Comparative Transcriptomic Analysis Reveals Diverse Expression Pattern Underlying Fatty Acid Composition among Different Beef Cuts

Comparison of Meat Quality, Including Fatty Acid Content and Amino Acid Profile, and Transcriptome Profile among Hanwoo, Korea Black Cattle, and Jeju Black Cattle

This study aimed to compare the meat quality, including fatty acid content, amino acid profile, and transcriptome profile, among three Korean cattle breeds: Hanwoo, Korean black cattle (KBC), and Jeju black cattle (JBC). We analyzed fatty acid compositions, revealing that Hanwoo had higher levels of saturated fatty acids such as pentadecanoic acid, palmitic acid, and margaric acid than other cattle breeds. In contrast, KBC showed higher levels of linolenic acid, which is one of the omega-3 polyunsaturated fatty acids. Free amino acid profiles showed that Hanwoo and JBC had significantly higher levels of glutamic acid, glycine, and phenylalanine compared to KBC. KBC had a significantly higher arginine content, while Hanwoo had a significantly higher serine content compared to the other two breeds. Regarding constituent amino acid content, JBC had a higher glutamic acid content, which is associated with umami, and exhibited a lower level of valine, arginine, isoleucine, and phenylalanine compared to the other breeds. RNA transcriptome analysis identified key differentially expressed genes involved in lipid metabolism and energy homeostasis, including MOGAT1, ANGPTL8, and SLC38A4. Network analysis highlighted substantial differences in muscle system processes, fat cell differentiation, and other pathways between the breeds. These findings provide foundational data for genetic selection programs aimed at enhancing meat quality and offer valuable insights into preserving the unique characteristics of Korean indigenous cattle.

Flavor, Lipid, and Transcriptomic Profiles of Chinese Wagyu Beef Cuts: Insights into Meat Quality Differences

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.

Identification and Co-expression Analysis of Differentially Expressed LncRNAs and mRNAs Regulate Intramuscular Fat Deposition in Yaks at Two Developmental Stages

Intramuscular fat (IMF) content is a key indicator of yak meat quality. This study aimed to identify lncRNAs that regulate IMF deposition in yaks. Three male calf yaks (3 months) and three male adult yaks (3 years) were used in the current study. After slaughter, the tissue morphology of the longissimus dorsi (LD) muscle was assessed using a cry-sectioning technique and differentially expressed lncRNAs and mRNAs (DELs and DEMs) were identified using RNA-Seq technology. The diameter and volume of fat droplets were significantly larger and bigger, respectively, in adults than in calves (P < 0.001). A total of 37,790 genes and 16,400 lncRNAs that regulate fat deposition were identified. Among them, 2327 mRNAs and 474 lncRNAs were differentially expressed between calves and adult yaks. DEGs stearoyl-CoA desaturase (SCD), fatty acid synthase (FASN), fatty acid binding protein 4 (FABP4) and fibronectin 1 (FN1) and DELs MSTRG.15795.4 and MSTRG.35028.6 were screened. The enrichment and pathway analysis regulated by the DMEs and DELs were predicted. We found significantly enriched biological processes and pathways involved in fat deposition, including the biosynthesis of unsaturated fatty acids, fatty acid biosynthesis, fatty acid elongation, and the mTOR signaling pathway. Co-expression network of the DELs and related genes, including MSTRG.10268.1-placenta associated 8 (PLAC8), MSTRG.16223.1-galectin 3 (LGALS3), MSTRG.34732.1-glycerol-3-phosphate acyltransferase, mitochondrial (GPAM), MSTRG.11907.11-fibroblast growth factor 1 (FGF1), MSTRG.34342.1-lipase A, lysosomal acid type (LIPA), and MSTRG.1667.2-integrin subunit beta 2 (ITGB2) was constructed. RT-qPCR verified the sequence results. The molecular regulatory mechanisms of lncRNAs on intramuscular fat deposition in yak were further explored.

Transcriptomic analysis reveals diverse expression patterns underlying the fiber diameter of oxidative and glycolytic skeletal muscles in steers

Skeletal muscles consist of heterogeneous fibers with various contractile and metabolic properties that affect meat quality. The size of muscle fibers contributes to muscle mass and myopathy. Thus, improved understanding of the expression patterns underlying fiber size might open possibilities to change them using genetic methods. The aim of this study was to reveal transcriptomic landscapes of one oxidative (Psoas major) and three glycolytic (Longissimus lumborum, Triceps brachii, and Semimembranosus) muscles. Principal component analysis (PCA) showed significant differences in gene expression among the four muscles. Specifically, 2777 differentially expressed genes (DEGs) were detected between six pairwise comparisons of the four muscles. Weighted gene co-expression network analysis (WGCNA) identified six modules, which were significantly associated with muscle fiber diameter. We also identified 23 candidate genes, and enrichment analysis showed that biosynthesis of amino acids (bta01230), sarcomere (GO:0030017), and regulation of actin cytoskeleton (bta04810) overlapped in DEGs and WGCNA. Nineteen of these genes (e.g., EEF1A2, FARSB, and PINK1) have been reported to promote or inhibit muscle growth and development. Our findings contribute to the understanding of fiber size differences among oxidative and glycolytic muscles, which may provide a basis for breeding to improve meat yield.

Comprehensive Analysis of the Longissimus Dorsi Transcriptome and Metabolome Reveals the Regulatory Mechanism of Different Varieties of Meat Quality

The beef quality significantly varies between breeds. Pingliang Red Cattle resembles Wagyu in fat deposition and flavor. To screen key factors affecting beef quality, we performed meat quality trait testing, RNA-seq, and metabolomics on the longissimus dorsi of Pingliang Red Cattle, Wagyu cross F1 generation, and Simmental cattle. The gene and metabolite expression profiles were similar between Pingliang Red Cattle and Wagyu cross F1 generation. Genes such as FASN, ACACA, PLIN1, and FABP4 were significantly upregulated in the Pingliang Red Cattle and Wagyu cross F1 generation (P < 0.05). Similarly, numerous metabolites, such as 3-iodo-l-tyrosine, arachidonic acid, and cis-aconitate, which may improve the beef quality such as fat deposition and tenderness, were found in higher levels in the Pingliang Red Cattle and Wagyu cross F1 generation. This study revealed differences in the transcriptional and metabolic levels between Pingliang Red Cattle and premium beef breeds, suggesting that Pingliang Red Cattle harbors the genetic potential for breeding high-grade beef cattle.

Characterization of fatty acid compositions in longissimus thoracis muscle and identification of candidate gene and SNPs related to polyunsaturated fatty acid in Hu sheep

Fatty acid (FA) composition contributes greatly to the quality and nutritional value of lamb meat. In the present study, FA was measured in longissimus thoracis (LT) muscles of 1,085 Hu sheep using gas chromatography. Comparative transcriptomic analysis was conducted in LT muscles to identify differentially expressed genes (DEGs) between six individuals with high polyunsaturated fatty acids (H-PUFA, 15.27% ± 0.42%) and six with low PUFA (L-PUFA, 5.22% ± 0.25%). Subsequently, the single nucleotide polymorphisms (SNPs) in a candidate gene PLIN2 were correlated with FA traits. The results showed a total of 29 FA compositions and 8 FA groups were identified, with the highest content of monounsaturated fatty acids (MUFA, 46.54%, mainly C18:1n9c), followed by saturated fatty acids (SFA, 44.32%, mainly C16:0), and PUFA (8.72%, mainly C18:2n6c), and significant correlations were observed among the most of FA traits. Transcriptomic analyses identified 110 upregulated and 302 downregulated DEGs between H-PUFA and L-PUFA groups. The functional enrichment analysis revealed three significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and 17 gene ontology (GO) terms, in which regulation of lipolysis in adipocytes, the AMPK signaling pathway, and the PPAR signaling pathway may play important roles in FA metabolism and biosynthesis. In addition, weighted gene co-expression network analysis (WGCNA) identified 37 module genes associated with PUFA-related traits. In general, PLIN1, LIPE, FABP4, LEP, ACACA, ADIPOQ, SCD, PCK2, FASN, PLIN2, LPL, FABP3, THRSP, and ACADVL may have a great impact on PUFA metabolism and lipid deposition. Four SNPs within PLIN2 were significantly associated with FA. Of those, SNP1 (g.287 G>A) was significantly associated with C18:1n9c and MUFA, and SNP4 (g.7807 T>C) was significantly correlated with PUFA (C18:3n3). In addition, the combined genotype of SNP1 (g.287 G>A), SNP3 (g.7664 T>C), and SNP4 (g.7807 T>C) were significantly correlated with C16:1, C17:0, C18:1C6, PUFA (C18:3n3, C22:6n3), and n-6/n-3 PUFA. These results contribute to the knowledge of the biological mechanisms and genetic markers involved in the composition of FA in Hu sheep.

Effects of Plant-Derived Glycerol Monolaurate (GML) Additive on the Antioxidant Capacity, Anti-Inflammatory Ability, Muscle Nutritional Value, and Intestinal Flora of Hybrid Grouper (Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂)

In a context where the search for plant-derived additives is a hot topic, glycerol monolaurate (GML) was chosen as our subject to study its effect on grouper (Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂). Seven gradient levels of GML (0, 600, 1200, 1800, 2400, 3000, and 3600 mg/kg) were used for the experiment. Based on our experiments, 1800 mg/kg GML significantly increased the final body weight (FBW) and weight gain rate (WGR). GML increased the activity of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) and decreased malondialdehyde (MDA). Adding 1800 mg/kg GML also significantly increased the levels of lauric acid (C12:0) (LA), n-3 polyunsaturated fatty acids (PFA), and the n-6 PFA-to-n-3/n-6 ratio, while significantly decreasing the levels of saturated fatty acids (SFA). Dietary supplementation with GML significantly inhibited the expression of pro-inflammatory factors and reduced the occurrence of inflammation. GML improved intestinal flora and the abundance of beneficial bacteria (Bacillus, Psychrobacter, Acinetobacter, Acinetobacter, Stenotrophomonas, and Glutamicibacter). It provides a theoretical basis for the application of GML in aquafeed and greatly enhances the possibility of using GML in aquafeed. Based on the above experimental results, the optimum level of GML in grouper feed is 1800 mg/kg.