Lipidomic and Transcriptomic Analysis of the Longissimus Muscle of Luchuan and Duroc Pigs

Identification of potential candidate genes for the Huoyan trait in developing Wulong goose embryos by transcriptomic analysis

1. The Wulong goose is a Chinese breed and a source of high-quality meat and eggs. A characteristic of the Wulong goose is that a proportion of the birds do not have eyelids, known as the Huoyon trait.2. Wulong geese exhibiting the Huoyan trait at embryonic stages of 9 days (E9), 12 days (E12) and 14 days (E14) were selected alongside those with normal eyelids for comprehensive transcriptome sequencing. Differentially expressed gene (DEG) and functional enrichment analyses were performed and finally, eight DEG were chosen to verify the accuracy of qPCR sequencing.3. Overall, 466, 962 and 550 DEG were obtained from the three control groups, D9 vs. N9, D12 vs. N12 and D14 vs. N14, respectively, by differential analysis (p < 0.05). CDKN1C, CRH, CROCC and TYSND1 were significantly expressed in the three groups. Enrichment analysis revealed the enrichment of CROCC and TYSND1 in pathways of cell cycle process, endocytosis, microtubule-based process, microtubule organising centre organisation, protein processing and protein maturation. CDKN1C and CRH were enriched in the cell cycle and cAMP signalling pathway.4. Some collagen family genes were detected among the DEGs, including COL3A1, COL4A5, COL4A2 and COL4A1. FREM1 and FREM2 genes were detected in both Huoyan and normal eyelids. There was a significant difference (p < 0.01) in FREM1 expression between ED9 and ED14 in female embryos, but this difference was not observed in male embryos.

Integrated analysis of the DNA methylome and RNA transcriptome during the development of skeletal muscle in Duroc pigs

BACKGROUND

Skeletal muscle development plays a crucial role in yield and quality of pork; however, this process is influenced by various factors. In this study, we employed whole-genome bisulfite sequencing (WGBS) and transcriptome sequencing to comprehensively investigate the longissimus dorsi muscle (LDM), aiming to identify key genes that impact the growth and development of Duroc pigs with different average daily gains (ADGs).

RESULTS

Eight pigs were selected and divided into two groups based on ADGs: H (774.89 g) group and L (658.77 g) group. Each pair of the H and L groups were half-siblings. The results of methylation sequencing revealed 2631 differentially methylated genes (DMGs) involved in metabolic processes, signalling, insulin secretion, and other biological activities. Furthermore, a joint analysis was conducted on these DMGs and the differentially expressed genes (DEGs) obtained from transcriptome sequencing of the same individual. This analysis identified 316 differentially methylated and differentially expressed genes (DMEGs), including 18 DMEGs in promoter regions and 294 DMEGs in gene body regions. Finally, LPAR1 and MEF2C were selected as candidate genes associated with muscle development. Bisulfite sequencing PCR (BSP) and quantitative real-time PCR (qRT-PCR) revealed that the promoter region of LPAR1 exhibited significantly lower methylation levels (P < 0.05) and greater expression levels (P < 0.05) in the H group than in the L group. Additionally, hypermethylation was observed in the gene body region of MEF2C, as was a low expression level, in the H group (P < 0.05).

CONCLUSIONS

These results suggest that the differences in the ADGs of Duroc pigs fed the same diet may be influenced by the methylation levels and expression levels of genes related to skeletal muscle development.

Comparison of Growth Performance, Carcass Properties, Fatty Acid Profile, and Genes Involved in Fat Metabolism in Nanyang and Landrace Pigs

This study compared the growth, carcass properties, fatty acid profile, lipid-producing enzyme activity, and expression pattern of genes involved in fat metabolism in Nanyang and Landrace pigs. In the study, 32 Nanyang (22.16 ± 0.59 kg) and 32 Landrace barrows (21.37 ± 0.57 kg) were selected and divided into two groups, each with eight pens and four pigs per pen. The trial period lasted 90 days. The findings showed that the Nanyang pigs had lower average daily weight gain and lean percentage and higher average backfat thickness and lipogenic enzyme activities, including for acetyl-CoA carboxylase, glucose-6-phosphate dehydrogenase, malic enzyme, and fatty acid synthase, than the Landrace pigs. A total of 14 long-chain fatty acids were detected using HPLC-MS, in which it was found that the levels of C14:0, C18:1n-9, C20:1n-9, C20:4n-6, and MUFA were up-regulated and C18:2n-6, C18:3n-3, PUFA n6, n3/n6, and total PUFA were down-regulated in the Nanyang pigs. Moreover, the mRNA levels for genes involved in fat metabolism, ME1, FAS, and LPL, were higher and the expression of SREBP1 mRNA was lower in the Nanyang pigs. Our results suggest genetic differences between the pig breeds in terms of growth, carcass traits, lipogenic enzyme activities, fatty acid profile, and the mRNA expression of genes involved in fat metabolism in subcutaneous fat tissue, which may provide a basis for high-quality pork production. Further studies are needed to investigate the regulation of lipid metabolism.

Integrative deep learning framework predicts lipidomics-based investigation of preservatives on meat nutritional biomarkers and metabolic pathways

Preservatives are added as antimicrobial agents to extend the shelf life of meat. Adding preservatives to meat products can affect their flavor and nutrition. This review clarifies the effects of preservatives on metabolic pathways and network molecular transformations in meat products based on lipidomics, metabolomics and proteomics analyses. Preservatives change the nutrient content of meat products via altering ionic strength and pH to influence enzyme activity. Ionic strength in salt triggers muscle triglyceride hydrolysis by causing phosphorylation and lipid droplet splitting in adipose tissue hormone-sensitive lipase and triglyceride lipase. DisoLipPred exploiting deep recurrent networks and transfer learning can predict the lipid binding trend of each amino acid in the disordered region of input protein sequences, which could provide omics analyses of biomarkers metabolic pathways in meat products. While conventional meat quality assessment tools are unable to elucidate the intrinsic mechanisms and pathways of variables in the influences of preservatives on the quality of meat products, the promising application of omics techniques in food analysis and discovery through multimodal learning prediction algorithms of neural networks (e.g., deep neural network, convolutional neural network, artificial neural network) will drive the meat industry to develop new strategies for food spoilage prevention and control.

Identification of a Candidate Gene Regulating Intramuscular Fat Content in Pigs through the Integrative Analysis of Transcriptomics and Proteomics Data

Pork is a widely consumed source of animal protein worldwide, and the intramuscular fat (IMF) content in pork plays a crucial role in determining its quality. In this study, we sought to identify candidate genes that regulate IMF deposition in pigs. We performed tandem mass tags (TMT)-based quantitative proteomics analysis using Longissimus dorsi (LD) muscle samples obtained from eight pigs with extremely high and low IMF content among a group of 28 Duroc pigs and identified 50 differentially abundant proteins (DAPs). Additionally, we compared the proteomics data with RNA-sequencing data obtained in our previous study and identified TUSC5 as a differentially expressed gene corresponding to the relevant DAP. To investigate the potential role of TUSC5 in adipogenesis, we suppressed TUSC5 expression in mouse 3T3-L1 preadipocytes using short hairpin RNA (shRNA) and observed a significant reduction in the differentiation of 3T3-L1 cells into adipocytes, as indicated by Oil Red O staining and triglyceride content. Moreover, we observed a reduction in the expression of genes associated with adipogenesis (PPARG, CEBPA, FABP4, and FASN) following TUSC5 suppression. Through an integrative analysis of transcriptomics and proteomics data, our study identified TUSC5 as a crucial candidate gene associated with the regulation of IMF content in pigs.

Integrative Analysis of Transcriptomic and Lipidomic Profiles Reveals a Differential Subcutaneous Adipose Tissue Mechanism among Ningxiang Pig and Berkshires, and Their Offspring

Adipose tissue composition contributes greatly to the quality and nutritional value of meat. Transcriptomic and lipidomic techniques were used to investigate the molecular mechanisms of the differences in fat deposition in Ningxiang pigs, Berkshires and F1 offspring. Transcriptomic analysis identified 680, 592, and 380 DEGs in comparisons of Ningxiang pigs vs. Berkshires, Berkshires vs. F1 offspring, and Ningxiang pigs vs. F1 offspring. The lipidomic analysis screened 423, 252, and 50 SCLs in comparisons of Ningxiang pigs vs. Berkshires, Berkshires vs. F1 offspring, and Ningxiang pigs vs. F1 offspring. Lycine, serine, and the threonine metabolism pathway, fatty acid biosynthesis and metabolism-related pathways were significantly enriched in comparisons of Berkshires vs. Ningxiang pigs and Berkshires vs. F1 offspring. The DEGs (PHGDH, LOC110256000) and the SCLs (phosphatidylserines) may have a great impact on the glycine, serine, and the threonine metabolism pathway. Moreover, the DEGs (FASN, ACACA, CBR4, SCD, ELOV6, HACD2, CYP3A46, CYP2B22, GPX1, and GPX3) and the SCLs (palmitoleic acid, linoleic acid, arachidonic acid, and icosadienoic acid) play important roles in the fatty acid biosynthesis and metabolism of fatty acids. Thus, the difference in fat deposition among Ningxiang pig, Berkshires, and F1 offspring may be caused by differences in the expression patterns of key genes in multiple enriched KEGG pathways. This research revealed multiple lipids that are potentially available biological indicators and screened key genes that are potential targets for molecular design breeding. The research also explored the molecular mechanisms of the difference in fat deposition among Ningxiang pig, Berkshires, and F1 pigs, and provided an insight into selection for backfat thickness and the fat composition of adipose tissue for future breeding strategies.

Genetic and Phenotypic Characteristics of Belted Pig Breeds: A Review

Belted pig breeds have unique, distinguishing phenotypic characteristics. This review summarises the current knowledge on pig breeds displaying a belted coat pattern. Belts of different widths and positions around the animal's trunk characterise specific pig breeds from all around the world. All the breeds included in the present paper have been searched through the FAO domestic animal diversity information system (DAD-IS), Every country was checked to identify all breeds described as having black or red piebald coat pattern variations. Advances in genomic technologies have made it possible to identify the specific genes and genetic markers associated with the belted phenotype and explore the genetic relationships between different local breeds. Thus, the origin, history, and production traits of these breeds, together with all the genomic information related to the mechanism of skin pigmentation, are discussed. By increasing our understanding of these breeds, we can appreciate the richness of our biological and cultural heritage and work to preserve the biodiversity of the world's animals.

BATF relieves hepatic steatosis by inhibiting PD1 and promoting energy metabolism

The rising prevalence of nonalcoholic fatty liver disease (NAFLD) has become a global health threat that needs to be addressed urgently. Basic leucine zipper ATF-like transcription factor (BATF) is commonly thought to be involved in immunity, but its effect on lipid metabolism is not clear. Here, we investigated the function of BATF in hepatic lipid metabolism. BATF alleviated high-fat diet (HFD)-induced hepatic steatosis and inhibited elevated programmed cell death protein (PD)1 expression induced by HFD. A mechanistic study confirmed that BATF regulated fat accumulation by inhibiting PD1 expression and promoting energy metabolism. PD1 antibodies alleviated hepatic lipid deposition. In conclusion, we identified the regulatory role of BATF in hepatic lipid metabolism and that PD1 is a target for alleviation of NAFLD. This study provides new insights into the relationship between BATF, PD1, and NAFLD.

Integrated multi-omics analysis reveals variation in intramuscular fat among muscle locations of Qinchuan cattle

BACKGROUND

Intramuscular fat (IMF) is closely related to the tenderness, marbling, juiciness, and flavor of meat. We used a combined transcriptome and metabolome analysis to investigate the molecular mechanisms underlying phenotypic variation among Qinchuan cattle.

RESULTS

The IMF content was relatively high in the meat of Qinchuan cattle bulls and differed among muscle locations, namely the high rib (15.86%), ribeye (14%), striploin (10.44%), and tenderloin (8.67%). CCDC80 and the HOX gene cluster may regulate intramuscular adipose tissue deposition. Moreover, erucic acid (EA) was found to be the main metabolite in Qinchuan beef cattle, with a high concentration in IMF. The deposition of IMF could be regulated by the metabolic pathway for unsaturated fatty acids involving EA and the ACOX3, HACD2, and SCD5 genes. In addition, differentially expressed genes and metabolites were enriched in three major KEGG pathways: purine metabolism, pyrimidine metabolism, and the metabolism of glycine, serine, and threonine.

CONCLUSIONS

We identified a significant metabolite, EA, with variation in IMF. Its closely related genes, ACOX3, HACD2, and SCD5, co-regulate the metabolism of unsaturated fatty acids, ultimately affecting the accumulation of intramuscular adipose tissue in Qinchuan cattle. Consequently, Qinchuan cattle are an elite cultivar for high-quality beef production and have great potential for breeding.

Transcriptome changes during osteogenesis of porcine mesenchymal stem cells derived from different types of synovial membranes and genetic background

Synovial membrane mesenchymal stem cells (SMSCs) often serve as in vitro model for bone disease, but the molecular mechanisms driving osteogenesis in SMSCs from different donor cells of various sources and breeds remain unclear. In this study, porcine SMSCs isolated from adipose synovium (FP) and fibrous synovium (FS) of Angeln Saddleback (AS) and German Landrace (DL) were used to discover the signaling network change after osteogenic induction. During osteogenic differentiation, mineral deposition was first observed at day 14 and further increased until day 21. Transcriptional changes between day 1 and day 21 were enriched in several signaling pathways, including Wnt, PI3K-Akt, and TGF-beta pathway. Certain pathways related to osteogenesis, including osteoblast differentiation, regulation of bone mineralization, and BMP signaling pathway, were enriched at late time points, as confirmed by the osteogenic markers ALPL, COL1A1, and NANOG. A fraction of differentially expressed genes (DEGs) were found between FP and FS, while DEGs between AS and DL increased during the differentiation phase until day 7 and then decreased from day 14 to day 21. These genes are involved in several important signaling pathways, including TGF-beta, Wnt, and lipid-related signaling pathways, suggesting that SMSCs from these two breeds have different osteogenic capabilities.

Single-nucleus and bulk RNA sequencing reveal cellular and transcriptional mechanisms underlying lipid dynamics in high marbled pork

Pork is the most consumed meat in the world, and its quality is associated with human health. Intramuscular fat (IMF) deposition (also called marbling) is a key factor positively correlated with various quality traits and lipo-nutritional values of meat. However, the cell dynamics and transcriptional programs underlying lipid deposition in highly marbled meat are still unclear. Here, we used Laiwu pigs with high (HLW) or low (LLW) IMF contents to explore the cellular and transcriptional mechanisms underlying lipid deposition in highly-marbled pork by single-nucleus RNA sequencing (snRNA-seq) and bulk RNA sequencing. The HLW group had higher IMF contents but less drip loss than the LLW group. Lipidomics results revelled the changes of overall lipid classes composition (e.g., glycerolipids including triglycerides, diglycerides, and monoglycerides; sphingolipids including ceramides and monohexose ceramide significantly increased) between HLW and LLW groups. SnRNA-seq revealed nine distinct cell clusters, and the HLW group had a higher percentage of adipocytes (1.40% vs. 0.17%) than the LLW group. We identified 3 subpopulations of adipocytes, including PDE4D⁺/PDE7B⁺ (in HLW and LLW), DGAT2⁺/SCD⁺ (mostly in HLW) and FABP5⁺/SIAH1⁺ cells (mostly in HLW). Moreover, we showed that fibro/adipogenic progenitors could differentiate into IMF cells and contribute to 43.35% of adipocytes in mice. In addition, RNA-seq revealed different genes involved in lipid metabolism and fatty acid elongation. Our study provides new insights into the cellular and molecular signatures of marbling formation; such knowledge may facilitate the development of new strategies to increase IMF deposition and the lipo-nutritional quality of high marbled pork.

Metabolome-Based Genome-Wide Association Study of Duck Meat Leads to Novel Genetic and Biochemical Insights

Meat is among the most consumed foods worldwide and has a unique flavor and high nutrient density in the human diet. However, the genetic and biochemical bases of meat nutrition and flavor are poorly understood. Here, 3431 metabolites and 702 volatiles in 423 skeletal muscle samples are profiled from a gradient consanguinity segregating population generated by Pekin duck × Liancheng duck crosses using metabolomic approaches. The authors identified 2862 metabolome-based genome-wide association studies (mGWAS) signals and 48 candidate genes potentially modulating metabolite and volatile levels, 79.2% of which are regulated by cis-regulatory elements. The level of plasmalogen is significantly associated with TMEM189 encoding plasmanylethanolamine desaturase 1. The levels of 2-pyrrolidone and glycerophospholipids are regulated by the gene expression of AOX1 and ACBD5, which further affects the levels of volatiles, 2-pyrrolidone and decanal, respectively. Genetic variations in GADL1 and CARNMT2 determine the levels of 49 metabolites including L-carnosine and anserine. This study provides novel insights into the genetic and biochemical basis of skeletal muscle metabolism and constitutes a valuable resource for the precise improvement of meat nutrition and flavor.

Integrative metabolomic and transcriptomic analysis reveals difference in glucose and lipid metabolism in the longissimus muscle of Luchuan and Duroc pigs

Luchuan pig, an obese indigenous Chinese porcine breed, has a desirable meat quality and reproductive capacity. Duroc, a traditional western breed, shows a faster growth rate, high feed efficiency and high lean meat rate. Given the unique features these two porcine breeds have, it is of interest to investigate the underlying molecular mechanisms behind their distinctive nature. In this study, the metabolic and transcriptomic profiles of longissimus dorsi muscle from Duroc and Luchuan pigs were compared. A total of 609 metabolites were identified, 77 of which were significantly decreased in Luchuan compared to Duroc, and 71 of which were significantly elevated. Most differentially accumulated metabolites (DAMs) upregulated in Luchuan were glycerophospholipids, fatty acids, oxidized lipids, alcohols, and amines, while metabolites downregulated in Luchuan were mostly amino acids, organic acids and nucleic acids, bile acids and hormones. From our RNA-sequencing (RNA-seq) data we identified a total of 3638 differentially expressed genes (DEGs), 1802 upregulated and 1836 downregulated in Luchuan skeletal muscle compared to Duroc. Combined multivariate and pathway enrichment analyses of metabolome and transcriptome results revealed that many of the DEGs and DAMs are associated with critical energy metabolic pathways, especially those related to glucose and lipid metabolism. We examined the expression of important DEGs in two pathways, AMP-activated protein kinase (AMPK) signaling pathway and fructose and mannose metabolism, using Real-Time Quantitative Reverse Transcription PCR (qRT-PCR). Genes related to glucose uptake, glycolysis, glycogen synthesis, fatty acid synthesis (PFKFB1, PFKFB4, MPI, TPI1, GYS1, SLC2A4, FASN, IRS1, ULK1) are more activated in Luchuan, while genes related to fatty acid oxidation, cholesterol synthesis (CPT1A, HMGCR, FOXO3) are more suppressed. Energy utilization can be a decisive factor to the distinctive metabolic, physiological and nutritional characteristics in skeletal muscle of the two breeds we studied. Our research may facilitate future porcine breeding projects and can be used to reveal the potential molecular basis of differences in complex traits between various breeds.

Identification of Differentially Expressed Genes in the Longissimus Dorsi Muscle of Luchuan and Duroc Pigs by Transcriptome Sequencing

The Duroc pig originated in the United States and is a typical lean-meat pig. The breed grows fast, and the body size is large, but the meat quality is poor. The Luchuan pig is one of eight excellent local breeds in China; it has tender meat but is small in size. To study the factors that determine growth, we selected the longissimus dorsi muscle of Luchuan and Duroc pigs for transcriptome sequencing. The results of the transcriptome showed that 3682 genes were differentially expressed (DEGs) in the longissimus dorsi muscle of Duroc and Luchuan pigs. We screened out genes related to muscle development and selected the MYL2 (Myosin light chain-2) gene to perform preliminary research. Gene Ontology (GO) enrichment of biological functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the gene products were mainly involved in the Akt/FoxO signaling pathway, fatty acid metabolism, arachidonic acid metabolism and glycine, serine and threonine metabolism. Such pathways contributed to skeletal muscle growth, fatty acid metabolism and intramuscular fat deposition. These results provide insight into the mechanisms underlying the formation of skeletal muscle and provide candidate genes to improve growth traits, as well as contribute to improving the growth and development traits of pigs through molecular breeding.

Flavor formation based on lipid in meat and meat products: A review

Meat product is popular throughout the world due to its unique taste. Flavor is one of the most important quality characteristics of meat products and also is a key influencing factor in the overall acceptability of meat products. The flavor of meat products is formed by precursors undergoing a series of complex reactions. During meat product processing, lipids are hydrolyzed by lipase to produce flavor precursors such as free fatty acid, then further oxidized to form volatile flavor compounds. This review summarizes lipolysis, lipid oxidation, and interaction of lipid with Maillard reaction and amino acid during meat products processing and storage as well as influencing factors on lipid degradation including raw meat (source of meat, feeding pattern, and castration), processing methods (thermal processing, nonthermal processing, salting, and fermentation) and additives. Meanwhile, the volatile compounds produced by lipids in meat products including aldehydes, alcohols, ketones, and hydrocarbons are summed up. Analytical methods of volatile compounds and the application of lipidomics analysis in mechanisms of flavor formation of meat products are also reviewed. PRACTICAL APPLICATIONS: Flavor is one of the most important quality characteristics of meat products, which influences the acceptability of meat products for consumption. Lipids play an important role in the flavor formation of meat products. Understanding the relationship between flavor compounds and changes in lipid compositions during the processing and storage of meat products will be helpful to control the quality of meat products.

Comprehensive lipidomics analysis reveals the changes in lipid profile of camellia oil affected by insect damage

Information on changes in lipid composition of seed oils under biotic stresses is scare. The camellia weevil, Curculio chinensis (Coleoptera: Curculionidae) as a notorious seed predator of Camellia species, has caused huge economic losses in China. Lipidomics is used in this study to reveal the lipid composition of camellia oil and its changes after insect damage. 278 lipids including glycerolipids (GL) (221), glycerophospholipids (GP) (34), fatty acyls (FA) (13), sphingolipids (SP) (8), prenol lipids (PR) (1) and sterol lipids (ST) (1) were determined in camellia oils. Insect damage had a significant impact on lipids, particularly FA and GL. Ten significantly different lipids [FFA(18:2), FFA(24:6), TG(14:1/18:2/18:2), TG(16:0/23:0/18:2), TG(20:1/24:1/18:2), TG(18:2/24:0/18:2), TG(16:3/18:2/22:5), PI(16:1/18:1), PE(16:0/18:1), PE(18:1/18:2)] were identified as potential biomarkers for distinguishing oil extracted from non-infested oilseeds and oil from infested oilseeds. We also detected four most important metabolic pathways by bioinformatics analysis to explore the mechanisms underlying changes. Our findings may be useful for future camellia oil production and may provide new insight into improving of nutritional quality of camellia oil.

Transcriptome Analysis of the Adipose Tissue of Luchuan and Duroc Pigs

Simple Summary

Fat is a vital body tissue of pigs and a crucial index that affects the production efficiency of pigs. In this study, Duroc pigs and Luchuan pigs were used as animal materials, transcriptome sequencing was used to compare the back adipose tissue of the two breeds, to explore the key reason of difference in fat deposition. The result provided new ideas and reference for further study of fat development.

Abstract

Fat deposition is a crucial element in pig production that affects production efficiency, quality and consumer choices. In this study, Duroc pigs, a Western, famous lean pig breed, and Luchuan pigs, a Chinese, native obese pig breed, were used as animal materials. Transcriptome sequencing was used to compare the back adipose tissue of Duroc and Luchuan pigs, to explore the key genes regulating fat deposition. The results showed that 418 genes were highly expressed in the Duroc pig, and 441 genes were highly expressed in the Luchuan pig. In addition, the function enrichment analysis disclosed that the DEGs had been primarily enriched in lipid metabolism, storage and transport pathways. Furthermore, significant differences in the metabolic pathways of alpha-linolenic acid, linoleic acid and arachidonic acid explained the differences in the flavor of the two kinds of pork. Finally, the gene set enrichment analysis (GSEA) exposed that the difference in fat deposition between Duroc and Luchuan pigs may be due to the differential regulation of the metabolism pathway of fatty acid. Therefore, this study described the differential expression transcriptional map of adipose tissue of Duroc pig and Luchuan pig, identified the functional genes regulating pig fat deposition, and provided new hypotheses and references for further study of fat development.

Lipidomics and Transcriptome Reveal the Effects of Feeding Systems on Fatty Acids in Yak’s Meat

The differences of fatty acids in yak’s meat under graze feeding (GF) and stall feeding (SF) regimes and the regulation mechanism of the feeding system on the fatty acids content in yak ’s meat was explored in this study. First, the fatty acids in yak’s longissimus dorsi (LD) muscle were detected by gas liquid chromatography (GLC). Compared with GF yaks, the absolute content of ΣSFAs, ΣMUFAs, ΣUFAs, ΣPUFAs and Σn-6PUFAs in SF yak’s LD were higher, whereas Σn-3PUFAs was lower; the relative content of ΣMUFAs, ΣPUFAs, Σn-3PUFAs and ΣUFAs in SF yak’s LD were lower, whereas ΣSFAs was higher. The GF yak’s meat is healthier for consumers. Further, the transcriptomic and lipidomics profiles in yak’s LD were detected by mRNA-Sequencing (mRNA-Seq) and ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS), respectively. The integrated transcriptomic and lipidomics analysis showed the differences in fatty acids were caused by the metabolism of fatty acids, amino acids, carbohydrates and phospholipids, and were mainly regulated by the FASN, FABP3, PLIN1, SLC16A13, FASD6 and SCD genes in the PPAR signaling pathway. Moreover, the SCD gene was the candidate gene for the high content of ΣMUFA, and FADS6 was the candidate gene for the high content of Σn-3PUFAs and the healthier ratio of Σn-6/Σn-3PUFAs in yak meat. This study provides a guidance to consumers in the choice of yak’s meat, and also established a theoretical basis for improving yak’s meat quality.

Effects of intramuscular fat on meat quality and its regulation mechanism in Tan sheep

Intramuscular fat (IMF) contributes importantly to various aspects of meat quality, and genetic regulation is an effective pathway to improve IMF deposition in sheep. In this study, we systematically explored the effect of IMF content on meat quality in Tan sheep and investigated the regulatory mechanism of flavor precursors metabolism and IMF deposition. The results revealed that IMF significantly affected meat color, total muscle fiber numbers, and muscle fiber types in Tan sheep. Widely-targeted metabolomic analysis showed that amino acids were the main differential flavor precursors between lambs with different IMF content. Importantly, the comparison of fatty acid profiles revealed that saturated fatty acids and monounsaturated fatty acids are beneficial for IMF deposition. Furthermore, integrated analysis between metabolome and transcriptome indicated that MME is a key gene resulting in the reduction of amino acids in lambs with high IMF content; and the joint analysis between fatty acid profiles and transcript profiles showed that ADIPOQ, FABP4, PLIN1, PPARGC1A, SLC2A1 accelerated IMF deposition through positive regulation of saturated fatty acids and monounsaturated fatty acids metabolism. These results revealed key changes in meat quality affected by IMF content and the corresponding genetic mechanism, which may provide a new insight for understanding the IMF differential deposition and for improving meat quality in Tan sheep.

Integration of RNA-seq and ATAC-seq identifies muscle-regulated hub genes in cattle

As the main product of livestock, muscle itself plays an irreplaceable role in maintaining animal body movement and regulating metabolism. Therefore, it is of great significance to explore its growth, development and regeneration to improve the meat yield and quality of livestock. In this study, we attempted to use RNA-seq and ATAC-seq techniques to identify differentially expressed genes (DEGs) specifically expressed in bovine skeletal muscle as potential candidates for studying the regulatory mechanisms of muscle development. Microarray data from 8 tissue samples were selected from the GEO database for analysis. First, we obtained gene modules related to each tissue through WGCNA analysis. Through Gene Ontology (GO) functional annotation, the module of lightyellow (ME_lightyellow) was closely related to muscle development, and 213 hub genes were screened as follow-up research targets. Further, the difference analysis showed that, except for PREB, all other candidate hub genes were up-regulated (muscle group vs. other-group). ATAC-seq analysis showed that muscle-specific accessible chromatin regions were mainly located in promoter of genes related to muscle structure development (GO:0061061), muscle cell development (GO:0055001) and muscle system process (GO:0003012), which were involved in cAMP, CGMP-PKG, MAPK, and other signaling pathways. Next, we integrated the results of RNA-seq and ATAC-seq analysis, and 54 of the 212 candidate hub genes were identified as key regulatory genes in skeletal muscle development. Finally, through motif analysis, 22 of the 54 key genes were found to be potential target genes of transcription factor MEF2C. Including CAPN3, ACTN2, MB, MYOM3, SRL, CKM, ALPK3, MAP3K20, UBE2G1, NEURL2, CAND2, DOT1L, HRC, MAMSTR, FSD2, LRRC2, LSMEM1, SLC29A2, FHL3, KLHL41, ATXN7L2, and PDRG1. This provides a potential reference for studying the molecular mechanism of skeletal muscle development in mammals.

A Divergent Selection on Breast Meat Ultimate pH, a Key Factor for Chicken Meat Quality, is Associated With Different Circulating Lipid Profiles

Background: Chicken meat has become a major source of protein for human consumption. However, the quality of the meat is not yet under control, especially since pH values that are too low or too high are often observed. In an attempt to get a better understanding of the genetic and biochemical determinants of the ultimate pH, two genetic lines of broilers were divergently selected for low (pHu−) or high (pHu+) breast meat pHu. In this study, the serum lipidome of 17-day-old broilers from both lines was screened for pHu markers using liquid-chromatography coupled with mass spectrometry (LC-HRMS).

Results: A total of 185 lipids belonging to 4 groups (glycerolipids, glycerophospholipids, sterols, sphingolipids) were identified in the sera of 268 broilers from the pHu lines by targeted lipidomics. The glycerolipids, which are involved in energy storage, were in higher concentration in the blood of pHu− birds. The glycerophospholipids (phosphatidylcholines, phosphatidylethanolamines) with long and polyunsaturated acyl chains were more abundant in pHu+ than in pHu− while the lysophosphatidylcholines and lysophosphatidylethanolamines, known to be associated with starch, were observed in higher quantity in the serum of the pHu− line. Finally, the concentration of the sterols and the ceramides, belonging to the sphingolipids class, were higher in the pHu+ and pHu−, respectively. Furthermore, orthogonal partial least-squares analyses highlighted a set of 68 lipids explaining 77% of the differences between the two broilers lines (R²Y = 0.77, Q² = 0.67). Among these lipids, a subset of 40 predictors of the pHu value was identified with a Root Mean Squared Error of Estimation of 0.18 pH unit (R²Y = 0.69 and Q² = 0.62). The predictive model of the pHu value was externally validated on 68 birds with a Root Mean Squared Error of Prediction of 0.25 pH unit.

Conclusion: The sets of molecules identified will be useful for a better understanding of relationship between serum lipid profile and meat quality, and will contribute to define easily accessible pHu biomarkers on live birds that could be useful in genetic selection.

Advanced Lipidomics in the Modern Meat Industry: Quality Traceability, Processing Requirement, and Health Concerns

Over the latest decade, lipidomics has been extensively developed to give robust strength to the qualitative and quantitative information of lipid molecules derived from physiological animal tissues and edible muscle foods. The main lipidomics analytical platforms include mass spectrometry (MS) and nuclear magnetic resonance (NMR), where MS-based approaches [e.g., “shotgun lipidomics,” ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF-MS)] have been widely used due to their good sensitivity, high availability, and accuracy in identification/quantification of basal lipid profiles in complex biological point of view. However, each method has limitations for lipid-species [e.g., fatty acids, triglycerides (TGs), and phospholipids (PLs)] analysis, and necessitating the extension of effective chemometric-resolved modeling and novel bioinformatic strategies toward molecular insights into alterations in the metabolic pathway. This review summarized the latest research advances regarding the application of advanced lipidomics in muscle origin and meat processing. We concisely highlighted and presented how the biosynthesis and decomposition of muscle-derived lipid molecules can be tailored by intrinsic characteristics during meat production (i.e., muscle type, breed, feeding, and freshness). Meanwhile, the consequences of some crucial hurdle techniques from both thermal/non-thermal perspectives were also discussed, as well as the role of salting/fermentation behaviors in postmortem lipid biotransformation. Finally, we proposed the inter-relationship between potential/putative lipid biomarkers in representative physiological muscles and processed meats, their metabolism accessibility, general nutritional uptake, and potency on human health.

A Comprehensive Review of Lipidomics and Its Application to Assess Food Obtained from Farm Animals

Lipids are one of the major macronutrients essential for adequate growth and maintenance of human health. Their structure is not only complex but also diverse, which makes systematic and holistic analyses challenging; consequently, little is known regarding the relationship between phenotype and mechanism of action. In recent years, rapid advancements have been made in the fields of lipidomics and bioinformatics. In comparison with traditional approaches, mass spectrometry-based lipidomics can rapidly identify as well as quantify >1,000 lipid species at the same time, facilitating comprehensive, robust analyses of lipids in tissues, cells, and body fluids. Accordingly, lipidomics is now being widely applied in various fields, particularly food and nutrition science. In this review, we discuss lipid classification, extraction techniques, and detection and analysis using lipidomics. We also cover how lipidomics is being used to assess food obtained from livestock and poultry. The information included herein should serve as a reference to determine how to characterize lipids in animal food samples, enhancing our understanding of the application of lipidomics in the field in animal husbandry.

Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Muscle of Luchuan and Duroc Pigs

Luchuan pig is a typical obese pig breed in China, and the diameter and area of its longissimus dorsi muscle fibers are significantly smaller than those of Duroc (lean) pig. Skeletal muscle fiber characteristics are related to meat quality of livestock. There is a significant correlation between the quality of different breeds of pork and the characteristics of muscle fiber, which is an important factor affecting the quality of pork. The diameter and area of muscle fibers are related to muscle growth and development. Therefore, we used the assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) analysis to investigate the potential mechanism underlying the difference in skeletal muscle growth and development between the two types of pigs. First, transposase-accessible chromatin was analyzed to map the landscape of open chromatin regions and transcription factor binding sites. We identified several transcription factors that potentially affected muscle growth and development, including TFAP4, MAX, NHLH1, FRX5, and TGIF1. We also found that transcription factors with basic helix-loop-helix structures had a preference for binding to genes involved in muscle development. Then, by integrating ATAC-seq and RNA-seq, we found that the Wnt signaling pathway, the mTOR signaling pathway, and other classical pathways regulate skeletal muscle development. In addition, some pathways that might regulate skeletal muscle growth, such as parathyroid hormone synthesis, secretion, and action, synthesis and degradation of ketone bodies, and the thyroid hormone signaling pathway, which were significantly enriched. After further study, we identified a number of candidate genes (ASNS, CARNS1, G0S2, PPP1R14C, and SH3BP5) that might be associated with muscle development. We also found that the differential regulation of chromatin openness at the level of some genes was contrary to the differential regulation at the level of transcription, suggesting that transcription factors and transcriptional repressors may be involved in the regulation of gene expression. Our study provided an in-depth understanding of the mechanism behind the differences in muscle fibers from two species of pig and provided an important foundation for further research on improving the quality of pork.

Determination of the Heterogeneity of Intramuscular Fat and Visceral Adipose Tissue From Dezhou Donkey by Lipidomics and Transcriptomics Profiling

Intramuscular fat (IMF) and visceral adipose tissue (VAT) are both lipids, but have significantly different deposition processes. Furthermore, the heterogeneity of lipid molecular characteristics and mechanisms is unclear. Accordingly, this study used non-targeted lipidomics and transcriptomics to analyze the lipid profiles and metabolism of longissimus dorsi muscle (LDM) and VAT from donkeys. A total of 1,146 and 1,134 lipids belonging to 18 subclasses were identified in LDM and VAT, respectively, with LDM having higher glycerophospholipid (GP) and lower glycerolipid (GL) contents. Polyunsaturated fatty acids (PUFAs) were distributed preferentially at the sn-1 positions in triglycerides (TGs), and sn-2 positions in phosphatidylcholine (PC) and phosphatidylethanolamine (PE). The percentage PUFA content in TGs was significantly lower in LDM than in VAT, while the opposite trend was observed for PUFAs in PC and PE. A total of 110 different lipid molecules (72 downregulated and 38 upregulated) were identified in LDM compared with VAT, of which 11 were considered potential lipid markers. These different lipids were involved in 17 metabolic pathways, including GL and GP metabolisms. Of the 578 differentially expressed genes screened, 311 were downregulated and 267 were upregulated in LDM compared with VAT. Enriched ontology analysis of the differentially expressed genes mainly involved sphingolipid signaling pathways, and GP, GL, and sphingolipid metabolisms. Overall, lipidomics and transcriptomics indicated differences in lipid profiles and metabolism in LDM and VAT, providing new perspectives for the study of heterogeneity in IMF and VAT.

Combined Transcriptomic and Lipidomic Analysis Reveals Dysregulated Genes Expression and Lipid Metabolism Profiles in the Early Stage of Fatty Liver Disease in Rats

Non-alcoholic fatty liver disease develops from simple steatosis to non-alcoholic steatohepatitis (NASH), which then potentially develops into liver cirrhosis. It is a serious threat to human health. Therefore, investigating the formation and development mechanism of non-alcoholic fatty liver disease (NAFLD) is of great significance. Herein, an early model of NAFLD was successfully established by feeding rats with a high-fat and choline-deficient diet. Liver tissue samples were obtained from rats in the fatty liver model group (NAFL) and normal diet control group (CON). Afterward, transcriptome and lipidomic analysis was performed. Transcriptome results revealed that 178 differentially expressed genes were detected in NAFL and CON groups. Out of which, 105 genes were up-regulated, 73 genes were downregulated, and 8 pathways were significantly enriched. A total of 982 metabolites were detected in lipidomic analysis. Out of which 474 metabolites were significantly different, 273 were up-regulated, 201 were downregulated, and 7 pathways were significantly enriched. Based on the joint analysis, 3 common enrichment pathways were found, including cholesterol metabolism and fat digestion and absorption metabolic pathways. Overall, in the early stage of NAFLD, a small number of genetic changes caused a strong response to lipid components. The strongest reflection was glycerides and glycerophospholipids. A significant increase in fatty acid uptake accompanied by cholesterol metabolism is the most prominent metabolic feature of the liver in the early stage of NAFLD. In the early stage of fatty liver, the liver had shown the characteristics of NASH.

Dietary calcium supplementation promotes the accumulation of intramuscular fat

BACKGROUND

In the livestock industry, intramuscular fat content is a key factor affecting meat quality. Many studies have shown that dietary calcium supplementation is closely related to lipid metabolism. However, few studies have examined the relationship between dietary calcium supplementation and intramuscular fat accumulation.

METHODS

Here, we used C2C12 cells, C57BL/6 mice (n = 8) and three-way cross-breeding pigs (Duroc×Landrace×Large white) (n = 10) to study the effect of calcium addition on intramuscular fat accumulation. In vitro, we used calcium chloride to adjust the calcium levels in the medium (2 mmol/L or 3 mmol/L). Then we measured various indicators. In vivo, calcium carbonate was used to regulate calcium levels in feeds (Mice: 0.5% calcium or 1.2% calcium) (Pigs: 0.9% calcium or 1.5% calcium). Then we tested the mice gastrocnemius muscle triglyceride content, pig longissimus dorsi muscle meat quality and lipidomics.

RESULTS

In vitro, calcium addition (3 mmol/L) had no significant effect on cell proliferation, but promoted the differentiation of C2C12 cells into slow-twitch fibers. Calcium supplementation increased triglyceride accumulation in C2C12 cells. Calcium addition increased the number of mitochondria and also increased the calcium level in the mitochondria and reduced the of key enzymes activity involved in β-oxidation such as acyl-coenzyme A dehydrogenase. Decreasing mitochondrial calcium level can alleviate lipid accumulation induced by calcium addition. In addition, calcium addition also reduced the glycolytic capacity and glycolytic conversion rate of C2C12 cells. In vivo, dietary calcium supplementation (1.2%) promoted the accumulation of triglycerides in the gastrocnemius muscle of mice. Dietary calcium supplementation (1.5%) had no effect on pig weight, but significantly improved the flesh color of the longissimus dorsi muscle, reduced the backfat thickness and increased intramuscular fat content in pigs. Besides, calcium addition had no effect on longissimus dorsi pH, electrical conductivity and shear force.

CONCLUSIONS

These results suggest that calcium addition promotes intramuscular fat accumulation by inhibiting the oxidation of fatty acids. These findings provide a new tool for increasing intramuscular fat content and an economical strategy for improving meat quality.