Identification of Biological Pathways Contributing to Marbling in Skeletal Muscle to Improve Beef Cattle Breeding

A review of sustainable cattle genetic improvement in the Peruvian Highlands

Cattle breeding in the highlands of Peru is an important economic activity at the level of the entire rural extension, because it serves as an economic reserve for rural families and forms an integral part of the agricultural producer's culture. This review aimed to provide a literature- and research-based approach to the fundamental aspects of a national genetic improvement plan, emphasising the efficacy of using a bovine germplasm of high genetic quality as an initiative to implement genetic improvement programmes. The concepts to be implemented in national livestock farming include high yield, feed conversion efficiency, and minimum greenhouse gas emissions. The use of a dual-purpose germplasm to maximise the usefulness of livestock farmers and the implementation of improvement programmes, with the expectation of achieving a differential increase in genetic merit, were also considered. In addition to aspects related to milk and carcase quality, there is a territorial approach, such as the case of breeds that adapt to terminal crossbreeding and consider reproductive aspects. One of the final aspects considered is the conservation and valuation of local animals within conservation and improvement plans owing to their resistance and adaptation to temperature and altitude conditions.

Genomic evidence for human-mediated introgressive hybridization and selection in the developed breed

BACKGROUND

The pig (Sus Scrofa) is one of the oldest domesticated livestock species that has undergone extensive improvement through modern breeding. European breeds have advantages in lean meat development and highly-productive body type, whereas Asian breeds possess extraordinary fat deposition and reproductive performance. Consequently, Eurasian breeds have been extensively used to develop modern commercial breeds for fast-growing and high prolificacy. However, limited by the sequencing technology, the genome architecture of some nascent developed breeds and the human-mediated impact on their genomes are still unknown.

RESULTS

Through whole-genome analysis of 178 individuals from an Asian locally developed pig breed, Beijing Black pig, and its two ancestors from two different continents, we found the pervasive inconsistent gene trees and species trees across the genome of Beijing Black pig, which suggests its introgressive hybrid origin. Interestingly, we discovered that this developed breed has more genetic relationships with European pigs and an unexpected introgression from Asian pigs to this breed, which indicated that human-mediated introgression could form the porcine genome architecture in a completely different type compared to native introgression. We identified 554 genomic regions occupied 63.30 Mb with signals of introgression from the Asian ancestry to Beijing Black pig, and the genes in these regions enriched in pathways associated with meat quality, fertility, and disease-resistant. Additionally, a proportion of 7.77% of genomic regions were recognized as regions that have been under selection. Moreover, combined with the results of a genome-wide association study for meat quality traits in the 1537 Beijing Black pig population, two important candidate genes related to meat quality traits were identified. DNAJC6 is related to intramuscular fat content and fat deposition, and RUFY4 is related to meat pH and tenderness.

CONCLUSIONS

Our research provides insight for analyzing the origins of nascent developed breeds and genome-wide selection remaining in the developed breeds mediated by humans during modern breeding.

Identification of Hub Genes and Target miRNAs Crucial for Milk Production in Holstein Friesian Dairy Cattle

Dairy milk production is a quantitative trait that is controlled by many biological and environmental factors. This study employs a network-driven systems approach and clustering algorithm to uncover deeper insights into its genetic associations. We analyzed the GSE33680 dataset from the GEO database to understand the biological importance of milk production through gene expression and modules. In this study, we employed CytoNCA and ClusterONE plugins within Cytoscape for network analysis. Moreover, miRWalk software was utilized to detect miRNAs, and DAVID was employed to identify gene ontology and pathways. The results revealed 140 up-regulated genes and 312 down-regulated genes. In addition, we have identified 91 influential genes and 47 miRNAs that are closely associated with milk production. Through our examination of the network connecting these genes, we have found significant involvement in important biological processes such as calcium ion transit across cell membranes, the BMP signaling pathway, and the regulation of MAPK cascade. The conclusive network analysis further reveals that GAPDH, KDR, CSF1, PYGM, RET, PPP2CA, GUSB, and PRKCA are closely linked to key pathways essential for governing milk production. Various mechanisms can control these genes, making them valuable for breeding programs aiming to enhance selection indexes.

Marinades Based on Natural Ingredients as a Way to Improve the Quality and Shelf Life of Meat: A Review

Marinating is a traditional method of improving the quality of meat, but it has been modified in response to consumer demand for "clean label" products. The aim of this review is to present scientific literature on the natural ingredients contained in marinades, the parameters of the marinating process, and certain mechanisms that bring about changes in meat. A review was carried out of publications from 2000 to 2023 available in Web of Science on the natural ingredients of meat marinades: fruit and vegetables, seasonings, fermented dairy products, wine, and beer. The review showed that natural marinades improve the sensory quality of meat and its culinary properties; they also extend its shelf life. They affect the safety of meat products by limiting the oxidation of fats and proteins. They also reduce biogenic amines and the formation of heterocyclic aromatic amines (HAAs) and polycyclic aromatic hydrocarbons (PAHs). This is possible due to the presence of biologically active substances and competitive microflora from dairy products. However, some marinades, especially those that are acidic, cause a slightly acidic flavour and an unfavourable colour change. Natural compounds in the ingredients of marinades are accepted by consumers. There are no results in the literature on the impact of natural marinades on the nutritional value and health-promoting potential of meat products, so it can be assumed that this is a future direction for scientific research.

Improving the textural and microstructural quality of cow meat by black chokeberry, grape, and hawthorn vinegar-based marination

This study was designed to investigate the effects of vinegar-based marinades on pH, technological properties, color, microstructure, texture, and sensory characteristics of 9-year-old Holstein meat which had tough texture. To marinate the Longissimus lumborum steaks, three different marinades were prepared depending on the different additions of vinegar: black chokeberry (BV), grape (GV), and hawthorn vinegars (HV). The group with water (without vinegar) was prepared as a control sample (C). The steak samples were dipped into the vinegar-based marinades and stored at 4°C for 24 h. Vinegar-based marinades decreased the pH and cooking loss of the samples (p < .05). The highest a* values were determined in the BV group, while the samples marinated with vinegar-based marinades had lower L* values than the control group (p < .05). The samples marinated with grape vinegar marinade had the lowest hardness, WBSF, and WBSE values (p < .05). SEM images and sensory analysis results also supported these texture results. The results suggest that grape vinegar-based marinade may be a promising natural tenderizer to improve textural characteristics of tough meats.

Effects of Marinades Prepared from Food Industry By-Products on Quality and Biosafety Parameters of Lamb Meat

This study aimed to develop marinade formulas based on by-products from the dairy, berry, and fruit industries and apply them to lamb meat (LM) treatments to improve the safety and quality characteristics of the meat. To fulfil this aim, six marinade (M) formulations were created based on acid whey (AW) fermented with Lacticaseibacillus casei (Lc) and Liquorilactobacillus uvarum (Lu), either alone or combined with freeze-dried apple (AP) or blackcurrant (BC) pomace. The most appropriate fermentation times for the marinades were selected according to the lower pH values and higher viable LAB counts in the samples. Additionally, the antimicrobial activity of the selected marinades against pathogenic and opportunistic bacterial strains was tested. The characteristics of the LM were analysed after 24 and 48 h of treatment, including physicochemical, technological, and microbiological parameters, as well as overall acceptability. It was established that, after 48 h of fermentation, all of the tested marinades, except M-AWLuBC, had lactic acid bacterial counts > 8.0 log10 CFU·mL−1 and pH values < 3.74. The broadest spectra of pathogen inhibition were observed in the M-AWLuAP and M-AWLuBC marinades. The latter formulations improved the water holding capacity (WHC) and overall acceptability of the LM, while, in the LM-AWLcAP samples, histamine, cadaverine, putrescine, tryptamine, and phenylethylamine were not formed. Lastly, LM treatment with the M-AWLcAP and M-AWLuAP formulas for 48 h achieved the highest overall acceptability (9.04 and 9.43), tenderness (1.53 and 1.47 kg·cm−2) and WHC (2.95% and 3.5%) compared to the control samples.

Exploring and Identifying Candidate Genes and Genomic Regions Related to Economically Important Traits in Hanwoo Cattle

The purpose of the current review was to explore and summarize different studies concerning the detection and characterization of candidate genes and genomic regions associated with economically important traits in Hanwoo beef cattle. Hanwoo cattle, the indigenous premium beef cattle of Korea, were introduced for their marbled fat, tenderness, characteristic flavor, and juiciness. To date, there has been a strong emphasis on the genetic improvement of meat quality and yields, such as backfat thickness (BFT), marbling score (MS), carcass weight (CW), eye muscle area (EMA), and yearling weight (YW), as major selection criteria in Hanwoo breeding programs. Hence, an understanding of the genetics controlling these traits along with precise knowledge of the biological mechanisms underlying the traits would increase the ability of the industry to improve cattle to better meet consumer demands. With the development of high-throughput genotyping, genomewide association studies (GWAS) have allowed the detection of chromosomal regions and candidate genes linked to phenotypes of interest. This is an effective and useful tool for accelerating the efficiency of animal breeding and selection. The GWAS results obtained from the literature review showed that most positional genes associated with carcass and growth traits in Hanwoo are located on chromosomes 6 and 14, among which LCORL, NCAPG, PPARGC1A, ABCG2, FAM110B, FABP4, DGAT1, PLAG1, and TOX are well known. In conclusion, this review study attempted to provide comprehensive information on the identified candidate genes associated with the studied traits and genes enriched in the functional terms and pathways that could serve as a valuable resource for future research in Hanwoo breeding programs.

Transcriptome analysis reveals the molecular regulatory network of muscle development and meat quality in Sunit lamb supplemented with dietary probiotic

Supplementing animal feed with probiotic additives can promote muscle production and improve meat quality. The study aimed to explore the effects of dietary probiotics supplementation on the performance, meat quality and muscle transcriptome profile in Sunit lamb. Overall, feeding probiotics significantly increased the body length, LT area, pH24h and intramuscular fat (IMF) content, but decreased cooking loss and meat shear force compared to the control group (P < .05). A total of 651 differentially expressed genes (DEGs) were found in probiotic supplemented lambs. Pathway analysis revealed that DEGs were involved in multiple pathways related to muscle development and fat deposition, such as the ECM-receptor interactions, the MAPK signaling pathway and the FoxO signaling pathway. Therefore, dietary probiotic supplementation can improve muscle development and final meat quality in Sunit lambs by altering gene expression profiles associated with key pathways, providing unique insights into the molecular mechanisms by which dietary probiotics regulate muscle development in the lamb industry.

Using Untargeted LC-MS Metabolomics to Identify the Association of Biomarkers in Cattle Feces with Marbling Standard Longissimus Lumborum

Background: To improve the grade of beef marbling has great economic value in the cattle industry since marbling has the traits of high quality and comprehensive nutrition. And because of the marbling’s importance and complexity, it is indispensable to explore marbled beef at multiple levels. This experiment studied the relationship between fecal metabolites and marbling characters, and further screened biomarkers. Results: We performed fecal metabolomics analysis on 30 individuals selected from 100 crossbreed cattle (Luxi Yellow cattle ♀ × Japanese Wagyu cattle ♂), 15 with an extremely high-grade marbling beef and 15 with an extremely low-grade marbling beef. A total of 9959 and 8389 m/z features were detected in positive ionization and negative ionization mode by liquid chromatography-mass spectrometry (LC-MS). Unfortunately, the sample separation in the PCA is not obvious, and the predictive ability of the orthogonal partial least squares discrimination analysis (OPLS-DA) model is not good. However, we got six differential metabolites filtered by VIP > 1 and p < 0.05. After that, we used weighted correlation network analysis (WGCNA) and found out a module in each positive and negative mode most related to the trait of marbling beef, and then identified three metabolites in positive mode. By further annotation of the Kyoto encyclopedia of genes and genomes (KEGG), it was found that these metabolites involved a variety of metabolic ways, including sphingomyelin metabolism, linoleic acid metabolism, glycerophospholipid metabolism, and so on. Finally, receiver operating characteristic (ROC) analysis was used to evaluate the predictability of metabolites, and the result showed that SM(d18:0/16:1(9Z)) (AUC = 0.72), PC(15:0/18:2(9Z,12Z)) (AUC = 0.72), ADP (AUC = 0.71), PC(16:0/16:0) (AUC = 0.73), and 3-O-Sulfogalactosylceramide (d18:1/18:0) (AUC = 0.69) have an accuracy diagnosis. Conclusions: In conclusion, this study supports new opinions for the successive evaluation of marbling beef through metabolites. Furthermore, six non-invasive fecal metabolites that can evaluate beef marbling grade were found, including SM(d18:0/16:1(9Z)), PC(15:0/18:2(9Z,12Z)), ADP, PC(16:0/16:0), and 3-O-Sulfogalactosylceramide.

Leptin gene contributes to beef marbling standard, meat brightness, meat firmness, and beef fat standard of the Kumamoto sub-breed of Japanese Brown cattle

The Kumamoto sub-breed of Japanese Brown cattle has unique characteristics, such as great growth rate, and their contribution as future breeding materials is expected. To develop a DNA marker for their breeding, we investigated the effects of Leptin gene, controlling energy homeostasis, on carcass traits of the Kumamoto sub-breed. Sequence comparison identified five single nucleotide polymorphisms (SNPs): four linked synonymous mutations and one nonsynonymous mutation. Statistical analysis revealed that c.239C > T (p.A80V) had significant effects on the traits related with quality grade: beef marbling standard (p = 0.0132), meat brightness (p = 0.0383), and meat firmness (p = 0.0115). The C allele showed favorable effects; these scores of the C/C cattle were significantly higher than those of the C/T cattle. On the other hand, the effect of c.399T > C was observed on meat firmness (p = 0.0172) and beef fat standards (BFS) (p = 0.0129). The C/C cattle showed higher values of these traits than the T/T cattle. Our data suggested that these SNPs in Leptin gene could be used as a DNA marker for breeding of the Kumamoto sub-breed.

Haplotype-Based Single-Step GWAS for Yearling Temperament in American Angus Cattle

Behavior is a complex trait and, therefore, understanding its genetic architecture is paramount for the development of effective breeding strategies. The objective of this study was to perform traditional and weighted single-step genome-wide association studies (ssGWAS and WssGWAS, respectively) for yearling temperament (YT) in North American Angus cattle using haplotypes. Approximately 266 K YT records and 70 K animals genotyped using a 50 K single nucleotide polymorphisms (SNP) panel were used. Linkage disequilibrium thresholds (LD) of 0.15, 0.50, and 0.80 were used to create the haploblocks, and the inclusion of non-LD-clustered SNPs (NCSNP) with the haplotypes in the genomic models was also evaluated. WssGWAS did not perform better than ssGWAS. Cattle YT was found to be a highly polygenic trait, with genes and quantitative trait loci (QTL) broadly distributed across the whole genome. Association studies using LD-based haplotypes should include NCSNPs and different LD thresholds to increase the likelihood of finding the relevant genomic regions affecting the trait of interest. The main candidate genes identified, i.e., ATXN10, ADAM10, VAX2, ATP6V1B1, CRISPLD1, CAPRIN1, FA2H, SPEF2, PLXNA1, and CACNA2D3, are involved in important biological processes and metabolic pathways related to behavioral traits, social interactions, and aggressiveness in cattle. Future studies should further investigate the role of these candidate genes.

Influence of Marination with Aromatic Herbs and Cold Pressed Oils on Black Angus Beef Meat

Beef aging is one of the most common methods used for improving its qualities. The main goal of the present study was to analyse the influence of different cold pressed oils and aromatic herbs during marination process on the nutritional, textural, and sensory attributes of the final grilled sirloin samples. In order to fulfil this goal, methods like GC-MS, HPLC/DAD/ESI-MS, HLPC-RID were performed to quantify fatty acids, phenolic acids, and organic acids, respectively. Textural and sensory analysis were performed with CT 3 Texture Analyser and hedonic test. The results showed high improvement of the meat grilled samples regarding the content of phenolic acids, and textural and sensory characteristics. Pearson values indicate strong positive correlations between raw and grilled samples regarding their content in phenolic acids. Hardness, chewiness, gumminess decreased during marination, meanwhile, resilience, and cohesiveness increased. Sensory analysis highlighted that meat samples marinated with olive oil and rosemary for 120 h reached the highest hedonic score among the tested samples.

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

Maintaining a high level of beef consumption requires paying attention not only to quantitative traits but also to the quality and dietary properties of meat. Growing consumer demands do not leave producers many options for how animals are selected for breeding and animal keeping. Meat and carcass fatness quality traits, which are influenced by multiple genes, are economically important in beef cattle breeding programs. The recent availability of genome sequencing methods and many previously identified molecular markers offer new opportunities for animal breeding, including the use of molecular information in selection programs. Many gene polymorphisms have thus far been analyzed and evaluated as potential candidates for molecular markers of meat quality traits. Knowledge of these markers can be further applied to breeding programs through marker-assisted selection. In this literature review, we discuss the most promising and well-described candidates and their associations with selected beef production traits.

Productivity of steers of different genotypes: forecast based on interior indicators

ABSTRACT Meat productivity and quality of beef are determined by a number of factors, including pedigree traits of animals. Meat productivity is closely related to the biological patterns of their growth and development. Considering the patterns that affect meat productivity enables effective growing and fattening of livestock and obtaining commercially viable beef. To predict economically useful traits in beef cattle breeding, interior indicators can be used, as they reflect the metabolic picture of the animal’s body. The research studies in physiology and biochemistry of livestock aimed at revealing the persistent mechanisms of a growing animal organism make them relevant. The article identifies a correlation between the interior indicators and the fattening indicators of three experimental groups of steers. The main forecasting factors of meat productivity indicators have been substantiated. Regression coefficients have been found and show how much the live weight varies depending on the determining factors. Meat productivity predicting procedures have been modeled with respect to the protein content in blood serum.

Characterization of the promoter region of bovine ATP5B: roles of MyoD and GATA1 in the regulation of basal transcription

Intramuscular fat (IMF) content is a key determinant of beef quality, making it a key topic of research interest. ATP5B serves as the catalytic component of the mitochondrial ATP synthase complex and plays essential roles in controlling fat contents and oxidative metabolism in bovine skeletal muscle. In this study, we determined that bovine ATP5B was highly expressed in longissimus thoracis. To elucidate the molecular mechanisms involved in bovine ATP5B regulation, we cloned and characterized the promoter region of ATP5B. Applying 5'-rapid amplification of cDNA end analysis (RACE), we identified two transcriptional start sites (TSSs) in its promoter region. Using a series of 5'-deletion promoter plasmids in luciferase reporter assay, we found that the proximal minimal promoter of ATP5B was located within the region -539/220 relative to the TSS. Site-directed mutation in combination with chromatin immunoprecipitation (ChIP) assays demonstrated that MyoD and GATA1 binding to the promoter region drives bovine ATP5B transcription. Taken together, these results provide new insight into the regulatory mechanisms of ATP5B transcription in mediating the IMF content of beef.