Comparative transcriptomic analysis reveals beneficial effect of dietary mulberry leaves on the muscle quality of finishing pigs

Effects of intensive and conventional farming on oxidative stress and meat quality biomarkers in holstein and simmental cattle

This study investigates the intricate factors influencing meat quality, including breed, rearing conditions, and processing, with a primary focus on oxidative stress in Holstein Friesian and Simmental cattle within conventional and intensive production systems. A notable difference in oxidative stress was found between animals subjected to intensive-farming versus conventional practices, with Holstein cattle showing a more pronounced antioxidant gene response than Simmental. The analysis revealed that intensive rearing conditions resulted in increased DNA repair activity and expression of stress-response proteins like heat shock proteins, suggestive of greater cellular damage and an adaptive stress response. Muscle tissue analyses, revealed a clear distinction in gene expression associated with meat quality between the breeds and the type of farming system. A negative correlation emerged between oxidative stress levels and genes related to muscle development, which affects meat quality. Intensive farming conditions altered the expressions of apoptotic proteins, impacting meat quality at the molecular level. These results underscore the profound effect rearing conditions have on meat quality, driven by stress-related molecular responses. This highlights the need for further research into the influence of husbandry practices on animal welfare and meat quality, with the intention of developing strategies to mitigate the negative consequences of intensive-farming.

A comparative analysis reveals the genomic diversity among 8 Muscovy duck populations

The Muscovy duck (Cairina moschata) is a waterfowl indigenous to the neotropical regions of Central and South America. It has low demand for concentrated feed and strong adaptability to different rearing conditions. After introduced to China through Eurasian commercial trade, Muscovy ducks have a domestication history of around 300 years in the Fujian Province of China. In the 1990s, the commodity Muscovy duck breed "Crimo," cultivated in Europe, entered the Chinese market for consumption and breeding purposes. Due to the different selective breeding processes, Muscovy ducks have various populational traits and lack transparency of their genetic background. To remove this burden in the Muscovy duck breeding process, we analyzed genomic data from 8 populations totaling 83 individuals. We identify 11.24 million single nucleotide polymorphisms (SNPs) and categorized these individuals into the Fujian-bred and the Crimo populations according to phylogenetic analyses. We then delved deeper into their evolutionary relationships through assessing population structure, calculating fixation index (FST) values, and measuring genetic distances. Our exploration of runs of homozygosity (ROHs) and homozygous-by-descent (HBD) uncovered genomic regions enriched for genes implicated in fatty acid metabolism, development, and immunity pathways. Selective sweep analyses further indicated strong selective pressures exerted on genes including TECR, STAT2, and TRAF5. These findings provide insights into genetic variations of Muscovy ducks, thus offering valuable information regarding genetic diversity, population conservation, and genome associated with the breeding of Muscovy ducks.

Effects of dietary mulberry leaves on growth, production performance, gut microbiota, and immunological parameters in poultry and livestock: a systematic review and meta-analysis

OBJECTIVE

This study aimed to assess the effects of dietary mulberry leaves on the growth, production performance, gut microbiota, and immunological parameters of poultry and livestock.

METHODS

The PubMed, Embase, and Scopus databases were systematically analyzed to identify pertinent studies up to December 2022. The effects of mulberry leaf diet was assessed using the weighted mean difference, and the 95% confidence interval was calculated using a random-effects model.

RESULTS

In total, 18 studies that sampled 2,335 poultry and livestock were selected for analysis. Mulberry leaves improved the average daily gain and reduced the feed/meat ratio in finishing pigs, and the average daily gain and average daily feed intake in chicken. In production performance, mulberry leaves lowered the half carcass weight, slaughter rate, and loin eye area in pigs, and the slaughter rate in chickens. Regarding meat quality in pigs, mulberry leaves reduced the cooked meat percentage, shear force, crude protein, and crude ash, and increased the 24 h pH and water content. In chickens, it increased the drip loss, shear force, 45 min and 24 h pH, crude protein, and crude ash. Mulberry leaves also affect the abundances of gut microbiota, including Bacteroides, Prevotella, Megamonas, Escherichia-Shigella, Butyricicoccus, unclassified Ruminococcaceae, Bifidobacterium, Lactobacillus, and Escherichia coli in poultry and livestock. Mulberry leaves at different doses were associated with changes in antioxidant capacity in chickens, and immune organ indexes in pigs. With respect to egg quality, mulberry leaves at different doses improved the shell strength, yolk color, eggshell thickness, and eggshell weight. However, moderate doses diminished the egg yolk ratio and the egg yolk moisture content.

CONCLUSION

In general, dietary mulberry leaves improved the growth, production performance, and immunological parameters in poultry and livestock, although the effects varied at different doses.

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.

RNA-seq analysis identifies differentially expressed gene in different types of donkey skeletal muscles

The main component of donkey meat is skeletal muscle, and different muscle fibers have been found to be associated with meat quality. However, RNA-seq technology has yet to be used to profile the transcriptomic changes of different muscles of the donkey. In this study, the characterizations of different muscles on the gene expression profiles of Dezhou donkey were obtained, the aim was to identify the important genes in donkey muscles, and aid in improving donkey meat quality via RNA-seq. In the donkey gluteus (DG) and donkey longissimus dorsi (DL) group, GO enrichment indicated that DEGs were mainly involved in the biological regulation and metabolic process, and KEGG analysis shows that a total of 427 DEGs were mapped to 216 KEGG pathways and 23 KEGG pathways were significantly enriched such as the ribosome, glycolysis/gluconeogenesis, glucagon signaling pathway and biosynthesis of amino acids pathways. Meanwhile, 504 DEGs were mapped to 223 KEGG pathways, in which 17 were significantly enriched including cardiac muscle contraction and oxytocin signaling pathway in donkey hamstring muscles (DH) and DL group. In addition, the tenderness in donkey meat might involve muscle fiber type and glucose metabolism, which might profit from the DEGs including MYH1, MYH7, TNNC1, TNNI3, TPM3, ALDOA, ENO3, and PGK1. The genes found in this study will provide some ideas for further understanding the molecular mechanism of donkey meat quality.

Plasma metabolomic profiling in two rabbit lines divergently selected for intramuscular fat content

This study provides a thorough comparison of the plasma metabolome of two rabbit lines divergently selected for intramuscular fat content (IMF). The divergent selection led to a correlated response in the overall adiposity, turning these lines into a valuable animal material to study also the genetics of obesity. Over 900 metabolites were detected, and the adjustment of multivariate models, both discriminant and linear, allowed to identify 322 with differential abundances between lines, which also adjusted linearly to the IMF content. The most affected pathways were those of lipids and amino acids, with differences between lines ranging from 0.23 to 6.04 standard deviations, revealing a limited capacity of the low-IMF line to obtain energy from lipids, and a greater branched-chain amino acids catabolism in the high-IMF line related to its increased IMF content. Additionally, changes in metabolites derived from microbial activity supported its relevant role in the lipid deposition. Future research will focus on the analysis of the metabolomic profile of the cecum content, and on the integration of the several -omics datasets available for these lines, to help disentangle the host and microbiome biological mechanisms involved in the IMF deposition.

Identification of Potential Sex-Specific Biomarkers in Pigs with Low and High Intramuscular Fat Content Using Integrated Bioinformatics and Machine Learning

Intramuscular fat (IMF) content is a key determinant of pork quality. Controlling the genetic and physiological factors of IMF and the expression patterns of various genes is important for regulating the IMF content and improving meat quality in pig breeding. Growing evidence has suggested the role of genetic factors and breeds in IMF deposition; however, research on the sex factors of IMF deposition is still lacking. The present study aimed to identify potential sex-specific biomarkers strongly associated with IMF deposition in low- and high-IMF pig populations. The GSE144780 expression dataset of IMF deposition-related genes were obtained from the Gene Expression Omnibus. Initially, differentially expressed genes (DEGs) were detected in male and female low-IMF (162 DEGs, including 64 up- and 98 down-regulated genes) and high-IMF pigs (202 DEGs, including 147 up- and 55 down-regulated genes). Moreover, hub genes were screened via PPI network construction. Furthermore, hub genes were screened for potential sex-specific biomarkers using the least absolute shrinkage and selection operator machine learning algorithm, and sex-specific biomarkers in low-IMF (troponin I (TNNI1), myosin light chain 9(MYL9), and serpin family C member 1(SERPINC1)) and high-IMF pigs (CD4 molecule (CD4), CD2 molecule (CD2), and amine oxidase copper-containing 2(AOC2)) were identified, and then verified by quantitative real-time PCR (qRT-PCR) in semimembranosus muscles. Additionally, the gene set enrichment analysis and single-sample gene set enrichment analysis of hallmark gene sets were collectively performed on the identified biomarkers. Finally, the transcription factor-biomarker and lncRNA-miRNA-mRNA (biomarker) networks were predicted. The identified potential sex-specific biomarkers may provide new insights into the molecular mechanisms of IMF deposition and the beneficial foundation for improving meat quality in pig breeding.

The Protective Effect of a Dietary Extract of Mulberry (Morus alba L.) Leaves against a High Stocking Density, Copper and Trichlorfon in Crucian Carp (Carassius auratus)

This study was designed to examine the protective effects of the extract of mulberry (Morus alba L.) leaves (EML) on crucian carp (Carassius auratus) against a high stocking density, Cu exposure and trichlorfon exposure, which adversely impact fish growth performance, feed intake and fish locomotion. High stocking densities decreased the activities of amylase, lipase, trypsin, Na+/K+-ATPase and alkaline phosphatase (AKP), and increased the content of malonaldehyde (MDA) in fish digestive organs, indicating an impairment of the digestive function and a disturbance of the antioxidant status. Cu exposure increased the activities of glutamate-oxaloacetate transaminase (GOT) and glutamate-pyruvate transaminase (GPT) in fish digestive organs, suggesting the activation of amino acid metabolism. Furthermore, trichlorfon exposure reduced the activities of lactate dehydrogenase (LDH), glutathione reductase (GR), GOT and GPT, and the capacities of the anti-superoxide anion (ASA) and anti-hydroxyl radical (AHR) in fish muscles, indicating a disruption of the bioenergetic homeostasis and antioxidant status. Our present study indicates that dietary EML supplementation relieved the detrimental effects induced by these stressors.

Mulberry leaf extract reduces abdominal fat deposition via adenosine-activated protein kinase/sterol regulatory element binding protein-1c/acetyl-CoA carboxylase signaling pathway in female Arbor Acre broilers

This experiment was carried out to investigate the mechanism of action of mulberry leaf extract (MLE) in reducing abdominal fat accumulation in female broilers. A total of 192 one-day-old female Arbor Acres (AA) broilers were divided into 4 diet groups, with each group consisting of 8 replicates with 6 birds per replicate. The diets contained a basal diet and 3 test diets with supplementation of 400, 800, or 1,200 MLE mg/kg, respectively. The trial had 2 phases that lasted from 1 to 21 d and from 22 to 56 d, respectively. The growth performance, abdominal fat deposition, fatty acid composition, serum biochemistry and mRNA expression of genes related to fat metabolism in liver were determined. The results showed that, 1) dietary supplementation with MLE had no significant impact on broilers final body weight, average daily gain (ADG), or feed to gain ration (F/G) (P > 0.05), but linearly reduced abdominal fat accumulation in both experimental phases (P < 0.05); 2) the total contents of monounsaturated fatty acids (MUFA) and polyunsaturated fatty acids (PUFA), such as palmitoleic acid, oleic acid, and eicosadienoic acid, were increased quadratically as a result of dietary supplements of 400, 800, and 1,200 mg/kg MLE (P < 0.01), while the total contents of saturated fatty acids (SFA), such as teracosanoic acid were decreased (P < 0.01); 3) the addition of 800 or 1,200 MLE mg/kg to the diet linearly reduced total cholesterol (TC) in the serum and liver (P < 0.05). Adenosine-activated protein kinase (AMPK) mRNA expression in the liver was quadratically increased by the addition of 800 or 1,200 MLE mg/kg to the diet (P < 0.05), and the mRNA expression of sterol regulatory element binding protein-1c (SREBP-1c), acetyl-CoA carboxylase (ACC), and acetyl-CoA carboxylate), fatty acid synthase (FAS) were linearly decreased (P < 0.05). In conclusion, MLE can be employed as a viable fat loss feed supplement in fast-growing broiler diets since it reduces abdominal fat deposition in female AA broilers via the AMPK/SREBP-1c/ACC signaling pathway. MLE can also be utilized to modify the fatty acid profile in female broilers (AA) at varied inclusion levels.

Protective Application of Morus and Its Extracts in Animal Production

Different components of the mulberry tree (fruits, leaves, twigs, and roots) are rich in active compounds, and have been reported to possess potent beneficial properties, including antioxidative, anti-inflammatory, antimicrobial, anticancer, anti-allergenic, antihypertensive, and neuroprotective. The mulberry and its extracts can effectively improve the growth performance and fitness of animals. They not only possess the properties of being safe and purely natural, but also they are not prone to drug resistance. According to the literature, the supplemental level of the mulberry and its extracts in animal diets varies with different species, physiological status, age, and the purpose of the addition. It has been observed that the mulberry and its extracts enhanced the growth performance, the quality of animal products (meat, egg, and milk), the antioxidant and the anti-inflammatory responses of animals. Furthermore, the mulberry and its extracts have antibacterial properties and can effectively moderate the relative abundance of the microbial populations in the rumen and intestines, thus improving the immunity function of animals and reducing the enteric methane (CH₄) production in ruminants. Furthermore, the mulberry and its extracts have the potential to depurate tissues of heavy metals. Collectively, this review summarizes the nutrients, active compounds, and biological functions of mulberry tree products, as well as the application in livestock production with an aim to provide a reference for the utilization of the mulberry and its extracts in animal production.

Mulberry plant as a source of functional food with therapeutic and nutritional applications: A review

Medicinal plants from the family Moraceae have diverse applications in agriculture, cosmetics, food, and the pharmaceutical industry. Their extensive spectrum of pharmacological activity for treating numerous inflammatory illnesses, cancer, cardiovascular diseases, and gastrointestinal problems reflects their biological and therapeutic value. This article summarizes the molecular mechanisms related to the biological implications of mulberry extracts, fractions, and isolated bioactive compounds from different parts in various health-related ailments. Additionally, the food industry and animal nutrition applications are summarized. Phytochemicals such as steroids, saponins, alkaloids, glycosides, polysaccharides, and phenolic compounds including terpenoids, flavonoids, anthocyanins, and tannins are found in this medicinal plant. The aqueous, ethanolic, and methanolic extracts, as well as bioactive compounds, have anti-oxidative, hypoglycemic, nephroprotective, antimicrobial, neuroprotective, anti-mutagenic, hepatoprotective, anthelmintic, immune-modulatory, cardioprotective, and skin protecting activities. Mulberry supplementation in food products improves the stability of phenolics, sensory properties, antioxidant activity, and antimicrobial properties. Mulberry leaves in animal feed increase the nutrient digestibility, growth parameters, antimicrobial, and antioxidant properties. PRACTICAL APPLICATIONS: This review summarized the in vivo and in vitro biological activities of the mulberry and isolated constituents in various health conditions. In addition, the food uses such as antioxidant potential, antimicrobial, and physicochemical properties were discussed. Furthermore, in vivo studies revealed mulberry as a significant protein source and its flavonoids as potential animal foliage.

Genome-wide detection of genetic structure and runs of homozygosity analysis in Anhui indigenous and Western commercial pig breeds using PorcineSNP80k data

Background

Runs of homozygosity (ROH) are continuous homozygous regions typically located in the DNA sequence of diploid organisms. Identifications of ROH that lead to reduced performance can provide valuable insight into the genetic architecture of complex traits. Here, we systematically investigated the population genetic structure of five Anhui indigenous pig breeds (AHIPs), and compared them to those of five Western commercial pig breeds (WECPs). Furthermore, we examined the occurrence and distribution of ROHs in the five AHIPs and estimated the inbreeding coefficients based on the ROHs (F_ROH) and homozygosity (F_HOM). Finally, we identified genomic regions with high frequencies of ROHs and annotated candidate genes contained therein.

Results

The WECPs and AHIPs were clearly differentiated into two separate clades consistent with their geographical origins, as revealed by the population structure and principal component analysis. We identified 13,530 ROHs across all individuals, of which 4,555 and 8,975 ROHs were unique to AHIPs and WECPs, respectively. Most ROHs identified in our study were short (< 10 Mb) or medium (10–20 Mb) in length. WECPs had significantly higher numbers of short ROHs, and AHIPs generally had longer ROHs. F_ROH values were significantly lower in AHIPs than in WECPs, indicating that breed improvement and conservation programmes were successful in AHIPs. On average, F_ROH and F_HOM values were highly correlated (0.952–0.991) in AHIPs and WECPs. A total of 27 regions had a high frequency of ROHs and contained 17 key candidate genes associated with economically important traits in pigs. Among these, nine candidate genes (CCNT2, EGR2, MYL3, CDH13, PROX1, FLVCR1, SETD2, FGF18, and FGF20) found in WECPs were related to muscular and skeletal development, whereas eight candidate genes (CSN1S1, SULT1E1, TJP1, ZNF366, LIPC, MCEE, STAP1, and DUSP) found in AHIPs were associated with health, reproduction, and fatness traits.

Conclusion

Our findings provide a useful reference for the selection and assortative mating of pig breeds, laying the groundwork for future research on the population genetic structures of AHIPs, ultimately helping protect these local varieties.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08583-9.

Comparative transcriptomic analysis reveals beneficial effect of dietary mulberry leaves on the muscle quality of finishing pigs

Background

The aim of this study was to investigate the effect of dietary mulberry leaves on the transcriptome profiles of finishing pigs. RNA‐Seq was used to identify differentially expressed genes (DEGs) in the longissimus dorsi of 56 pigs fed either a traditional diet or diets supplemented with 3%, 6% or 9% mulberry leaf powder, and both gene ontology (GO) function and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses were performed. Furthermore, protein–protein interaction (PPI) network and the subnet module analysis were used to identify genes with beneficial potential, and quantitative real‐time polymerase chain reaction (qRT‐PCR) was used to validate the expression patterns revealed by RNA‐Seq.

Results

Pigs fed with the 6% mulberry diet exhibited greater average daily gain, lower water loss and lower shear force than the control group and yielded 531 DEGs, including 271 and 260 upregulated and downregulated genes, respectively. Function analysis revealed that the DEGs were significantly enriched in functions related to muscle growth and development. Furthermore, several genes (i.e. ACOT4, ECHS1, HACD1, NPR1, ADCY2, MGLL and IRS1) were enriched in a KEGG pathway that was associated with fatty acid metabolism, and in the PPI subnet module, four of eight node genes, namely TNNC1, MYL3, TCAP and TNNT1, were associated with muscle formation and development. The upregulation of these genes, including TNNC1, TNNT1 and MYL3, was confirmed by qRT‐PCR.

Conclusions

Dietary mulberry leaves (6%) may improve the muscle quality of pigs by modulating the expression of several key genes, such as TNNC1, MYL3 and TNNT1.

The study was aimed to explain the effect of the inclusion of mulberry in the diet of pigs on transcriptome profiling. The inclusion of mulberry in the diet might be helpful in muscle formation and development of pigs by modulating the expression levels of three genes including TNNC1, MYL3 and TNNT1