Search Results (36)

While bulk RNA sequencing provides a comprehensive view of transcriptomes, it lacks cell type specificity. Single-cell RNA sequencing (scRNA-seq) overcomes this limitation by providing detailed insights at the individual cell level, though it involves higher costs. Deconvolution methods can estimate cell type proportions in bulk RNA-seq data, but their results may vary based on the scRNA-seq reference data and software used. This study investigates the estimation of muscle fiber type proportions through deconvolution analysis of Longissimus dorsi muscle bulk RNA-seq data from late-gestation Holstein Friesian multiparous cows. Four software tools (i.e., CIBERSORTx, Cellanneal, DeconvR-NNLS, and DeconvR-RLM) were compared using scRNA-seq reference data from Brahman and Wagyu cattle breeds, which included proportions of types I, IIa, and IIx myofibers. Kruskal–Wallis and Dunn’s tests revealed that the breed of reference data significantly influenced the proportions of type IIa and IIx muscle fibers across different deconvolution methods. To the best of our knowledge, this is the first study to show that the cattle breed used in reference scRNA-seq data can substantially impact deconvolution outcomes, highlighting a critical consideration for accurate cell type proportion estimation in livestock genomics. These findings suggest that future deconvolution studies should carefully consider breed compatibility between reference and target datasets. Full article

Beef fat injection technology, used to enhance the perceived quality of lower-grade meat, often results in artificially marbled beef that mimics the visual traits of Wagyu, characterized by dense fat distribution. This practice, driven by the high cost of Wagyu and the affordability of fat-injected beef, has led to the proliferation of mislabeled “Wagyu-grade” products sold at premium prices, posing potential food safety risks such as allergen exposure or consumption of unverified additives, which can adversely affect consumer health. Addressing this, this study introduces a smart sensing system integrated with handheld mobile devices, enabling consumers to capture beef images during purchase for real-time health-focused assessment. The system analyzes surface texture and color, transmitting data to a server for classification to determine if the beef is artificially marbled, thus supporting informed dietary choices and reducing health risks. Images are processed by applying a region of interest (ROI) mask to remove background noise, followed by partitioning into grid blocks. Local binary pattern (LBP) texture features and RGB color features are extracted from these blocks to characterize surface properties of three beef types (Wagyu, regular, and fat-injected). A support vector machine (SVM) model classifies the blocks, with the final image classification determined via majority voting. Experimental results reveal that the system achieves a recall rate of 95.00% for fat-injected beef, a misjudgment rate of 1.67% for non-fat-injected beef, a correct classification rate (CR) of 93.89%, and an F1-score of 95.80%, demonstrating its potential as a human-centered healthcare tool for ensuring food safety and transparency. Full article

Intramuscular fat (IMF) content in beef cattle is a critical determinant of beef meat quality, as it positively influences juiciness, tenderness, and palatability. In China, the crossbreeding of Wagyu and Angus is a prevalent method for achieving a better marbling level. However, the molecular mechanisms governing IMF regulation in these crossbreeds remain poorly understood. To elucidate the mechanism of IMF deposition in these crossbred cattle, we conducted a comparative transcriptomic analysis of longissimus dorsi muscles and livers from cattle with divergent IMF content. RNA-seq revealed 940 and 429 differentially expressed genes (DEGs) in the liver and muscle, respectively, with 60 genes co-differentially expressed (co-DEGs) in both tissues. Functional enrichment highlighted lipid metabolism pathways including fatty acid β-oxidation, PPAR signaling, and glycerolipid metabolism. A total of eleven genes including ACAA2, ACADL, ACOX2, CPT1B, CPT2, LPL, SLC27A1, ACAT1, GK, ACOX3, and ACSM5, were screened as key candidate genes for IMF deposition. A “liver–muscle” regulatory network of IMF deposition was built to illustrate the tissues’ interaction. The reliability of the transcriptomic data was verified by quantitative reverse real-time PCR (qRT-PCR). Our findings provide novel molecular markers for increasing the IMF content and accelerating the genetic improvement of beef quality traits in crossbred cattle. Full article

Objectives: This study investigated the long-term effects of maternal undernutrition on overall muscle metabolism, growth performance, and muscle characteristics in postnatal offspring of Wagyu (Japanese Black) cattle. Methods: Wagyu cows were divided into nutrient-adequate (control, CNT; n = 4, 120% of requirements) and nutrient-restricted groups (NR; n = 4; 60% of requirements), and treated from day 35 of gestation until parturition. Diets were delivered on the basis of crude protein requirements, meeting 100% and 80% of dry matter requirements in CNT and NR groups, respectively. All offspring were provided with the same diet from birth to 300 days of age (d). Longissimus thoracis muscle (LM) samples were collected from the postnatal offspring. Results: The NR offspring had lower birth body weight, but their body weight caught up before weaning. These offspring showed enhanced efficiency in nutrient utilization during the post-weaning growth period. Comprehensive analyses of metabolites and transcripts revealed the accumulation of proteinogenic amino acid, asparagine, in NR offspring LM at 300 d, while the abundance of nicotinamide adenine dinucleotide (NADH) and succinate were reduced. These changes were accompanied by decreased gene expression of nicotinamide phosphoribosyltransferase (NAMPT), NADH: ubiquinone oxidoreductase subunit A12 (NDUFA12), and NADH dehydrogenase subunit 5 (ND5), which are essential for mitochondrial energy production. Additionally, NR offspring LM exhibited decreased abundance of neurotransmitter, along with a higher proportion of slow-oxidative myofibers and a lower proportion of fast-oxidative myofibers at 300 d. Conclusions: Offspring from nutrient-restricted cows might suppress muscle energy production, primarily in the mitochondria, and conserve energy expenditure for muscle protein synthesis. These findings suggest that maternal undernutrition programs a thrifty metabolism in offspring muscle, with long-term effects. Full article

This study aimed to investigate the flavor formation and meat quality differences among different beef cuts in Chinese Wagyu cattle. The metabolites and gene expression profiles of chuck, neck, rump, tenderloin, and longissimus lumborum cuts were analyzed. The results revealed that a total of 240 volatile organic compounds and 779 lipid molecules were detected among the beef cuts, with hydrocarbons (accounting for 29.71%) and triglycerides (representing 41.21%) emerging as the most prominent compounds, respectively. The sensory-directed analysis highlighted the significance of sweet and fruity aroma compounds, which contributed to the distinct aroma profiles among different beef cuts. Additionally, a total of 60 key lipid molecular markers, including FA(18:1), PC(40:5), TG(18:0_16:1_18:1), and TG(36:0_18:1), etc., were identified as playing crucial roles in the generation of essential lipid compounds across five different beef cuts. Integrative analysis of multi-omics data pinpointed a cluster of differentially expressed genes (e.g., DLD, ACADM, PCCA, SCD), which were involved in the regulation of valine, leucine, and isoleucine degradation pathways and lipid metabolism. Taken together, this study has identified key metabolites and candidate genes influencing meat quality across different beef cuts, providing a valuable resource for the molecular breeding of high-quality traits in beef cattle. Full article

Background: Japanese Black beef is known for its high intramuscular fat content, an important factor in its distinctive Wagyu aroma. Wet aging, which involves vacuum-packing meat and storing it at low temperatures, enhances flavor, texture, and tenderness and is essential for maintaining and improving meat quality. In this study, changes in metabolites and lipid profiles were investigated during the wet aging of Japanese Black and Holstein beef. Methods/Results: Gas chromatography–mass spectrometry identified 113 metabolites in Japanese Black beef and 94 in Holstein beef, with significant increases in metabolites like aspartic acid and maleic acid over the aging period. Regarding lipid composition, total free fatty acids significantly increased with wet aging, with Japanese Black beef showing significantly higher concentrations of oleic and linoleic acids than Holstein beef. Additionally, lipid analysis by liquid chromatography–mass spectrometry revealed a reduction in specific phospholipids, particularly lysophosphatidylcholine (LPC) and lysophosphatidylethanolamine (LPE), with notable decreases in LPC (18:1), LPC (18:2), LPE (18:1), and LPE (18:2). Conclusions: These results suggest that wet aging influences the stability of membrane lipids, facilitating the degradation of phospholipids into free fatty acids, and improving the flavor of Japanese Black beef. Full article

This study investigated the factors influencing gestation length in a herd of Wagyu cattle in Rio Grande do Sul, Brazil. Fifty-five multiparous purebred Wagyu cows underwent a Fixed-Time Artificial Insemination (FTAI) protocol using semen from a bull randomly selected from five bulls representing three distinct genetic lines. Following birth, we recorded the calves’ gender, weight, and gestation length. The ANOVA test was employed to assess genetic effects on calf weight and gestation length, with significance set at p < 0.05. The 55 inseminations resulted in 52 births, comprising 34 females and 18 males. The average calf weight was 25.9 kg, with 25.2 kg for females and 27.2 kg for males (p = 0.38). No significant effect was observed for birth weight concerning the sire’s genetic line (p = 0.42), although there was a trend towards an effect from the maternal grandfather (p = 0.09). The mean duration of pregnancy was 283.8 ± 5.91 days, with no significant effect of gender on gestation length (p = 0.6). However, when evaluating the genetic influences on gestation length, we observed significant effects from the sire’s genetic line (p < 0.0001) and the maternal grandfather (p < 0.0001). Notably, longer pregnancies resulted in heavier calves (p < 0.0001). This is the first study to identify the effects of Wagyu breed lines on pregnancy length. Full article

(1) Background: Target capture sequencing (TCS) is potentially a cost-effective way to detect single-nucleotide polymorphisms (SNPs) and an alternative to SNP array-based genotyping. (2) Methods: We evaluated the effectiveness and reliability of TCS in cattle breeding scenarios using 48 female and 8 male samples. DNA was extracted from blood samples, targeted for 71,746 SNPs with TWIST probes, and sequenced on an MGI platform. GATK and BCFtools were evaluated for the best genotyping calling tool. The genotypes were compared to existing genotypes from the Versa50K SNP array of the same animals by measuring accuracy as concordance (%) and R². (3) Results: In this study, 71,553 SNPs and 166 indels were identified. The genotype comparison of 37,130 common SNPs between TCS and SNP arrays yielded high agreement, with a mean concordance of 98%, R² of 0.98 and Cohen’s kappa of 0.97. The concordances of sex prediction, parent verification and validation of five genotype markers of interest important for Wagyu breeding were 100% between TCS and SNP array. The elements of the genomic relationship matrix (GRM) constructed from the SNP array and TCS data demonstrated a correlation coefficient approaching unity (r = 0.9998). (4) Conclusions: Compared to the SNP array, TCS is a comparable, cost-effective and flexible platform for genotyping SNPs, including non-model organisms and underrepresented commercial animal populations. Full article

Wagyu beef is gaining worldwide popularity, primarily due to the fineness of its marbling. Currently, the evaluation of this marbling is performed visually by graders. This method has several issues: varying evaluation standards among graders, reduced accuracy due to long working hours and external factors causing fatigue, and fluctuations in grading standards due to the grader’s mood at the time. This paper proposes the use of fractal analysis for the grading evaluation of beef marbling to achieve automatic grading without the inconsistencies caused by human factors. In the experiments, cross-sectional images of the parts used for visual judgment were taken, and fractal analysis was performed on these images to evaluate them using fractal dimensions. The results confirmed a correlation between the marbling evaluation and the fractal dimensions, demonstrating that quantitative evaluation can be achieved, moving away from qualitative visual assessments. Full article

We aimed to determine the effects of maternal nutrient restriction (MNR) on the DNA methylation and gene expression patterns associated with metabolism and immunopoiesis in the thymuses of fetal Wagyu cattle. Pregnant cows were allocated to two groups: a low-nutrition (LN; 60% nutritional requirement; n = 5) and a high-nutrition (HN; 120% nutritional requirement, n = 6) group, until 8.5 months of gestation. Whole-genome bisulfite sequencing (WGBS) and RNA sequencing were used to analyze DNA methylation and gene expression, while capillary electrophoresis–Fourier transform mass spectrometry assessed the metabolome. WGBS identified 4566 hypomethylated and 4303 hypermethylated genes in the LN group, with the intergenic regions most frequently being methylated. Pathway analysis linked hypoDMGs to Ras signaling, while hyperDMGs were associated with Hippo signaling. RNA sequencing found 94 differentially expressed genes (66 upregulated, 28 downregulated) in the LN group. The upregulated genes were tied to metabolic pathways and oxidative phosphorylation; the downregulated genes were linked to natural killer cell cytotoxicity. Key overlapping genes (GRIA1, CACNA1D, SCL25A4) were involved in cAMP signaling. The metabolomic analysis indicated an altered amino acid metabolism in the MNR fetuses. These findings suggest that MNR affects DNA methylation, gene expression, and the amino acid metabolism, impacting immune system regulation during fetal thymus development in Wagyu cattle. Full article

Past and ongoing selection shapes the genomes of livestock breeds. Identifying such signatures of selection allows for uncovering the genetic bases of affected phenotypes, including economically important traits and environmental adaptations, for the further improvement of breed genetics to respond to climate and economic challenges. Turano-Mongolian cattle are a group of taurine breeds known for their adaptation to extreme environmental conditions and outstanding production performance. Buryat Turano-Mongolian cattle are among the few breeds adapted to cold climates and poor forage. Wagyu, on the other hand, is famous for high productivity and unique top-quality marbled meat. We used hapFLK, the de-correlated composite of multiple signals (DCMS), PBS, and F_ST methods to search for signatures of selection in their genomes. The scans revealed signals in genes related to cold adaptation (e.g., STAT3, DOCK5, GSTM3, and CXCL8) and food digestibility (SI) in the Buryat breed, and growth and development traits (e.g., RBFOX2 and SHOX2) and marbling (e.g., DGAT1, IQGAP2, RSRC1, and DIP2B) in Wagyu. Several putatively selected genes associated with reproduction, immunity, and resistance to pathogens were found in both breed genomes. The results of our work could be used for creating new productive adapted breeds or improving the extant breeds. Full article

Numerous studies have shown that combining populations from similar or closely related genetic breeds improves the accuracy of genomic predictions (GP). Extensive experimentation with diverse Bayesian and genomic best linear unbiased prediction (GBLUP) models have been developed to explore multi-breed genomic selection (GS) in livestock, ultimately establishing them as successful approaches for predicting genomic estimated breeding value (GEBV). This study aimed to assess the effectiveness of using BayesR and GBLUP models with linkage disequilibrium (LD)-weighted genomic relationship matrices (GRMs) for genomic prediction in three different beef cattle breeds to identify the best approach for enhancing the accuracy of multi-breed genomic selection in beef cattle. Additionally, a comparison was conducted to evaluate the predictive precision of different marker densities and genetic correlations among the three breeds of beef cattle. The GRM between Yunling cattle (YL) and other breeds demonstrated modest affinity and highlighted a notable genetic concordance of 0.87 between Chinese Wagyu (WG) and Huaxi (HX) cattle. In the within-breed GS, BayesR demonstrated an advantage over GBLUP. The prediction accuracies for HX cattle using the BayesR model were 0.52 with BovineHD BeadChip data (HD) and 0.46 with whole-genome sequencing data (WGS). In comparison to the GBLUP model, the accuracy increased by 26.8% for HD data and 9.5% for WGS data. For WG and YL, BayesR doubled the within-breed prediction accuracy to 14.3% from 7.1%, outperforming GBLUP across both HD and WGS datasets. Moreover, analyzing multiple breeds using genomic selection showed that BayesR consistently outperformed GBLUP in terms of predictive accuracy, especially when using WGS. For instance, in a mixed reference population of HX and WG, BayesR achieved a significant accuracy of 0.53 using WGS for HX, which was a substantial enhancement over the accuracies obtained with GBLUP models. The research further highlights the benefit of including various breeds in the reference group, leading to enhanced accuracy in predictions and emphasizing the importance of comprehensive genomic selection methods. Our research findings indicate that BayesR exhibits superior performance compared to GBLUP in multi-breed genomic prediction accuracy, achieving a maximum improvement of 33.3%, especially in genetically diverse breeds. The improvement can be attributed to the effective utilization of higher single nucleotide polymorphism (SNP) marker density by BayesR, resulting in enhanced prediction accuracy. This evidence conclusively demonstrates the significant impact of BayesR on enhancing genomic predictions in diverse cattle populations, underscoring the crucial role of genetic relatedness in selection methodologies. In parallel, subsequent studies should focus on refining GRM and exploring alternative models for GP. Full article

Efficient cold-chain delivery is essential for maintaining a sustainable global food supply. This study used metabolomic analysis to examine meat quality changes during the “wet aging” of crossbred Wagyu beef during cold storage. The longissimus thoracic (Loin) and adductor muscles (Round) of hybrid Wagyu beef, a cross between the Japanese Black and Holstein–Friesian breeds, were packaged in vacuum film and refrigerated for up to 40 days. Sensory evaluation indicated an increase in the umami and kokumi taste owing to wet aging. Comprehensive analysis using gas chromatography-mass spectrometry identified metabolite changes during wet aging. In the Loin, 94 metabolites increased, and 24 decreased; in the Round, 91 increased and 18 decreased. Metabolites contributing to the umami taste of the meat showed different profiles during wet aging. Glutamic acid increased in a cold storage-dependent manner, whereas creatinine and inosinic acid degraded rapidly even during cold storage. In terms of lipids, wet aging led to an increase in free fatty acids. In particular, linoleic acid, a polyunsaturated fatty acid, increased significantly among the free fatty acids. These results provide new insight into the effects of wet aging on Wagyu-type beef, emphasizing the role of free amino acids, organic acids, and free fatty acids generated during cold storage. Full article

Wagyu cattle are well known for their greater intramuscular fat content which improves eating quality for consumers. These experiments were designed to investigate the impact of olive cake supplementation on Wagyu steer growth performance, longissimus muscle fatty acid composition, and in vitro rumen fermentation characteristics. We hypothesized that feeding with olive cake would improve animal performance and increase oleic acid (C18:1cis9) composition in the longissimus muscle. Experiment 1: Eighty-three American Wagyu steers (725 ± 10.7 kg) were used in this experiment. Steers were blocked by initial body weight (BW) and randomly assigned within blocks to one of two treatments. Treatments consisted of (1) control (basal ration with no olive cake) or (2) control diet + 5% supplemental olive. Steers were housed in feedlot pens (n = 4 steers/pen; 11 replicates/treatment) and fed a finishing diet typical for Wagyu cattle. Steers were individually weighed every 28 d throughout the 177 d experiment. Longissimus muscle samples were obtained for fatty acid analysis at the time of slaughter. Experiment 2: Rumen fluid from three beef steers (480 ± 10 kg) fitted with rumen canulae was used to investigate the impact of olive cake on in vitro rumen fermentation characteristics. Treatments consisted of (1) control (no olive cake) or (2) 5% olive cake. Results: Experiment 1: Steers receiving olive cake had a lower (p < 0.05) final BW and DM intake when compared to steers receiving the control diet. Longissimus muscle C18:2 and C22:6 n-3 were greater (p < 0.05) and C18:1cis9 tended (p < 0.06) to be greater in steers receiving olive cake when compared to controls. Experiment 2: Dry matter, acid detergent fiber, and neutral detergent fiber disappearance and molar proportions of short chain fatty acids were similar across treatments. The weight percentage of C14:1 was greater in in vitro rumen fluid fermented with olive cake when compared to controls. All other long chain fatty acids were similar across treatments. Under the conditions of this experiment, feeding olive cake at 5% of the diet DM reduced live animal performance and had minimal impacts on longissimus muscle fatty acid composition and in vitro rumen fermentation characteristics. Full article

Congenital abnormalities in animals, including abnormalities of the cleft lip and jaw and hypospadias have been reported in all domesticated species. They are a major concern for breeders due to the increased economic loss they entail. In this article, we described a congenital bilateral cheilognathoschisis (cleft lip and jaw) with campylognathia in association with penile hypospadias and preputial hypoplasia with failure of preputial fusion in a Bos taurus crossbred Piedmontese × Wagyu calf. Clinical examination, computed tomography, and whole genome sequencing were performed to describe and identify a possible cause of the abnormalities. Clinical examination revealed a bilateral cheilognathoschisis of approximately 4 cm in length and 3 cm in width in the widest part, with computer tomography analyses confirming the bilateral absence of the processus nasalis of the incisive bone and the lateral deviation of the processus palatinus towards the left side. Genomic data analyses identified 13 mutations with a high impact on the products of the following overlapped genes: ACVR1, ADGRA2, BHMT2, BMPR1B, CCDC8, CDH1, EGF, F13A1, GSTP1, IRF6, MMP14, MYBPHL, and PHC2 with ADGRA2, EGF, F13A1, GSTP1, and IRF6 having mutations in a homozygous state. The whole genome investigation indicates the involvement of multiple genes in the birth defects observed in this case. Full article