-1 gene in bulls and in the GHR gene in heifers, which should be considered when breeding with heterogeneous parental pairs. The negative effect of the allele substitution in the IGF-1 C472T polymorphism was observed in the LW of heifers (-3.25 kg) at the age of 8 months and bulls (-6.05 kg) at 15 months. The substitution in the GH C2141G polymorphism was associated with a significant reduction in DMI by 0.036 kg (p < 0.05) and an increase in feed efficiency by 0.023 kg (p < 0.05) during the rearing of heifers. These results can improve the production efficiency of mature herds of Kazakh white-headed cattle.

Cis-eQTL Analysis and Functional Validation of Candidate Genes for Carcass Yield Traits in Beef Cattle

Carcass yield traits are of considerable economic importance for farm animals, which act as a major contributor to the world’s food supply. Genome-wide association studies (GWASs) have identified many genetic variants associated with carcass yield traits in beef cattle. However, their functions are not effectively illustrated. In this study, we performed an integrative analysis of gene-based GWAS with expression quantitative trait locus (eQTL) analysis to detect candidate genes for carcass yield traits and validate their effects on bovine skeletal muscle satellite cells (BSCs). The gene-based GWAS and cis-eQTL analysis revealed 1780 GWAS and 1538 cis-expression genes. Among them, we identified 153 shared genes that may play important roles in carcass yield traits. Notably, the identified cis-eQTLs of PON3 and PRIM2 were significantly (p < 0.001) enriched in previous GWAS loci for carcass traits. Furthermore, overexpression of PON3 and PRIM2 promoted the BSCs’ proliferation, increased the expression of MYOD and downregulated the expression of MYOG, which indicated that these genes may inhibit myogenic differentiation. In contrast, PON3 and PRIM2 were significantly downregulated during the differentiation of BSCs. These findings suggested that PON3 and PRIM2 may promote the proliferation of BSCs and inhibit them in the pre-differentiation stage. Our results further contribute to the understanding of the molecular mechanisms of carcass yield traits in beef cattle.

Bibliometric Analysis of Research on the Main Genes Involved in Meat Tenderness

Simple Summary

A bibliometric analysis was carried out to know the evolution of research on genes associated with meat tenderness, of interest for the development of selection programs. Since 1993, studies have been limited to a few researchers in high-income countries due to the costs associated with the techniques. The main findings showed that the scientific production had a discontinuous growth because science experienced a significant change since approximately 2010. Marker-assisted selection was widely used, evaluating mainly CAPN (calpain) and CAST (calpastatin) genes for their contribution to meat tenderness, especially in cattle. However, the effects are small; therefore, genomic selection was implemented by genotyping thousands of single nucleotide polymorphisms (SNPs) for further explanation of genetic variation. The results shown are important for scholars to identify emerging methodologies and gaps in the literature and to know who the prolific authors and institutions in the field for possible collaborations, etc., are.

Abstract

Tenderness is one of the main characteristics of meat because it determines its price and acceptability. This is the first bibliometric study on the trend of research on the role of genes in meat tenderness. A total of 175 original and English-language articles published up to 2021 were retrieved from Scopus. The bibliometric analysis was carried out with VOSviewer (version 1.6.18, Eck and Waltman, Leiden, Netherlands) and complemented with the Analyze search results service from Scopus. Erroneous and duplicate data were eliminated, and incomplete information was added to standardize the results. Scientific production was evaluated by means of quantity, quality and structure indicators. As a first glance, 8.816% of authors have published more than 50% of papers mainly related to genes encoding the calpain (CAPN)-calpastatin (CAST) system and single nucleotide polymorphisms (SNPs). Among other findings, a strong link was found between the contribution of the main countries (led by the United States with) and their institutions (led by the USDA Agricultural Research Service with) to their gross domestic product. Most studies on the topic are published in the Journal of Animal Science, and other journals with high impact according to the number of citations and different metrics. Finally, when evaluating the most cited articles, the occurrence and association of the main keywords, it was confirmed that research is focused on the role of CAPN and CAST genes and of SNPs in beef tenderness. The change in science was emphasized; although marker-assisted selection is still used, genes have an infinitesimal effect on complex traits. Therefore, since about 2010, new research groups adopted genomic selection to evaluate dense panels of SNPs and better explain genetic variation in meat tenderness.

Assessment of the association of the MOGAT1 and MOGAT3 gene with growth traits in different growth stages in Holstein calves

The members of the monoacylglycerol acyltransferase (MOGAT) family are essential candidate genes that influence economic traits associated with triglyceride synthesis, dietary fat absorption, and storage in livestock. In addition, the MOGAT gene family may also play an essential function in human polygenic diseases, like type 2 diabetes and obesity. The present study was conducted on Holstein calves to find the association between MOGAT1, MOGAT3/g.A229G, and MOGAT3/g.G1627A and growth traits. The polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) method was performed for genotyping the MOGAT1, MOGAT3/g.A229G, and MOGAT3/g.G1627A genes' locus using the TaqI, MspI, and BsuRI restriction enzyme. The allele frequency of A and G of the MOGAT1 locus was 0.79 and 0.21, respectively, while the genotype frequency was 0.65, 0.28, and 0.07 for AA, AG, and GG, respectively. While the allele and genotype frequencies of the MOGAT3/g.A229G locus were 00.57(A1), 0.43(G1), 0.35(A1A1), 0.45(A1G1), and 0.20(G1G1), the allele and genotype frequencies of the MOGAT3/g.G1627A locus were 0.49(A2), 0.51(G2), 0.25(A2A2), 0.49(A2G2), and 0.26(G2G2). Chi-square analysis showed that MOGAT3/g.G1627A distribution was at the Hardy–Weinberg disequilibrium (p < 0.05), and MOGAT1 and MOGAT3/g.A229G distribution was at the Hardy–Weinberg equilibrium (p > 0.05). In total, two statistical methods (general linear model (GLM) and PROC MIXED) were used to identify an association between gene locus and growth traits. An association analysis showed a statistically significant difference between the MOGAT1 and body weight, body length, and chest circumference, MOGAT3/g.A229G with average daily gain (ADG) and withers height, and MOGAT3/g.G1627A with body weight and body length (p < 0.05). The results confirmed that the MOGAT1, MOGAT3/g.A229G, and MOGAT3/g.G1627A locus are strong candidate genes that could be considered molecular markers for growth traits in cattle breeding.

Towards Sustainable Sources of Omega-3 Long-Chain Polyunsaturated Fatty Acids in Northern Australian Tropical Crossbred Beef Steers through Single Nucleotide Polymorphisms in Lipogenic Genes for Meat Eating Quality

This study aimed to identify single nucleotide polymorphisms (SNP) in lipogenic genes of northern Australian tropically adapted crossbred beef cattle and to evaluate associations with healthy lipid traits of the Longissimus dorsi (loin eye) muscle. The hypothesis tested was that there are significant associations between SNP loci encoding for the fatty acid binding protein 4 (FABP4), stearoyl-CoA desaturase (SCD) and fatty acid synthase (FASN) genes and human health beneficial omega-3 long-chain polyunsaturated fatty acids (ω3 LC-PUFA) within the loin eye muscle of northern Australian crossbred beef cattle. Brahman, Charbray, and Droughtmaster crossbred steers were fed on Rhodes grass hay augmented with desmanthus, lucerne, or both, for 140 days and the loin eye muscle sampled for intramuscular fat (IMF), fat melting point (FMP), and fatty acid composition. Polymorphisms in FABP4, SCD, and FASN genes with significant effects on lipid traits were identified with next-generation sequencing. The GG genotype at the FABP4 g.44677239C>G locus was associated with higher proportion of linoleic acid than the CC and CG genotypes (p < 0.05). Multiple comparisons of genotypes at the SCD g.21266629G>T locus indicated that the TT genotype had significantly higher eicosapentaenoic, docosapentaenoic, and docosahexaenoic acids than GG genotype (p < 0.05). Significant correlations (p < 0.05) between FASN SNP and IMF, saturated and monounsaturated fatty acids were observed. These results provide insights into the contribution of lipogenic genes to intramuscular fat deposition and SNP marker-assisted selection for improvement of meat-eating quality, with emphasis on alternate and sustainable sources of ω3 LC-PUFA, in northern Australian tropical crossbred beef cattle, hence an acceptance of the tested hypothesis.

Dr. Novel missense variant L46Q of fatty acid synthase gene and fatty acids content in Awassi sheep

This study was conducted to investigate the association between the polymorphism of the FASN gene with fatty acid content in Awassi sheep. A total of 100 male Awassi sheep between the ages of one and two and a half years old were used in this study. Phenotypic measurement was recorded at slaughter, and from each animal, the longissimus dorsi (LD) muscle samples were taken to analyze the fatty acid profile. Genotyping, sequencing reactions, and in silico tools were performed to confirm the variants in amplified fragments. The result of genotyping revealed two genotypes (AA and AB) of the ovine FASN gene (exon 3). Novel SNP (L46Q) was discovered only within the FASN gene (AB genotype). All utilized in silico tools revealed remarkably deleterious effects for the L46Q on the mutant protein structure, function, and stability. Association analysis revealed that the AB genotype has significantly (p < 0.05) higher levels of animal length and monounsaturated fatty acids (MUFA) with lower amounts of saturated fatty acids (SFA) content than the AA genotype. In conclusion, novel SNP (L46Q) was discovered within the FASN gene (AB genotype), made the animals that has the AB genotype associated with good meat quality traits and this polymorphism may serve as markers for meat quality.

Genome-Wide Association Study of Potential Meat Quality Trait Loci in Ducks

With continuously increasing living standards and health requirements of consumers, meat quality is becoming an important consideration while buying meat products. To date, no genome-wide association study (GWAS) for copy number variants (CNVs) and single nucleotide polymorphisms (SNPs) has been conducted to reveal the genetic effects on meat quality in ducks. This study analyzed the phenotypic correlation and heritability of fat, water, collagen, and protein content of duck breast muscle. To identify the candidate variants for meat quality, we performed a GWAS using 273 ducks from an F2 population. The results of the SNP GWAS showed that the BARHL2, COPS7B, and CCDC50 genes were associated with fat content; BLM, WDR76, and EOMES with water content; CAMTA1, FGD5, GRM7, and RAPGEF5 with collagen production; and RIMS2, HNRNPU, and SPTBN1 with protein content. Additionally, 3, 7, 1, and 3 CNVs were associated with fat, water, collagen, and protein content, respectively, in duck breast muscle. The genes identified in this study can serve as markers for meat quality. Furthermore, our findings may help devise effective breeding plans and selection strategies to improve meat quality.