Polymorphism of Genes and Their Impact on Beef Quality

Genetic parameters, genomic prediction, and identification of regulatory regions located on chromosome 14 for weight traits in Nellore cattle

This study aimed to investigate functional variants in chromosome 14 (BTA14) and its impact in genomic selection for birth weight (BW), weaning weight (WW), and yearling weight (YW) in Nellore cattle. Genetic parameter estimation and the weighted single-step genomic best linear unbiased prediction (WssGBLUP) analyses were performed. Direct additive heritability estimates were high for WW and YW, and moderate for BW. Trait-associated variants distributed across multiple regions on BTA14 were observed in the weighted single-step genome-wide association studies (WssGWAS) results, implying a polygenic genetic architecture for weight in different ages. Several genes have been found in association with the weight traits, including the CUB And Sushi multiple domains 3 (CSMD3), thyroglobulin (TG), and diacylglycerol O-acyltransferase 1 (DGAT1) genes. The variance explained per SNP was higher in six functional classes of gene regulatory regions (5UTR, CpG islands, downstream, upstream, long non-coding RNA, and transcription factor binding sites (TFBS)), highlighting their importance for weight traits in Nellore cattle. A marginal increase in accuracy was observed when the selected functional variants (SV) information was considered in the WssGBLUP method, probably because of the small number of SV available on BTA14. The identified genes, pathways, and functions contribute to a better understanding of the genetic and physiological mechanisms regulating weight traits in the Nellore breed.

Polymorphisms of TXK and PLCE1 Genes and Their Correlation Analysis with Growth Traits in Ashidan Yaks

The tyrosine protein kinase (TXK) gene, as a member of the non-receptor tyrosine kinase Tec family, plays a vital role in signal transduction mediation. Phospholipase C epsilon 1 (PLCE1), a membrane-associated enzyme, is of paramount importance for the differentiation of myoblasts and the normal functioning of muscle tissue. In recent years, both of these genes have been reported to be associated with the economic traits of animals. This study aimed to investigate the relationship between single nucleotide polymorphisms (SNPs) in the TXK and PLCE1 genes and growth traits in Ashidan yaks and to search for potential molecular marker loci that can influence Ashidan yak breeding. A cGPS liquid microarray was utilized to genotype 232 Ashidan yaks and to analyze correlations between two SNP loci in the TXK and PLCE1 genes and yak body weight, body height, body length, and chest circumference at different periods. The results indicated that the g.55,999,531C>T locus of the TXK gene and the g.342,350T>G locus of the PLCE1 gene were significantly correlated with the growth traits of Ashidan yaks. Among these, individuals with the CC genotype at the g.55,999,531C>T locus showed a significantly higher body length at 6 months old compared to TT individuals, and those with the CT genotype at 12 months old had a significantly higher chest circumference than TT individuals. At the g.342,350T>G locus, the body height of GG genotype individuals at 18 months of age was significantly higher than that of TT genotype individuals and TG genotype individuals. The above findings can be used as theoretical support for the subsequent improvement of Ashidan yak breeding.

Genetic characterization of LEP and TG5 gene polymorphisms in crossbred beef cattle populations

Objective

This study aimed to investigate the single nucleotide polymorphisms (SNPs) in the intron 2 region of the leptin (LEP) gene and the 5' untranslated region of the thyroglobulin (TG5) gene across four crossbred beef cattle populations, including Blanc Bleu Belge × Lai Brahman (BLB), Charolais × Lai Brahman (CLB), Droughtmaster × Lai Brahman (DLB), and Red Angus × Lai Brahman (RLB) raised in Central Vietnam.

Materials and Methods

A total of 200 tail hair root samples (50 per group) were collected, and genomic DNA was extracted. The PCR-RFLP method was utilized to analyze the LEP and TG5 gene polymorphisms using the restriction enzymes Sau3AI and PsuI, respectively.

Results

The SNPs of LEP/Sau3AI and TG5/PsuI were present in all populations, with a lower frequency of the LEPB allele compared to LEPA. The LEPAA genotype was most common, followed by LEPAB and LEPBB; notably, the LEPBB genotype was absent in the CLB group. The Hardy-Weinberg equilibrium was observed for LEP/Sau3AI in the CLB and BLB populations. Conversely, the TG5CT genotype dominated all groups, with no individuals exhibiting the TG5TT genotype. None of the populations achieved Hardy-Weinberg equilibrium for TG5/PsuI. The level of polymorphism was moderate for LEP/Sau3AI in RLB and BLB and for TG5/PsuI across all groups.

Conclusion

The SNPs of LEP/Sau3AI and TG5/PsuI may serve as valuable tools for genomic selection. By focusing on increasing the frequency of the TG5T allele, breeding programs can more effectively enhance beef marbling and other important traits, leading to improved beef quality and greater economic outcomes in the cattle industry.

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.

Leveraging Functional Genomics for Understanding Beef Quality Complexities and Breeding Beef Cattle for Improved Meat Quality

Consumer perception of beef is heavily influenced by overall meat quality, a critical factor in the cattle industry. Genomics has the potential to improve important beef quality traits and identify genetic markers and causal variants associated with these traits through genomic selection (GS) and genome-wide association studies (GWAS) approaches. Transcriptomics, proteomics, and metabolomics provide insights into underlying genetic mechanisms by identifying differentially expressed genes, proteins, and metabolic pathways linked to quality traits, complementing GWAS data. Leveraging these functional genomics techniques can optimize beef cattle breeding for enhanced quality traits to meet high-quality beef demand. This paper provides a comprehensive overview of the current state of applications of omics technologies in uncovering functional variants underlying beef quality complexities. By highlighting the latest findings from GWAS, GS, transcriptomics, proteomics, and metabolomics studies, this work seeks to serve as a valuable resource for fostering a deeper understanding of the complex relationships between genetics, gene expression, protein dynamics, and metabolic pathways in shaping beef quality.

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.

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.

A review of the role of epigenetic studies for intramuscular fat deposition in beef cattle

Intramuscular fat (IMF) deposition profoundly influences meat quality and economic value in beef cattle production. Meanwhile, contemporary developments in epigenetics have opened new outlooks for understanding the molecular basics of IMF regulation, and it has become a key area of research for world scholars. Therefore, the aim of this paper was to provide insight and synthesis into the intricate relationship between epigenetic mechanisms and IMF deposition in beef cattle. The methodology involves a thorough analysis of existing literature, including pertinent books, academic journals, and online resources, to provide a comprehensive overview of the role of epigenetic studies in IMF deposition in beef cattle. This review summarizes the contemporary studies in epigenetic mechanisms in IMF regulation, high-resolution epigenomic mapping, single-cell epigenomics, multi-omics integration, epigenome editing approaches, longitudinal studies in cattle growth, environmental epigenetics, machine learning in epigenetics, ethical and regulatory considerations, and translation to industry practices from perspectives of IMF deposition in beef cattle. Moreover, this paper highlights DNA methylation, histone modifications, acetylation, phosphorylation, ubiquitylation, non-coding RNAs, DNA hydroxymethylation, epigenetic readers, writers, and erasers, chromatin immunoprecipitation followed by sequencing, whole genome bisulfite sequencing, epigenome-wide association studies, and their profound impact on the expression of crucial genes governing adipogenesis and lipid metabolism. Nutrition and stress also have significant influences on epigenetic modifications and IMF deposition. The key findings underscore the pivotal role of epigenetic studies in understanding and enhancing IMF deposition in beef cattle, with implications for precision livestock farming and ethical livestock management. In conclusion, this review highlights the crucial significance of epigenetic pathways and environmental factors in affecting IMF deposition in beef cattle, providing insightful information for improving the economics and meat quality of cattle production.

Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project

More people in the world depend on water buffalo for their livelihoods than on any other domesticated animals, but its genetics is still not extensively explored. The 1000 Buffalo Genomes Project (1000BGP) provides genetic resources for global buffalo population study and tools to breed more sustainable and productive buffaloes. Here we report the most contiguous swamp buffalo genome assembly (PCC_UOA_SB_1v2) with substantial resolution of telomeric and centromeric repeats, ∼4-fold more contiguous than the existing reference river buffalo assembly and exceeding a recently published male swamp buffalo genome. This assembly was used along with the current reference to align 140 water buffalo short-read sequences and produce a public genetic resource with an average of ∼41 million single nucleotide polymorphisms per swamp and river buffalo genome. Comparison of the swamp and river buffalo sequences showed ∼1.5% genetic differences, and estimated divergence time occurred 3.1 million years ago (95% CI, 2.6-4.9). The open science model employed in the 1000BGP provides a key genomic resource and tools for a species with global economic relevance.