Transcriptomic analysis of the longissimus thoracis muscle in pigs has identified molecular regulatory patterns associated with meat quality.

Meat quality is a critical aspect of pig breeding. In addition to genetics, meat quality is also influenced by nutritional and environmental factors. In this study, three pig breeds, Shengxianhua, Jiaxing, and Qinglian Black (SXH, JXB and QLB), were used as experimental animals. Transcriptional analysis was performed on the longissimus thoracis (LT) muscle to investigate variations in intramuscular fat (IMF), inosine monophosphate (IMP), amino acids, and muscle fiber morphology across different breeds. Ingenuity canonical pathway analysis (IPA) identified biological processes and key driver genes related to metabolism and muscle development. Additionally, weighted gene co-expression network analysis (WGCNA) revealed gene modules associated with IMP. KEGG and GO analyses identified specific biological processes and signaling pathways related to IMP, including the Oxidative Phosphorylation pathway and rRNA Metabolic Processes. These findings provide novel insights into the molecular regulatory mechanisms underlying meat quality variations among pig breeds.

Transcriptome changes associated with fat deposition in the longissimus thoracis of Korean cattle following castration.

The castration of bulls increases the intramuscular fat (IMF) content in skeletal muscle. However, the biological processes of IMF accumulation in skeletal muscle after castration are not completely understood at the molecular level. This study examined the global transcriptomic changes in the longissimus thoracis muscle (LT) of bulls following castration using RNA sequencing (RNA-Seq) and identified new genes or pathways associated with beef quality. Ten bulls and 10 steers castrated at 6 months of age were slaughtered at 26 and 32 months of age respectively. For transcriptome analysis, six LT samples from three bulls and three steers were selected based on age, carcass weight, carcass quantity and beef quality grades. Using RNA-Seq, transcriptomic profiles of the LT were compared between bulls and steers. In all, 640 of the 18,027 genes identified through RNA-Seq were differentially expressed genes (DEGs) between bulls and steers. Pathway analysis of these 640 DEGs showed significant (p < .05) changes in seven Kyoto Encyclopedia of Genes and Genomes pathways, and the most significant terms were complement and coagulation cascade pathways. The transcriptomic expression patterns of 10 genes in the complement and coagulation cascades were validated using all animals through quantitative real-time polymerase chain reaction analysis. In conclusion, transcriptome changes associated with the complement and coagulation cascade pathways provide novel insights into understanding molecular mechanisms responsible for IMF accumulation following castration in beef cattle.

Comparative proteomics reveals genetic mechanisms of body weight in Hu sheep and Dorper sheep.

Body weight (BW) is a critical economic trait for meat production in sheep, and it is a complex trait affected by numerous elements. The aim of this study was to investigate the genetic mechanisms of sheep BW by a label-free proteomics approach. The result showed, a total of 27, 14, 61, and 65 differentially abundant proteins (DAPs) were identified in the Hu_HBW vs. Hu_LBW, DP_HBW vs. DP_LBW, Hu_HBW vs. DP_HBW, and Hu_LBW vs. DP_LBW comparisons, respectively. Five proteins (including ILK, AHCYL2, MLIP, CYB5A, and SMTNL1) related to fat synthesis and muscle development were detected in the Hu sheep group. In the Dorper sheep group, the screened DAPs strictly related to muscle development and fat synthesis were significantly enriched in MAP kinase activity (MAPK12), Arachidonic acid metabolism, and Steroid hormone biosynthesis (PGFS, LOC101107119) pathways. Several DAPs related to immune responses (SERPINA1, FGG, SERPINC1, and LOC101108131), fat deposition (APOH, GC, AHSG, SKP1, ACSL1, ACAT1, and ACADS), and muscle development (LMOD3 and LRRC39) were detected in the Hu vs. Dorper sheep comparison. These analyses indicated that the BW of sheep is regulated via a variety of pathways, and these DAPs can be further investigated as candidate markers for predicting the BW of sheep. SIGNIFICANCE: Body weight is one of the key traits in sheep and involves multiple coordinated regulatory mechanisms, but the genetic mechanism of BW is still unclear in sheep. In the current study, the label-free method was used to identify the proteins and pathways related to BW using LT muscle of Hu sheep and Dorper sheep with different BW. These findings will provide new candidate proteins and vital pathways into the molecular mechanisms involved growth traits in sheep.

Integrative analysis of transcriptomics and proteomics of longissimus thoracis of the Hu sheep compared with the Dorper sheep.

Meat quality is becoming more important for sheep breeding programs. Meat quality is a complex trait affected by genetic and environmental factors. In the present study, an integrative analysis of the longissimus thoracis tissue transcriptome and proteome was conducted to identify genes, proteins, and pathways related to meat quality in sheep. The sheep breeds Hu and Dorper were considered. These breeds were compared for the differences in muscle fiber structure, chemical composition, and amino acid composition. In the Hu sheep vs. Dorper sheep comparison, 22 DEGs/DEPs showed the same mRNA and protein expression trends. These genes are associated with lipid transport, lipid metabolism, and muscular system development. Moreover, some pathways such as "lipid transport", "lipoprotein metabolic process", "Alanine, aspartate and glutamate metabolism", and "Arginine biosynthesis" were significantly enriched in this study. The reliability of the RNA-Seq results was verified by qRT-PCR. These findings provide new insights into the molecular mechanisms of meat quality in sheep.

Comparison of Beef Palatability Characteristics between Longissimus Thoracis and Vastus Lateralis Muscles from Different Grades during Postmortem Aging.

The objectives of this study was to compare palatability changes of the longissimus thoracis (LT) and vastus lateralis (VL) muscles of Hanwoo steers from different beef quality grades (1+ and 1) during 28 d of wet-aging in order to improve the utilization of the VL muscle as a steak. The VL muscle showed a higher collagen content and a lower intramuscular fat content than the LT muscle (p<0.05). As expected, the Warner-Bratzler shear force value was greater in the LT 1 grade (LT-1) muscle than the LT-1+ muscle (p<0.05); whereas no difference was observed between the grades in the VL muscle at 24 h postmortem. Compared to 0 d of aging, tenderness scores significantly increased after 14 and 21 d of aging in the LT and VL muscles, respectively (p<0.05). Additionally, there was no difference in tenderness score between the VL-1+ aged for 21 d and the LT-1 at 24 h postmortem, although tenderness score was greater in the LT than the VL at each period (p<0.05). Moreover, the VL-1+ steak exhibited a higher tenderness score than the VL-1 steak at 21 and 28 d of aging (p<0.05). On the other hand, the effect of aging time on juiciness and flavor in the VL muscle was somewhat limited unlike the LT muscle. Taken together, the VL muscle requires a longer aging time than the LT muscle to improve consumer preference. Considering the tenderness, using a higher quality grade for aging is more useful in the VL muscle.

The longissimus thoracis muscle proteome in Alentejana bulls as affected by growth path.

Beef production is an important economic activity. In Southern Europe there are two types of beef production systems based on growth paths: continuous (CG) versus discontinuous growth (DG). DG is a traditional system dependent on pasture; whereas in CG animals are supplemented on concentrate feed. We compare the protein abundance profiles of the longissimus thoracis (LT) muscle in CG and DG animals using label-free quantitative proteomics. Twenty three Alentejana male calves (9months-old, 239kg live-weight) were allocated to two feeding regimens. In CG (n=12) production system, animals were fed ad libitum on concentrates plus hay and slaughtered at 18months. In DG (n=11) production system, animals were fed ad libitum on hay from 9 to 15months of age and then the same diet provided to the CG group and slaughtered at 24months. The LT muscle was sampled and protein abundance profiles determined using label-free quantification. We identified 510 proteins, of which 26 showed differential abundance. Several proteins (e.g. Myozenin-2, glyoclythic enzymes and 14-3-3 protein zeta/delta) are proposed as indicators of a more intensive growth path. Myosin binding protein H had higher abundance in the DG group, suggesting it could be associated to discontinuous growth path.

Carnosine content in the porcine longissimus thoracis muscle and its association with meat quality attributes and carnosine-related gene expression.

Muscle carnosine has pH-buffering, antioxidant and carbonyl scavenging properties, which may affect pork quality attributes. Study objectives were to: (1) compare muscle carnosine content and carnosine-related gene mRNA abundance in purebred pigs (n=282), (2) study the effect of muscle carnosine content on pork quality attributes and gene expression across breeds, and (3) study transcript abundance of carnosine-related genes in various tissues. Pigs were raised under similar conditions and slaughtered at 120±4.5kg. Longissimus thoracis muscles were sampled on the dressing line for gene expression and at 24h for meat quality measurements. Muscle carnosine content and carnosine-related gene mRNA abundance were modulated according to pig breeds. Greater pH24h, better water holding capacity and improved meat color values were found in pigs with high muscle carnosine content. Data suggest that high muscle carnosine is associated with improved pork meat quality attributes. The pig genetic background may be a key determinant for muscle carnosine content regulation.

Identification of single nucleotide polymorphisms in carnosine-related genes and effects of genotypes on pork meat quality attributes.

Carnosine has pH-buffering and antioxidant properties that may bring advantages in terms of meat quality attributes. This study aimed at identifying polymorphisms in carnosine-related genes (CARNS1, SLC6A6, SLC15A3, SLC15A4) that might associate with muscle carnosine content and meat quality traits in pigs (Duroc, Landrace, Yorkshire). Twenty seven SNPs were identified and association analyses performed for SLC15A3 c.*35C>T and c.*52C>T (3' UTR region), and SLC15A4 c.658A>G (Ile220Val) and c.818G>A (Ser273Asn) SNPs. Associations were observed for SNP c.658A>G with carnosine content, color b* and L*, drip and cooking losses, pH24h and glycolytic potential values (P≤0.05). The same associations were observed for SNP c.818G>A, but they were not significant after FDR correction. Results suggest that specific SLC15A4 gene variants might increase muscle carnosine content and improve meat quality. With a minor allele frequency of 0.17 for SNP c.658A>G in Yorkshire pigs, selection in favor of the c.658A allele may be considered as a mean to improve pork quality attributes.

Dietary supplementation of Lonicera macranthoides leaf powder improves amino acid profiles in serum and longissimus thoracis muscle of growing-finishing pigs.

A 60-days feeding trial was conducted to determine the effect of dietary supplementation of Lonicera macranthoides leaf (LML) on growth performance, meat quality, and free amino acid profiles in growing-finishing pigs. L. macranthoides leaves were harvested, air-dried and milled to powder. A total of 288 crossbred barrows (Large White × Landrace) with an average initial BW of 54.0 ± 3.4 kg were randomly allocated to 3 treatment groups and fed either a basal diet or a diet supplemented with 0.5% or 1.0% LML powder. Results showed that diet supplemented with LML powder did not affect average daily feed intake (ADFI) and feed: gain ratio (P > 0.05) in growing-finishing pigs. Moreover, diet supplemented with LML powder showed no significant effects on carcass traits (P > 0.05) including dressing percentage, backfat thickness and loin muscle area, and meat quality traits (P > 0.05) including meat color, intramuscular fat and cooking loss. However, diet supplemented with LML powder significantly improved free amino acid profiles in serum and longissimus thoracis muscle in growing-finishing pigs. Most importantly, dietary LML powder increased total free amino acids content (P < 0.001) and essential free amino acid content (P < 0.001) in longissimus thoracis muscle. These results indicate that LML has the potential to improve the nutritional value of meat through improving free amino acid profiles.