Effects of muscle fiber type on glycolytic potential and meat quality traits in different Tibetan pig muscles and their association with glycolysis-related gene expression

Comparative Study on the Postmortem Proteolysis and Shear Force during Aging of Pork and Beef Semitendinosus Muscles

The differences in the proteolytic patterns and shear force of pork and beef during aging were evaluated. Pork and beef semitendinosus muscles were obtained at 24 and 48 h postmortem, respectively, and aged at 4°C for 0 (Day 0), 7 (Day 7), and 14 days (Day 14). Changes in the electrical conductivity were observed in pork on Day 7 and beef on Day 14. The calpain activity increased in pork (p<0.05) after 14 days of aging, whereas that of beef decreased on Day 7 (p<0.05). The cathepsin B activity in pork and beef increased between Day 7 and 14 (p<0.05). The content of α-amino group in the 10% trichloroacetic acid-soluble fraction increased between Day 7 and 14 in pork (p<0.05), but increased steadily in beef throughout aging (p<0.05). The electrophoretogram of the myofibrillar proteins revealed a 30 kDa protein band only in the beef lane on Day 14. The cooked pork had no significant changes in the shear force during aging periods (p>0.05), while the gradual decrease in the shear force with the increasing aging periods was shown in the cooked beef (p<0.05). Circular dichroism analysis of myosin extracts from pork and beef revealed thermal denaturation temperatures of 55°C and 58°C, respectively. This study highlights the different post-mortem proteolytic patterns and thermal denaturation temperatures of myosin in pork and beef semitendinosus muscles, which contribute to distinct changes in the shear force during aging between pork and beef.

Research Progress on the Regulating Factors of Muscle Fiber Heterogeneity in Livestock: A Review

The type of muscle fiber plays a crucial role in the growth, development, and dynamic plasticity of animals' skeletal muscle. Additionally, it is a primary determinant of the quality of both fresh and processed meat. Therefore, understanding the regulatory factors that contribute to muscle fibers' heterogeneity is of paramount importance. Recent advances in sequencing and omics technologies have enabled comprehensive cross-verification of research on the factors affecting the types of muscle fiber across multiple levels, including the genome, transcriptome, proteome, and metabolome. These advancements have facilitated deeper exploration into the related biological questions. This review focused on the impact of individual characteristics, feeding patterns, and genetic regulation on the proportion and interconversion of different muscle fibers. The findings indicated that individual characteristics and feeding patterns significantly influence the type of muscle fiber, which can effectively enhance the type and distribution of muscle fibers in livestock. Furthermore, non-coding RNA, genes and signaling pathways between complicated regulatory mechanisms and interactions have a certain degree of impact on muscle fibers' heterogeneity. This, in turn, changes muscle fiber profile in living animals through genetic selection or environmental factors, and has the potential to modulate the quality of fresh meat. Collectively, we briefly reviewed the structure of skeletal muscle tissue and then attempted to review the inevitable connection between the quality of fresh meat and the type of muscle fiber, with particular attention to potential events involved in regulating muscle fibers' heterogeneity.

Type 2 diabetes mellitus related sarcopenia: a type of muscle loss distinct from sarcopenia and disuse muscle atrophy

Muscle loss is a significant health concern, particularly with the increasing trend of population aging, and sarcopenia has emerged as a common pathological process of muscle loss in the elderly. Currently, there has been significant progress in the research on sarcopenia, including in-depth analysis of the mechanisms underlying sarcopenia caused by aging and the development of corresponding diagnostic criteria, forming a relatively complete system. However, as research on sarcopenia progresses, the concept of secondary sarcopenia has also been proposed. Due to the incomplete understanding of muscle loss caused by chronic diseases, there are various limitations in epidemiological, basic, and clinical research. As a result, a comprehensive concept and diagnostic system have not yet been established, which greatly hinders the prevention and treatment of the disease. This review focuses on Type 2 Diabetes Mellitus (T2DM)-related sarcopenia, comparing its similarities and differences with sarcopenia and disuse muscle atrophy. The review show significant differences between the three muscle-related issues in terms of pathological changes, epidemiology and clinical manifestations, etiology, and preventive and therapeutic strategies. Unlike sarcopenia, T2DM-related sarcopenia is characterized by a reduction in type I fibers, and it differs from disuse muscle atrophy as well. The mechanism involving insulin resistance, inflammatory status, and oxidative stress remains unclear. Therefore, future research should further explore the etiology, disease progression, and prognosis of T2DM-related sarcopenia, and develop targeted diagnostic criteria and effective preventive and therapeutic strategies to better address the muscle-related issues faced by T2DM patients and improve their quality of life and overall health.

Impact of cooking temperature on pork longissimus, and muscle fibre type, on quality traits and protein denaturation of four pork muscles

Variations in pork quality impact consumer acceptance, and fibre type differences between muscles contribute to this variation. The aim was to investigate the influence of variations in muscle fibre types and protein denaturation peaks across four pork muscles and the influence of ageing and cooking temperature on longissimus quality traits. The longissimus, masseter, cutaneous trunci, and psoas major from 13 carcases were removed 1-day postmortem and subjected to 0- or 14-days ageing (d0, d14). Quality traits, protein denaturation peak temperature (DSC), fibre diameter and fibre type proportions were measured. Cook loss for longissimus was similar on d0 and d14, but was higher on d14 for masseter, cutaneous trunci, and psoas major. Warner-Bratzler shear force was highest, and ultimate pH was lowest, for longissimus, and similar among cutaneous trunci, masseter, and psoas major. Masseter had lowest L* and highest a* and longissimus and cutaneous trunci had highest L* and lowest a*. The DSC temperature peaks for longissimus occurred at lower temperatures relative to the other muscles. Fibre diameter was largest for type-IIb fibres relative to type-IIa and type-I. Longissimus and cutaneous trunci had predominantly type-IIb glycolytic (71%, 51% respectively), masseter had predominantly type-IIa intermediate (50%) and psoas major had predominantly type-I oxidative (48%) fibres. The glycolytic longissimus had the lowest DSC temperature peaks and the lowest quality meat. Masseter had the highest proportion of type-I fibres but was generally similar in quality traits to psoas major, and also similar to cutaneous trunci which had more glycolytic fibres than masseter.

Effects of Five Lipid Sources on Growth, Hematological Parameters, Immunity and Muscle Quality in Juvenile Largemouth Bass (Micropterus salmoides)

This study investigated the effects of fish oil (FO), soybean oil (SO), rapeseed oil (RO), peanut oil (PO) and lard oil (LO) on growth, immunity and muscle quality in juvenile largemouth bass. After 8 weeks, the results showed that FO and RO could increase weight gain and serum alkaline phosphatase and apelin values compared with LO (p < 0.05). Except lower crude lipid contents, higher amounts of n-3 polyunsaturated fatty acids (15.83% and 14.64%) were present in the dorsal muscle of the FO and RO groups. Meanwhile, FO and RO could heighten mRNA levels of immune defense molecules (lysozyme, hepcidin, and transforming growth factor β1) compared with PO (p < 0.05). While SO could increase potential inflammatory risk via rising counts of white blood cells, platelets, neutrophils and monocytes, and mRNA levels of interleukins (IL-1β, IL-8, IL-12 and IL-15), FO and RO could improve hardness, chewiness and springiness through increasing amounts of hydroxyproline, collagen and lysyl oxidase, and mRNA levels of collagen 1α2 and prolyl hydroxylase in the fish dorsal muscle. Moreover, FO and RO could improve firmness through increasing glycogen and glycogen synthase 1 levels when compared with LO (p < 0.05). Therefore, these results could provide dietary lipid source references during the feeding process of adult largemouth bass.

The long noncoding RNA lnc-H19 is important for endurance exercise by maintaining slow muscle fiber types

Skeletal muscle consists of different muscle fiber types whose heterogeneity is characterized by different metabolic patterns and expression of MyHC isomers. The transformation of muscle fiber types is regulated by a complex molecular network in which long noncoding (lnc) RNAs play an important role. In this study, we found that lnc-H19 is more enriched in slow muscle fibers. In vitro, interference of lnc-H19 by siRNA significantly promoted the expression of fast muscle fiber gene MyHC IIB and inhibited the expression of the slow muscle fiber gene MyHC I, thereby leading to a fast muscle fiber phenotype. In addition, interference of lnc-H19 significantly inhibited mRNA expression of the mitochondrial genes, such as COX5A, COX-2, UQCRFSL, FABP3, and CD36. Overexpression of lnc-H19 resulted in an opposite result. In vivo, knockdown of lnc-H19 by AAV-shRNA-H19 suppressed the mRNA expression of the slow muscle fiber gene MyHC I and the protein expression of slow-MyHC. Simultaneously, mitochondria were reduced in number, swollen, and vacuolated. The activities of succinate dehydrogenase, lactic dehydrogenase, and superoxide dismutase were significantly inhibited, and malondialdehyde content was significantly increased, indicating that deficiency of lnc-H19 leads to decreased oxidative metabolism and antioxidant capacity in muscle. Furthermore, inhibition of lnc-H19 decreased the weight-bearing swimming time and limb suspension time of mice. In conclusion, our results revealed the role of lnc-H19 in maintaining slow muscle fiber types and maintaining exercise endurance, which may help to further improve the regulatory network of lnc-H19 in muscle function.

Ubiquitin-Specific Proteases (USPs) and Metabolic Disorders

Ubiquitination and deubiquitination are reversible processes that modify the characteristics of target proteins, including stability, intracellular localization, and enzymatic activity. Ubiquitin-specific proteases (USPs) constitute the largest deubiquitinating enzyme family. To date, accumulating evidence indicates that several USPs positively and negatively affect metabolic diseases. USP22 in pancreatic β-cells, USP2 in adipose tissue macrophages, USP9X, 20, and 33 in myocytes, USP4, 7, 10, and 18 in hepatocytes, and USP2 in hypothalamus improve hyperglycemia, whereas USP19 in adipocytes, USP21 in myocytes, and USP2, 14, and 20 in hepatocytes promote hyperglycemia. In contrast, USP1, 5, 9X, 14, 15, 22, 36, and 48 modulate the progression of diabetic nephropathy, neuropathy, and/or retinopathy. USP4, 10, and 18 in hepatocytes ameliorates non-alcoholic fatty liver disease (NAFLD), while hepatic USP2, 11, 14, 19, and 20 exacerbate it. The roles of USP7 and 22 in hepatic disorders are controversial. USP9X, 14, 17, and 20 in vascular cells are postulated to be determinants of atherosclerosis. Moreover, mutations in the Usp8 and Usp48 loci in pituitary tumors cause Cushing syndrome. This review summarizes the current knowledge about the modulatory roles of USPs in energy metabolic disorders.

Integration of multi-omics data reveals cis-regulatory variants that are associated with phenotypic differentiation of eastern from western pigs

Background

The genetic mechanisms that underlie phenotypic differentiation in breeding animals have important implications in evolutionary biology and agriculture. However, the contribution of cis-regulatory variants to pig phenotypes is poorly understood. Therefore, our aim was to elucidate the molecular mechanisms by which non-coding variants cause phenotypic differences in pigs by combining evolutionary biology analyses and functional genomics.

Results

We obtained a high-resolution phased chromosome-scale reference genome with a contig N50 of 18.03 Mb for the Luchuan pig breed (a representative eastern breed) and profiled potential selective sweeps in eastern and western pigs by resequencing the genomes of 234 pigs. Multi-tissue transcriptome and chromatin accessibility analyses of these regions suggest that tissue-specific selection pressure is mediated by promoters and distal cis-regulatory elements. Promoter variants that are associated with increased expression of the lysozyme (LYZ) gene in the small intestine might enhance the immunity of the gastrointestinal tract and roughage tolerance in pigs. In skeletal muscle, an enhancer-modulating single-nucleotide polymorphism that is associated with up-regulation of the expression of the troponin C1, slow skeletal and cardiac type (TNNC1) gene might increase the proportion of slow muscle fibers and affect meat quality.

Conclusions

Our work sheds light on the molecular mechanisms by which non-coding variants shape phenotypic differences in pigs and provides valuable resources and novel perspectives to dissect the role of gene regulatory evolution in animal domestication and breeding.

Effects of oxidative stability variation on lamb meat quality and flavor during postmortem aging

This study evaluated the effects of oxidative stability variation on meat quality and flavor in biceps femoris (BF) and longissimus dorsi (LD) muscles of lambs during postmortem aging. The samples were stored at 4±1℃; the meat quality, flavor and muscle oxidative stability were measured on day 0, 1, 2, 3, and 4 of postmortem aging. The results showed that malondialdehyde (MDA) content increased in both muscle types; superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-Px) activities decreased, as did total antioxidative capacity (T-AOC). LD muscle showed lower MDA content and antioxidative activity than BF muscle. Meat quality analyses indicated that aging increased the lightness (L*), redness (a*), and yellowness (b*) values of meat while improving its tenderness. Gas chromatography-mass spectrometry results showed that volatile flavor compounds were more abundant in LD muscle than in BF muscle. As the aging time extended, relative contents of aldehyde and alcohol increased in both muscles. The key flavor compounds during postmortem aging including heptanal, octanal, nonanal, and decanal were screened by relative odor activity value (ROAV), and the content of key flavor compounds showed the trend of increasing, which were usually associated with fresh green grass, nutty, and fat descriptors. In conclusion, the oxidative muscles displayed better antioxidative capacity, and postmortem aging altered the oxidative stability of lamb muscle, which affected the meat quality and flavor. PRACTICAL APPLICATION: Meat aging is an important strategy to improve the quality of various meat traits (including flavor). The results of this work could be of interest to meat professionals who will be able to apply in actual production by choosing the best aging time based on flavor and meat quality for different muscle parts.

Comprehensive Analysis of Long Noncoding RNA Modified by m6A Methylation in Oxidative and Glycolytic Skeletal Muscles

N⁶-methyladenosine (m⁶A) is the most common modification in eukaryotic RNAs. Accumulating evidence shows m⁶A methylation plays vital roles in various biological processes, including muscle and fat differentiation. However, there is a lack of research on lncRNAs’ m⁶A modification in regulating pig muscle-fiber-type conversion. In this study, we identified novel and differentially expressed lncRNAs in oxidative and glycolytic skeletal muscles through RNA-seq, and further reported the m⁶A-methylation patterns of lncRNAs via MeRIP-seq. We found that most lncRNAs have one m⁶A peak, and the m⁶A peaks were preferentially enriched in the last exon of the lncRNAs. Interestingly, we found that lncRNAs’ m⁶A levels were positively correlated with their expression homeostasis and levels. Furthermore, we performed conjoint analysis of MeRIP-seq and RNA-seq data and obtained 305 differentially expressed and differentially m⁶A-modified lncRNAs (dme-lncRNAs). Through QTL enrichment analysis of dme-lncRNAs and PPI analysis for their cis-genes, we finally identified seven key m⁶A-modified lncRNAs that may play a potential role in muscle-fiber-type conversion. Notably, inhibition of one of the key lncRNAs, MSTRG.14200.1, delayed satellite cell differentiation and stimulated fast-to-slow muscle-fiber conversion. Our study comprehensively analyzed m⁶A modifications on lncRNAs in oxidative and glycolytic skeletal muscles and provided new targets for the study of pig muscle-fiber-type conversion.

Effects of sheep slaughter age on myogenic characteristics in skeletal muscle satellite cells

Objective

The objective of this study was to investigate the effects of sheep slaughter age on myogenic characteristics in skeletal muscle satellite cells (SMSCs).

Methods

Primary SMSCs were isolated from hind leg biceps femoris muscles of Wurank lambs (slaughtered at three months, Mth-3) and adults (slaughtered at fifteen months, Mth-15). SMSCs were selected by morphological observation and fluorescence staining. Myogenic regulatory factors (MRF) and myosin heavy chain (MyHC) expressions of SMSCs were analyzed on days 1, 3, 4, and 5.

Results

The expressions of myogenic factor 5 (Myf5), myogenic differentiation (MyoD), Myf6, and myogenin (MyoG) in Mth-15 were significantly higher in Mth-15 than in Mth-3 on days 1, 3, and 4 (p<0.05). However, MyoG expression in Mth-15 was significantly lower than in Mth-3 on day 5 (p<0.05). The expressions of MyHC I, MyHC IIa, and MyHC IIx in Mth-15 were significantly higher than in Mth-3 on days 1 and 3 (p<0.05), and MyHC IIb were significantly lower than in Mth-3 on days 3 and 4 (p<0.05). In contrast, the expression of MyHC IIx in Mth-15 was significantly lower and MyHC IIb was significantly higher than in Mth-3 on days 5 (p<0.05).

Conclusion

The slaughter age altered the expression of MRFs and MyHCs in SMSCs while differentiation, which caused the variation of myogenic characteristics, and thus may affect the meat quality of Wurank sheep.

miR-152 targets pyruvate kinase to regulate the glycolytic activity of pig skeletal muscles and affects pork quality

As a type of non-coding RNA, microRNAs are widely involved in the biological processes of animals. In the present study, the expression of miR-152 in glycolytic muscle fibers (Longissimus thoracis, LT) was lower than that of oxidative muscle fibers (Psoas major, PM). Using dual luciferase assay, miR-152 was shown to target muscle pyruvate kinase (PKM) to perform biological functions. Moreover, overexpression of miR-152 in primary porcine cells inhibited PKM gene expression and reduced lactic acid production in cells, whereas inhibition of miR-152 expression promoted PKM gene expression and increased lactic acid production. Correlation analysis showed that the expression of miR-152 was significantly positively correlated with the ultimate pH of LT after slaughter, while the expression of the PKM gene was significantly negatively correlated with the final pH of LT. In vivo and in vitro experiments discussed herein suggest that miR-152 may affect muscle pH by targeting the expression of the PKM gene. Our findings enrich the understanding of the genetic regulatory network that influences pork quality.

Analysis of potential regulatory LncRNAs and CircRNAs in the oxidative myofiber and glycolytic myofiber of chickens

SART and PMM are mainly composed of oxidative myofibers and glycolytic myofibers, respectively, and myofiber types profoundly influence postnatal muscle growth and meat quality. SART and PMM are composed of lncRNAs and circRNAs that participate in myofiber type regulation. To elucidate the regulatory mechanism of myofiber type, lncRNA and circRNA sequencing was used to systematically compare the transcriptomes of the SART and PMM of Chinese female Qingyuan partridge chickens at their marketing age. The luminance value (L*), redness value (a*), average diameter, cross-sectional area, and density difference between the PMM and SART were significant (p < 0.05). ATPase staining results showed that PMMs were all darkly stained and belonged to the glycolytic type, and the proportion of oxidative myofibers in SART was 81.7%. A total of 5 420 lncRNAs were identified, of which 365 were differentially expressed in the SART compared with the PMM (p < 0.05). The cis-regulatory analysis identified target genes that were enriched for specific GO terms and KEGG pathways (p < 0.05), including striated muscle cell differentiation, regulation of cell proliferation, regulation of muscle cell differentiation, myoblast differentiation, regulation of myoblast differentiation, and MAPK signaling pathway. Pathways and coexpression network analyses suggested that XR_003077811.1, XR_003072304.1, XR_001465942.2, XR_001465741.2, XR_001470487.1, XR_003077673.1 and XR_003074785.1 played important roles in regulating oxidative myofibers by TBX3, QKI, MYBPC1, CALM2, and PPARGC1A expression. A total of 10 487 circRNAs were identified, of which 305 circRNAs were differentially expressed in the SART compared with the PMM (p < 0.05). Functional enrichment analysis showed that differentially expressed circRNAs were involved in host gene expression and were enriched in the AMPK, calcium signaling pathway, FoxO signaling pathway, p53 signaling pathway, and cellular senescence. Novel_circ_004282 and novel_circ_002121 played important roles in regulating oxidative myofibers by PPP3CA and NFATC1 expression. Using lncRNA-miRNA/circRNA-miRNA integrated analysis, we identified many candidate interaction networks that might affect muscle fiber performance. Important lncRNA-miRNA-mRNA networks, such as lncRNA-XR_003074785.1/miR-193-3p/PPARGC1A, regulate oxidative myofibers. This study reveals that lncXR_003077811.1, lncXR_003072304.1, lncXR_001465942.2, lncXR_001465741.2, lncXR_001470487.1, lncXR_003077673.1, XR_003074785.1, novel_circ_004282 and novel_circ_002121 might regulate oxidative myofibers. The lncRNA-XR_003074785.1/miR-193-3p/PPARGC1A pathway might regulate oxidative myofibers. All these findings provide rich resources for further in-depth research on the regulatory mechanism of lncRNAs and circRNAs in myofibers.

High-throughput sequencing reveals crucial miRNAs in skeletal muscle development of Bian chicken

1. Growth performance is significant for chickens. MicroRNAs (miRNAs) have been found to play important roles in the post-transcriptional regulation of skeletal muscle growth. However, the mechanism of miRNAs in this process has not been elucidated.2. This study involved collecting leg muscle from slow- and fast-growing groups of Bian chicken at 16 weeks of age for high-throughput sequencing. A total of 42 differentially expressed miRNAs (DEMs) were identified. Among them, 22 DEMs were up-regulated and 20 DEMs were down-regulated.3. Biological process terms, relating to growth, were found by GO enrichment for target genes of DEMs and KEGG pathway analysis of target genes. This revealed some significantly enriched pathways closely related to skeletal muscle development, such as the calcium signalling pathway, ECM-receptor interaction, lysine degradation, apoptosis and tight junctions. Network interaction analysis of DEMs and target genes showed that the top fifty hub genes were targeted by thirteen DEMs.4. Four important miRNAs (novel_miR_158, novel_miR_144, novel_miR_291, and miR-205a) as well as some other valuable miRNAs, such as gga-miR-214 and gga-miR-3525 were identified. The qPCR results of five DEMs were highly consistent with that of sequencing between the two groups, which proved the reliability of miRNA-seq.5. The study will help to improve the molecular mechanism of miRNAs in chickens and guide future experiments concerning miRNA function in chicken growth.

Transcriptomics analysis reveals the effect of Broussonetia papyrifera L. fermented feed on meat quality traits in fattening lamb

To date, utilization of feed grains is increasing, which competes for human food. It is imperative to develop and utilize unconventional feed materials. Broussonetia papyrifera L. (B. papyrifera) is a good feeding material with high crude protein, crude fat, and low crude fiber, which is widely distributed in China. In this study, 12 Dorper ♂×Hu ♀  crossbred weaned male lambs were seleted into four groups based on the feed that ratio of the B. papyrifera fermented feed in the total mixed diet (0%, 6%, 18%, and 100%), to character the lambs' longissimus dorsi (LD) fatty acids, morphology and transcriptome. Results showed that the muscle fiber's diameter and area were the smallest in the 100% group. The highest content of beneficial fatty acids and the lowest content of harmful fatty acids in group 18%. RNA-seq identified 443 differentially expressed genes (DEGs) in the LD of lambs from 4 groups. Among these genes, 169 (38.1%) were up-regulated and 274 (61.9%) were down-regulated. The DEGs were mostly enriched in in fatty acid metabolism, arginine and proline metabolism, and PPAR signaling pathways. Our results provide knowledge to understand effect of different ratios of B. papyrifera fermented feed on sheep meat quality traits, also a basis for understanding of the molecular regulation mechanism of B. papyrifera fermented feed affecting on sheep meat quality.

LncRNA-FKBP1C regulates muscle fiber type switching by affecting the stability of MYH1B

Long non-coding RNAs (lncRNAs) are well-known to participate in a variety of important regulatory processes in myogenesis. In our previous RNA-seq study (accession number GSE58755), we found that lncRNA-FKBP1C was differentially expressed between White Recessive Rock (WRR) and Xinghua (XH) chicken. Here, we have further demonstrated that lncRNA-FKBP1C interacted directly with MYH1B by biotinylated RNA pull-down assay and RNA immunoprecipitation (RIP). Protein stability and degradation experiments identified that lncRNA-FKBP1C enhanced the protein stability of MYH1B. Overexpression of lncRNA-FKBP1C inhibited myoblasts proliferation, promoted myoblasts differentiation, and participated in the formation of skeletal muscle fibers. LncRNA-FKBP1C could downregulate the fast muscle genes and upregulate slow muscle genes. Conversely, its interference promoted cell proliferation, repressed cell differentiation, and drove the transformation of slow-twitch muscle fibers to fast-twitch muscle fibers. Similar results were observed after knockdown of the MYH1B gene, but the difference was that the MYH1B gene had no effects on fast muscle fibers. In short, these data demonstrate that lncRNA-FKBP1C could bound with MYH1B and enhance its protein stability, thus affecting proliferation, differentiation of myoblasts and conversion of skeletal muscle fiber types.

A maternal high-fat/low-fiber diet impairs glucose tolerance and induces the formation of glycolytic muscle fibers in neonatal offspring

PURPOSE

In our previous study, the maternal high-fat/low-fiber (HF-LF) diet was suggested to induce metabolic disorders and placental dysfunction of the dam, but the effects of this diet on glucose metabolism of neonatal offspring remain largely unknown. Here, a neonatal pig model was used to evaluate the effects of maternal HF-LF diet during pregnancy on glucose tolerance, transition of skeletal muscle fiber types, and mitochondrial function in offspring.

METHODS

A total of 66 pregnant gilts (Guangdong Small-ear Spotted pig) at day 60 of gestation were randomly divided into two groups: control group (CON group; 2.86% crude fat, 9.37% crude fiber), and high-fat/low-fiber diet group (HF-LF group; 5.99% crude fat, 4.13% crude fiber).

RESULTS

The maternal HF-LF diet was shown to impair the glucose tolerance of neonatal offspring, downregulate the protein level of slow-twitch fiber myosin heavy chain I (MyHC I), and upregulate the protein levels of fast-twitch fiber myosin heavy chain IIb (MyHC IIb) and IIx (MyHC IIx) in soleus muscle. Additionally, compared with the CON group, the HF-LF offspring showed inhibition of insulin signaling pathway and decrease in mitochondrial function in liver and soleus muscle.

CONCLUSION

Maternal HF-LF diet during pregnancy impairs glucose tolerance, induces the formation of glycolytic muscle fibers, and decreases the hepatic and muscular mitochondrial function in neonatal piglets.

The role of histidine dipeptides on postmortem acidification of broiler muscles with different energy metabolism

It is generally held that the content of several free amino acids and dipeptides is closely related to the energy-supplying metabolism of skeletal muscles. Metabolic characteristics of muscles are involved in the variability of meat quality due to their ability to influence the patterns of energy metabolism not only in living animal but also during postmortem time. Within this context, this study aimed at establishing whether the concentration of histidine dipeptides can affect muscle postmortem metabolism, examining the glycolytic pathway of 3 chicken muscles (pectoralis major, extensor iliotibialis lateralis, and gastrocnemius internus as glycolytic, intermediate, and oxidative-type, respectively) selected based on their histidine dipeptides content and ultimate pH. Thus, a total of 8 carcasses were obtained from the same flock of broiler chickens (Ross 308 strain, females, 49 d of age, 2.8 kg body weight at slaughter) and selected immediately after evisceration from the line of a commercial processing plant. Meat samples of about 1 cm³ were excised from bone-in muscles at 15, 60, 120, and 1,440 min postmortem, instantly frozen in liquid nitrogen and used for the determination of pH, glycolytic metabolites, buffering capacity as well as histidine dipeptides content through ¹H-NMR. Overall results suggest that glycolysis in leg muscles ceased already after 2 h postmortem, whereas in breast muscle continued until 24 h, when it exhibited significantly lower pH values (P < 0.05). However, considering its remarkable glycolytic potential, pectoralis major muscle should have exhibited a greater and faster acidification, suggesting that its higher (P < 0.05) histidine dipeptides' content might have prevented a potentially stronger acidification process. Accordingly, breast muscle also showed greater (P < 0.05) buffering ability in the pH range 6.0–7.0. Therefore, anserine and carnosine, being highly positively correlated with muscle's buffering capacity (P < 0.001), might play a role in regulating postmortem pH decline, thus exerting an effect on muscle metabolism during prerigor phase and the quality of the forthcoming meat. Overall results also suggest that total histidine dipeptides content along with muscular ultimate pH represent good indicators for the energy-supplying metabolism of chicken muscles.

Expression of Myosin Heavy Chain and Some Energy Metabolism-Related Genes in the Longissimus Dorsi Muscle of Krškopolje Pigs: Effect of the Production System

The Slovenian Krškopolje pig is the only preserved local autochthonous breed, appreciated mainly for its good meat quality and considered more appropriate for processing into dry-cured products. However, the biological characteristics of the skeletal myofibers of the Krškopolje breed, specifically the heavy myosin chain-based contractile and metabolic phenotypes that could affect meat quality, have not been established under different husbandry systems. The breed is generally maintained in either conventional indoor or organic systems. In the present study, the morphological, contractile, and metabolic properties of myofibers of the longissimus dorsi muscle were compared between animals reared in either an organic or a conventional indoor system. The myofibers were studied using immunohistochemical and succinate dehydrogenase (SDH) activity-based classification, histomorphometric assessment, and qPCR. Results revealed that the organic production system influenced the composition of the longissimus dorsi myofiber type, characterized by a smaller myofiber cross-sectional area, a shift toward oxidative (SDH-positive) myofiber types, increased relative expression of myosin heavy chain (MyHC) isoforms I, IIa, and IIx, and downregulation of MyHC IIb. On the contrary, no apparent effect was observed on the metabolic phenotype of the myofiber as assessed through relative mRNA expression of energy metabolism-related genes [peroxisome proliferator-activated receptor gamma, coactivator 1 alpha (PGC-1α), peroxisome proliferator-activated receptor gamma (PPARγ), lipoprotein-lipase (LPL), carnitine palmitoyltransferase 1B (CPT1B), glycogen synthase 1 (GYS1), hexokinase 2 (HK2), and fatty acid synthase (FASN)]. Differences in MyHC expression were largely corroborated by the histochemical classification, indicating that the contractile protein content is directly regulated by the MyHC genes. A correlation between the muscle contractile and metabolic phenotypes was not established, except for that between the HK2 and MyHC I genes. In conclusion, the present study showed an evident effect of rearing on the longissimus dorsi myofiber contractile phenotype but not the metabolic phenotype. Moreover, obtained data suggest that rearing the Krškopolje pig breed in a conventional system would result in an increased fiber size and a greater proportion of type IIb myofibers, which are known to be negatively correlated with some meat quality traits.

Changes in Physical Meat Traits, Protein Solubility, and the Microstructure of Different Beef Muscles during Post-Mortem Aging

This study was performed to compare the differences in pH, myofibril fragmentation index (MFI), total protein solubility (TPS), sarcoplasmic protein solubility (SPS), myofibrillar protein solubility (MPS), and the microstructure of seven beef muscles during aging. From the six beef carcasses of Xinjiang brown cattle, a total of 252 samples from semitendinosus (ST), longissimus thoracis (LT), rhomboideus (RH), gastrocnemius (GN), infraspinatus (IN), psoas major (PM), and biceps femoris (BF) muscles were collected, portioned, and assigned to six aging periods (1, 3, 7, 9, 11, and 14 day/s) and 42 samples were used per storage period. IN muscle showed the highest pH (p < 0.05) from 1 to 14 days and the lowest TPS (p < 0.01) from 9 to 14 days with respect to the other muscles. Moreover, the changes in IN were further supported by transmission electron microscopy due to the destruction of the myofibril structure. The highest value of MFI was tested in ST muscle from 7 to 14 days. The total protein solubility in PM, RH, and GN muscles were not affected (p > 0.05) as the aging period increased. The lowest TPS was found in the RH muscle on day 1, 3, and 7 and in the IN muscle on day 9, 11, and 14. The pH showed negative correlations with the MFI, TPS, and MPS (p < 0.01). The results suggest that changes in protein solubility and muscle fiber structure are related to muscle location in the carcass during aging. These results provide new insights to optimize the processing and storage of different beef muscles and enhance our understanding of the biological characteristics of Xinjiang brown cattle muscles.

Effect of feeding regimen on meat quality, MyHC isoforms, AMPK, and PGC-1α genes expression in the biceps femoris muscle of Mongolia sheep

The effects of two feeding regimens on meat quality, myosin heavy chain (MyHC) types, and key factors regulating muscle fiber type (AMP-activated protein kinase [AMPK] and peroxisome proliferator-activated receptor-coactivator-1α [PGC-1α]) in the biceps femoris muscle of Mongolia sheep were investigated. A total of 20 Mongolia sheep were weaning for 90 days and divided into two groups (pasture group (P) and confinement group (C)) at 10.36 ± 0.35 kg of weaning weight. After weaning, sheep were pasture fed or confinement fed for 9 months. The results showed that live weights, carcass weight, intramuscular fat (IMF), and Warner-Bratzler shear force (WBSF) in P group were significantly lower (p < .05) than that in C group. Compared with P group, color evaluations with respect to L* and b* values were significantly higher (p < .05) in C group. Expression of the MyHC I gene in the P group was significantly higher, while MyHC IIa and MyHC IIb genes expression was significantly lower (p < .05) than that in C group. Also, AMPK activity and expression of AMPKα2 and PGC-1α genes were significantly higher (p < .05) in P group compared with C group. The present study indicated that muscle fiber composition was one of the key differences leading to the differences of meat quality in different feeding regimens. AMPK, particularly AMPKα2, and PGC-1α were considered to be two key factors regulating muscle fiber types in Mongolia sheep. The results support that AMPK activity and the expression of AMPKα2 and PGC-1α genes may affect the composition of muscle fibers; thus, AMPK activity and the expression of AMPKα2 and PGC-1α genes had an effect on meat quality by changed composition of muscle fibers.

Transcriptome for the breast muscle of Jinghai yellow chicken at early growth stages

Background

The meat quality of yellow feathered broilers is better than the quality of its production. Growth traits are important in the broiler industry. The exploration of regulation mechanisms for the skeletal muscle would help to increase the growth performance of chickens. At present, some progress has been made by researchers, but the molecular mechanisms of the skeletal muscle still remain unclear and need to be improved.

Methods

In this study, the breast muscles of fast- and slow-growing female Jinghai yellow chickens (F4F, F8F, F4S, F8S) and slow-growing male Jinghai yellow chickens (M4S, M8S) aged four and eight weeks were selected for transcriptome sequencing (RNA-seq). All analyses of differentially expressed genes (DEGs) and functional enrichment were performed. Finally, we selected nine DEGs to verify the accuracy of the sequencing by qPCR.

Results

The differential gene expression analysis resulted in 364, 219 and 111 DEGs (adjusted P-value ≤ 0.05) for the three comparison groups, F8FvsF4F, F8SvsF4S, and M8SvsM4S, respectively. Three common DEGs (ADAMTS20, ARHGAP19, and Novel00254) were found, and they were all highly expressed at four weeks of age. In addition, some other genes related to growth and development, such as ANXA1, COL1A1, MYH15, TGFB3 and ACTC1, were obtained. The most common DEGs (n = 58) were found between the two comparison groups F8FvsF4F and F8SvsF4S, and they might play important roles in the growth of female chickens. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway also showed some significant enrichment pathways, for instance, extracellular matrix (ECM)-receptor interaction, focal adhesion, cell cycle, and DNA replication. The two pathways that were significantly enriched in the F8FvsF4F group were all contained in that of F8SvsF4S. The same two pathways were ECM–receptor interaction and focal adhesion, and they had great influence on the growth of chickens. However, many differences existed between male and female chickens in regards to common DEGs and KEGG pathways. The results would help to reveal the regulation mechanism of the growth and development of chickens and serve as a guideline to propose an experimental design on gene function with the DEGs and pathways.

miR-222 is involved in the regulation of genistein on skeletal muscle fiber type

In skeletal muscle, the composition of the fiber types has a profound impact on athletic performance, such as endurance or strength output. The proportions of muscle fiber types have also been associated with certain diseases, including dyskinesia, obesity and insulin resistance. Genistein, a natural estrogen, has been demonstrated to regulate fatty acid oxidation and insulin sensitivity in skeletal muscle. However, it is unknown whether genistein can regulate skeletal muscle fiber types. Furthermore, the mechanism of its effect on skeletal muscle energy metabolism is not entirely clear. In this study, in vivo and in vitro experiments were used to explore the effect of genistein on the muscle fiber-type transitions and muscle metabolism. The results indicated that genistein not only promotes skeletal muscle development but increases the expression of slow muscle fibers in mice as well. It was also demonstrated that genistein altered the ratios of fiber type and promoted mitochondrial biogenesis in C2C12 myoblasts. Interestingly, the expression of miR-222 was decreased by genistein, and it was demonstrated that this microRNA targets the PGC1α gene. In C2C12 myoblasts, miR-222 appears to regulate fiber type conversion and mitochondrial biogenesis. However, this function was significantly reduced following genistein treatment. These results suggest that miR-222 may be involved in the regulation of genistein on skeletal muscle fiber and muscle metabolism, and genistein may be used to improve muscle health.

In-depth mapping of the proteome of Tibetan pig tenderloin (longissimus dorsi) using offline high-pH reversed-phase fractionation and LC-MS/MS

In recent years, Tibetan pig breeding and meat processing have developed rapidly. However, the basic physiological and biochemical characteristics of Tibetan pork have not been systematically explored. The present study conducted a high-throughput analysis of the tenderloin (longissimus dorsi) proteome of the Tibetan pigs and performed a functional annotation and bioinformatics analysis of the identified proteins. Based on offline two-dimensional liquid chromatography fractionation and MS/MS identification, a total of 1,723 proteins were identified in the tenderloin of Tibetan pigs. Gene ontology analysis and pathway enrichment analysis revealed that the proteins involved in respiration (oxidative phosphorylation, glycolysis/gluconeogenesis, citric acid cycle, and pyruvate metabolism) and protein synthesis and metabolism (proteasome, amino acid biosynthesis, endoplasmic reticulum protein processing, and ribosomes) were significantly enriched, indicating that the energy production and protein metabolism are the most important physiological processes in Tibetan pig tenderloin. Practical applications The in-depth mapping of the tenderloin (longissimus dorsi) proteome of the Tibetan pigs gives a panoramic perspective at the protein molecular level and provides important information on the mechanisms of postmortem muscle physiology and meat quality formation. Furthermore, the development of Tibetan pork storage and processing technologies would also benefit from the characterization of the biochemical properties of Tibetan pork.

Comprehensive Analysis of lncRNAs and circRNAs Reveals the Metabolic Specialization in Oxidative and Glycolytic Skeletal Muscles

The biochemical and functional differences between oxidative and glycolytic muscles could affect human muscle health and animal meat quality. However, present understanding of the epigenetic regulation with respect to lncRNAs and circRNAs is rudimentary. Here, porcine oxidative and glycolytic skeletal muscles, which were at the growth curve inflection point, were sampled to survey variant global expression of lncRNAs and circRNAs using RNA-seq. A total of 4046 lncRNAs were identified, including 911 differentially expressed lncRNAs (p < 0.05). The cis-regulatory analysis identified target genes that were enriched for specific GO terms and pathways (p < 0.05), including the oxidation-reduction process, glycolytic process, and fatty acid metabolic. All these were closely related to different phenotypes between oxidative and glycolytic muscles. Additionally, 810 circRNAs were identified, of which 137 were differentially expressed (p < 0.05). Interestingly, some circRNA-miRNA-mRNA networks were found, which were closely linked to muscle fiber-type switching and mitochondria biogenesis in muscles. Furthermore, 44.69%, 39.19%, and 54.01% of differentially expressed mRNAs, lncRNAs, and circRNAs respectively were significantly enriched in pig quantitative trait loci (QTL) regions for growth and meat quality traits. This study reveals a mass of candidate lncRNAs and circRNAs involved in muscle physiological functions, which may improve understanding of muscle metabolism and development from an epigenetic perspective.

Relationship between pork fatty acid content in selected muscles and carcass tissues

Pork plays a central role in culinary tradition in Central Europe. Most of the studies determine the fatty acid (FA) content separately in muscles and subcutaneous fat. However, it is also important to determine the FA content of meat products, which contain a mixture of muscles and fat. The determination of FA in carcass tissues is difficult and leads to the destruction of the whole carcass. Thus, the aim of this study was to estimate the FA content of carcass meat (muscles with inter- and intramuscular fat, MC), and carcass soft tissues (muscles with inter- and intramuscular fat and subcutaneous fat, SC) based on a single muscle. Fatty acids were analysed using gas chromatography. Thirty crossbred pigs were fed diets differing in their fatty acid content and n-6:n-3 polyunsaturated fatty acid (PUFA) ratio. Samples of Longissimus thoracis et lumborum (LL), Biceps femoris (BF), Semitendinosus (ST), and Semimembranosus (SM) muscles, MC, and SC were taken. Correlation between linolenic, eicosapentaenoic and docosahexaenoic acids contents and n-6:n-3 PUFA in examined muscles and MC ranged from 0.809 (SM) to 0.961 (LL), from 0.708 (LL) to 0.954 (ST), from 0.907 (SM) to 0.941 (ST), respectively (P = 0.000). Correlation between linolenic, eicosapentaenoic and docosahexaenoic acids contents and n-6:n-3 PUFA in examined muscles and SC ranged from 0.773 (SM) to 0.954 (LL), 0.763 (LL) to 0.983 (BF), and from 0.909 (LL) to 0.940 (ST), respectively (P = 0.000). Results allow estimate the FA content of MC and SC based on their content in single muscles.

A genome-wide detection of selection signatures in conserved and commercial pig breeds maintained in Poland

BACKGROUND

Identification of selection signatures can provide a direct insight into the mechanism of artificial selection and allow further disclosure of the candidate genes related to the animals' phenotypic variation. Domestication and subsequent long-time selection have resulted in extensive phenotypic changes in domestic pigs, involving a number of traits, like behavior, body composition, disease resistance, reproduction and coat color. In this study, based on genotypes obtained from PorcineSNP60 Illumina assay we attempt to detect both diversifying and within-breed selection signatures in 530 pigs belonging to four breeds: Polish Landrace, Puławska, Złotnicka White and Złotnicka Spotted, of which the last three are a subject of conservative breeding and substantially represent the native populations.

RESULTS

A two largely complementary statistical methods were used for signatures detection, including: pairwise F_ST and relative extended haplotype homozygosity (REHH) test. Breed-specific diversifying selection signals included several genes involved in processes connected with fertility, growth and metabolism which are potentially responsible for different phenotypes of the studied breeds. The diversifying selection signals also comprised PPARD gene that was previously found to have a large effect on the shape of the external ear in pigs or two genes encoding neuropeptide Y receptors (Y2 and Y5) involved in fat deposition and stress response which are important features differentiating the studied breeds. REHH statistics allowed detecting several within-breed selection signatures overlapping with genes connected with a range of functions including, among others: metabolic pathways, immune system response or implantation and development of the embryo.

CONCLUSIONS

The study provides many potential candidate genes with implication for traits selected in the individual breeds and gives strong basis for further studies aiming at identification of sources of variation among the studied pig breeds.

Chromium, CLA, and ractopamine for finishing pigs

This study aimed to evaluate the effects of dietary chromium, CLA, and ractopamine on performance, carcass traits, and pork quality of finishing pigs slaughtered at 115 kg BW. Ninety-six crossbred barrows (initial BW = 70.21 ± 1.98 kg) were randomly assigned to 1 of 6 dietary treatments. There were 8 replicates per treatment (48 pens; 2 pigs/pen). A diet formulated according to the nutritional requirements was used as the control (CON). The other 5 diets were based on the CON and supplemented as follows: 0.4 mg/kg Cr yeast (CrY); 0.5% CLA; 0.4 mg/kg CrY and 0.5% CLA (CrY + CLA); 20 mg/kg ractopamine (RAC); 0.4 mg/kg CrY and 20 mg/kg RAC (CrY + RAC). Lysine levels on diets containing ractopamine were raised by 20% compared to CON to meet the greater requirements of pigs fed ractopamine. Pigs fed RAC and CrY + RAC were fed CON for the first 17 d, and then the respective diets for the last 28 d on trial. Data were analyzed in a model including the fixed effect of treatment (6 levels) and initial BW as a covariate for all characteristics, with the exception of carcass traits, in which final BW was used as a covariate. Least-squares means were separated using Tukey-Kramer's method. Differences were considered when probability values were lower than 0.05. Pigs fed RAC and CrY + RAC had the greatest ( < 0.001) final BW and ADG. Pigs fed CrY + RAC had greater ( < 0.001) G:F than pigs within the other groups, except for those fed RAC. Pigs fed CrY + RAC and RAC had similar G:F, both greater ( < 0.001) than pigs fed CON. Average daily feed intake was similar ( = 0.83) for all diets. Pigs fed CrY + RAC had greater LM area ( = 0.01) and carcass yield ( < 0.02) than pigs fed CON, CrY, CLA, and CrY + CLA. Loin muscle area and carcass yield of pigs fed RAC were not different from pigs fed the others diets. Pigs fed CON diets had greater BF ( = 0.02) than pigs fed CLA diet. Additives did not affect ( > 0.05) pork quality, except for color. No differences ( > 0.05) were observed for carcasses pH and temperature. The values for pigs fed RAC were greater ( = 0.01) than pigs fed other diets. Pigs fed RAC had lower ( < 0.01) values compared to pigs fed other experimental diets. Serum urea nitrogen concentration (SUN) was lower ( = 0.02) in pigs fed CrY + RAC than in pigs fed CON and RAC and similar to pigs fed the other feeding additives. In summary, it was demonstrated that, when combined, CrY and RAC increase LM area and carcass yield, and reduce SUN, suggesting that chromium could improve nutrient utilization by muscle cells in RAC-fed pigs. Additionally, the additives have no major effects on pork quality.

Screening for candidate genes related with histological microstructure, meat quality and carcass characteristic in pig based on RNA-seq data

Objective

The aim of the present study was to identify genetic variants based on RNA-seq data, obtained via transcriptome sequencing of muscle tissue of pigs differing in muscle histological structure, and to verify the variants’ effect on histological microstructure and production traits in a larger pig population.

Methods

RNA-seq data was used to identify the panel of single nucleotide polymorphisms (SNPs) significantly related with percentage and diameter of each fiber type (I, IIA, IIB). Detected polymorphisms were mapped to quantitative trait loci (QTLs) regions. Next, the association study was performed on 944 animals representing five breeds (Landrace, Large White, Pietrain, Duroc, and native Puławska breed) in order to evaluate the relationship of selected SNPs and histological characteristics, meat quality and carcasses traits.

Results

Mapping of detected genetic variants to QTL regions showed that chromosome 14 was the most overrepresented with the identification of four QTLs related to percentage of fiber types I and IIA. The association study performed on a 293 longissimus muscle samples confirmed a significant positive effect of transforming acidic coiled-coil-containing protein 2 (TACC2) polymorphisms on fiber diameter, while SNP within forkhead box O1 (FOXO1) locus was associated with decrease of diameter of fiber types IIA and IIB. Moreover, subsequent general linear model analysis showed significant relationship of FOXO1, delta 4-desaturase, sphingolipid 1 (DEGS1), and troponin T2 (TNNT2) genes with loin ‘eye’ area, FOXO1 with loin weight, as well as FOXO1 and TACC2 with lean meat percentage. Furthermore, the intramuscular fat content was positively associated (p<0.01) with occurrence of polymorphisms within DEGS1, TNNT2 genes and negatively with occurrence of TACC2 polymorphism.

Conclusion

This study’s results indicate that the SNP calling analysis based on RNA-seq data can be used to search candidate genes and establish the genetic basis of phenotypic traits. The presented results can be used for future studies evaluating the use of selected SNPs as genetic markers related to muscle histological profile and production traits in pig breeding.

Studies on meat color, myoglobin content, enzyme activities, and genes associated with oxidative potential of pigs slaughtered at different growth stages

Objective

This experiment investigated meat color, myoglobin content, enzyme activities, and expression of genes associated with oxidative potential of pigs slaughtered at different growth stages.

Methods

Sixty 4-week-old Duroc×Landrace×Yorkshire pigs were assigned to 6 replicate groups, each containing 10 pigs. One pig from each group was sacrificed at day 35, 63, 98, and 161 to isolate longissimus dorsi and triceps muscles.

Results

Meat color scores were higher in pigs at 35 d than those at 63 d and 98 d (p<0.05), and those at 98 d were lower than those at 161 d (p<0.05). The total myoglobin was higher on 161 d compared with those at 63 d and 98 d (p<0.05). Increase in the proportions of metmyoglobin and deoxymyoglobin and a decrease in oxymyoglobin were observed between days 35 and 161 (p<0.05). Meat color scores were correlated to the proportion of oxymyoglobin (r = 0.59, p<0.01), and negatively correlated with deoxymyoglobin and metmyoglobin content (r = −0.48 and −0.62, p<0.05). Malate dehydrogenase (MDH) activity at 35 d and 98 d was higher than that at 161 d (p<0.05). The highest lactate dehydrogenase/MDH ratio was achieved at 161 d (p<0.05). Calcineurin mRNA expression decreased at 35 d compared to that at 63 d and 98 d (p<0.05). Myocyte enhancer factor 2 mRNA results indicated a higher expression at 161 d than that at 63 d and 98 d (p<0.05).

Conclusion

Porcine meat color, myoglobin content, enzyme activities, and genes associated with oxidative potential varied at different stages.

Proteomic signature of muscle fibre hyperplasia in response to faba bean intake in grass carp

Fish muscle growth is important for the rapidly developing global aquaculture industry, particularly with respect to production and quality. Changes in muscle fibre size are accomplished by altering the balance between protein synthesis and proteolysis. However, our understanding regarding the effects of different protein sources on fish muscle proteins is still limited. Here we report on the proteomic profile of muscle fibre hyperplasia in grass carp fed only with whole faba bean. From the results, a total of 99 significantly changed proteins after muscle hyperplasia increase were identified (p < 0.05, ratio <0.5 or >2). Protein–protein interaction analysis demonstrated the presence of a network containing 56 differentially expressed proteins, and muscle fibre hyperplasia was closely related to a protein–protein network of 12 muscle component proteins. Muscle fibre hyperplasia was also accompanied by decreased abundance in the fatty acid degradation and calcium signalling pathways. In addition, metabolism via the pentose phosphate pathway decreased in grass carp after ingestion of faba bean, leading to haemolysis. These findings could provide a reference for the prevention and treatment of human glucose-6-phosphate dehydrogenase deficiency (“favism”).

Genome-wide landscape of DNA methylomes and their relationship with mRNA and miRNA transcriptomes in oxidative and glycolytic skeletal muscles

The physiological, biochemical and functional differences between oxidative and glycolytic muscles play important roles in human metabolic health and in animal meat quality. To explore these differences, we determined the genome-wide landscape of DNA methylomes and their relationship with the mRNA and miRNA transcriptomes of the oxidative muscle psoas major (PMM) and the glycolytic muscle longissimus dorsi (LDM). We observed the hypo-methylation of sub-telomeric regions. A high mitochondrial content contributed to fast replicative senescence in PMM. The differentially methylated regions (DMRs) in promoters (478) and gene bodies (5,718) were mainly enriched in GTPase regulator activity and signaling cascade-mediated pathways. Integration analysis revealed that the methylation status within gene promoters (or gene bodies) and miRNA promoters was negatively correlated with mRNA and miRNA expression, respectively. Numerous genes were closely related to distinct phenotypic traits between LDM and PMM. For example, the hyper-methylation and down-regulation of HK-2 and PFKFB4 were related to decrease glycolytic potential in PMM. In addition, promoter hypo-methylation and the up-regulation of miR-378 silenced the expression of the target genes and promoted capillary biosynthesis in PMM. Together, these results improve understanding of muscle metabolism and development from genomic and epigenetic perspectives.