The meat of local livestock breeds often has unique qualities and flavors. In this study, three Shanghai native pig breeds (MSZ, SWT, and SHB) exhibited better meat quality traits than globalized commercial pig breeds (DLY). Subsequently, metabolomic and lipidomic differences in the longissimus dorsi (L) and gluteus (T) muscles of the Shanghai native pig breeds and DLY pig breed were compared using liquid chromatography-mass spectrometry (LC-MS). The results demonstrated that the metabolites mainly consisted of (28.16%) lipids and lipid-like molecules, and (25.87%) organic acids and their derivatives were the two most dominant groups. Hundreds of differential expression metabolites were identified in every compared group, respectively. One-way ANOVA was applied to test the significance between multiple groups. Among the 20 most abundant differential metabolites, L-carnitine was significantly different in the muscles of the four pig breeds (p-value = 7.322 × 10-11). It was significantly higher in the L and T muscles of the two indigenous black pig breeds (MSZ and SWT) than in the DLY pigs (p-value < 0.001). Similarly, lipidomic analysis revealed the PA (18:0/18:2) was significantly more abundant in the muscle of these two black breeds than that in the DLY breed (p-value < 0.001). These specific metabolites and lipids might influence the meat quality and taste properties and lead to customer preferences. Therefore, this study provided insights into the characterization of meat metabolites and lipids in Shanghai native pig breeds.

Periparturient dairy cattle undergo physiological adaptations to support fetal growth and colostrum synthesis in late gestation and milk production in early lactation. To support energy and protein demands dairy cattle mobilize body tissue reserves. The objective of this study was to determine the effects of prepartum skeletal muscle reserves and supplementation of branched-chain volatile fatty acids (BCVFA) on body composition measurements, metabolic markers related to health, protein, and energy status, and subsequent milk yield in multiparous dairy cows. Skeletal muscle reserves were assessed by 3 ultrasounds of the longissimus dorsi muscle depth (LDD) measured 42 d before expected calving (BEC), and cows (n = 48) were assigned to either high muscle (HM; > 4.6 cm) or low muscle (LM; ≤ 4.6 cm) groups. Cows were then randomly assigned to either control (CON) of soyhull pellets (80 g/d) or BCVFA treatment which contained isobutyrate (40 g/d), isovalerate (20 g/d), and 2-methylbutyrate (20 g/d) calcium salt products. Treatments were top dressed from 42 BEC until parturition, resulting in 4 combinations of muscle groups and treatments: HM-CON (n = 13), HM-BCVFA (n = 13), LM-CON (n = 11), and LM-BCVFA (n = 11). Measurements of the LDD, BW, and BCS were taken on the following days relative to calving -42, -35, -21, -7, 0, 7, 14, 21, 28. Weekly blood samples were taken to measure glucose, BHB, and insulin concentrations, and 5 of the blood sample time points were utilized to determine 3-methylhistidine and creatinine blood concentrations. Milk yield was recorded daily for the first 28 d of lactation, and samples were taken from both milkings once a wk for the first 4 wk to determine components. The statistical model included the fixed effects of treatment, group, time, their interactions, and the random effect of cow nested within group and treatment. Prepartum muscle mobilization varied between muscle groups, as LM cows accreted muscle prepartum, and HM cows mobilized muscle. The HM cows had higher milk fat, protein, lactose, and energy corrected milk yields. The BCVFA supplementation tended to increase blood glucose concentrations both prepartum and postpartum and decreased milk urea nitrogen concentrations. Higher prepartum skeletal muscle reserves improve productivity of early lactation cows likely due to differences in muscle mobilization, and BCVFA supplementation improves glucose dynamics during the transition period, which may improve the metabolic health of the periparturient dairy cow.

Many studies have shown that long non-coding RNAs (lncRNAs) play key regulatory roles in various biological processes. However, the importance and molecular regulatory mechanisms of lncRNAs in donkey intramuscular fat deposition remain to be further investigated. In this study, we used published transcriptomic data from the longissimus dorsi muscle of Guangling donkeys to identify lncRNAs and obtained 196 novel lncRNAs. Compared with the coding genes, the novel lncRNAs and the known lncRNAs exhibited some typical features, such as shorter transcript length and smaller exons. A total of 272 coding genes and 52 lncRNAs were differentially expressed between the longissimus dorsi muscles of the low-fat and high-fat groups. The differentially expressed genes were found to be involved in various biological processes related to lipid metabolism. The potential target genes of differentially expressed lncRNAs were predicted by cis and trans. Functional analysis of lncRNA targets showed that some lncRNAs may act on potential target genes involved in lipid metabolism processes and regulate lipid deposition in the longissimus dorsi muscle. This study provides valuable information for further investigation of the molecular mechanisms of lipid deposition traits in donkeys, which may improve meat traits and facilitate the selection process of donkeys in future breeding.

In order to investigate the effect of slaughter weight (SW) on carcass characteristics and meat quality, we measured the carcass characteristics, meat quality, and amino acid metabolomics characteristics of longissimus dorsi (LD) muscle from Tianfu finishing (TF) pigs. Based on SW, 13 pigs were divided into three groups (100-kg group, 125-kg group, and 150-kg group with 3, 5, 5 pigs in each group, respectively). Raising SW to 125 kg or 150 kg increased average backfat thickness (P < 0.01) and intramuscular fat content (P < 0.01), and decreased shear force (P < 0.01). A total of 231 amino acid metabolome from three amino acid classes identified with metabolomics were analyzed, and 93 differentially expressed metabolites (DEMs) were identified (69 up-regulated DEMs and 24 down-regulated DEMs). The DEMs, including urea, 3-iodo-L-tyrosine, N-glycyl-L-leucine, and N, N-dimethylglycine with amino acid metabolism, were significantly induced (P < 0.01). KEGG pathway analysis showed that these DEMs were significantly enriched (P < 0.01) in 135 metabolism pathways, including pathways related to amino acid metabolism, such as arginine and proline metabolism, glycine, serine and threonine metabolism, alanine, aspartate and glutamate metabolism, tryptophan metabolism, and beta-alanine metabolism. Our research findings provided new insights into the impact of SW on amino acid distribution and theoretical support for genetic breeding of meat quality of TF pigs. However, raising SW to 125 kg, or more, decreased the carcass leanness of live TF pigs and had no benefits to pork quality attributes.

In this study, we measured the growth performance and intramuscular fat (IMF) content of the Longissimus dorsi (LD) of Fuqing goats (FQs) and Nubian goats (NBYs), which exhibit extreme phenotypic differences in terms of their production and meat quality traits. RNA-Seq analysis was performed, and transcriptome data were obtained from the LD tissue of 3-month fetuses (E3), 0-month lambs (0M), 3-month lambs (3M), and 12-month lambs (12M) to reveal the differences in the molecular mechanisms regulating the muscle development and IMF deposition between FQs and NBYs. The results showed that a higher body weight and average daily gain were observed in the NBYs at three developmental stages after birth, whereas a higher IMF content was registered in the FQs at 12M. Additionally, transcriptome profiles during the embryonic period and after birth were completely different for both FQs and NBYs. Moreover, DEGs (KIF23, CCDC69, CCNA2, MKI67, KIF11, RACGAP1, NUSAP1, SKP2, ZBTB18, NES, LOC102180034, CAPN6, TUBA1A, LOC102178700, and PEG10) significantly enriched in the cell cycle (ko04110) at E3 (FQs vs. NBYs), and DEGs (MRPS7, RPS8, RPL6, RPL4, RPS11, RPS10, RPL5, RPS6, RPL8, RPS13, RPS24, RPS15, RPL23) significantly enriched in ribosomes (ko03010) at 0M (FQs vs. NBYs) related to myogenic differentiation and fusion were identified. Meanwhile, the differences in glucose and lipid metabolism began at the E3 timepoint and continued to strengthen as growth proceeded in FQs vs. NBYs. DEGs (CD36, ADIROQR2, ACACA, ACACB, CPT1A, IGF1R, IRS2, LDH-A, PKM, HK2, PFKP, PCK1, GPI, FASN, FADS1, ELOVL6, HADHB, ACOK1, ACAA2, and ACSL4) at 3M (FQs vs. NBYs) and 12M (FQs vs. NBYs) significantly enriched in the AMPK signaling pathway (ko04152), insulin resistance (ko04931), the insulin signaling pathway (ko04910), fatty acid metabolism (ko01212), and glycolysis/gluconeogenesis (ko00010) related to IMF deposition were identified. Further, the results from this study provide the basis for future studies on the mechanisms regulating muscle development and IMF deposition in different breeds of goats, and the candidate genes identified could be used in the selection process.

Skeletal muscle grows in response to a combination of genetic and environmental factors, and its growth and development influence the quality of pork. Elucidating the molecular mechanisms regulating the growth and development of skeletal muscle is of great significance to both animal husbandry and farm management. The Jiangquan black pig is an excellent pig breed based on the original Yimeng black pig, importing the genes of the Duroc pig for meat traits, and cultivated through years of scientific selection and breeding. In this study, full-length transcriptome sequencing was performed on three growth stages of Jiangquan black pigs, aiming to study the developmental changes in Jiangquan black pigs at different developmental stages at the molecular level and to screen the key genes affecting the growth of skeletal muscle in Jiangquan black pigs. We performed an enrichment analysis of genes showing differential expression and constructed a protein-protein interaction network with the aim of identifying core genes involved in the development of Jiangquan black pigs. Notably, genes such as TNNI2, TMOD4, PLDIM3, MYOZ1, and MYH1 may be potential regulators of muscle development in Jiangquan black pigs. Our results contribute to the understanding of the molecular mechanisms of skeletal muscle development in this pig breed, which will facilitate molecular breeding efforts and the development of pig breeds to meet the needs of the livestock industry.

The Ningxiang pig, a distinguished local breed in China, is recognized for its good meat quality traits. This study examines the proteomics of Ningxiang pigs at three developmental stages and delves into the upstream transcriptomics of these proteomics. Such an analysis facilitates a deeper understanding of the molecular interplay between proteins and transcriptomes in the Ningxiang pig muscle, influencing muscle growth and development. In this research, we analyzed the muscles of Ningxiang pigs at three developmental stages: 30 days in weaned piglets, 90 days in nursery pigs, and 210 days in late fattening pigs. There a total of 16 differentially co-expressed miRNAs (ssc-miRNA-1, ssc-miRNA-378, ssc-miRNA-143, ssc-miRNA-30e, etc.), 74 differentially co-expressed mRNA (PLIN3, CPT2, IGF2 and HSP90AB1, etc.) have been identified in the three stages. 572 differentially abundant proteins (DAPs) (APOC3, NDUFA2, HSPD1, ATP5E, PDHA1, etc.) were readily identified by comparing different time periods. According to the KEGG enrich pathway results that DAPs most enriched in growth and development pathways, immune mechanism pathways and maintaining functions of physical. Through short time-series expression miner (STEM) association analysis, a total of 571 negative miRNA-mRNA interaction pairs and 2 negative miRNA-mRNA-protein (Chr05_11955-Pig.17268.1-ATP5F1B, ssc-miR-194a-3p-Pig.15802.1-ACY1) interaction pairs were found. Our study provides a theoretical basis on molecular mechanism for the study of IMF deposition, muscle growth and immunity in Ningxiang pig breed.

The aim of this study was to investigate the effects of dietary l-glutamine (Gln) supplementation on the morphology and function of the intestine and the growth of muscle in piglets. In this study, sixteen 21-day-old piglets were randomly divided into two groups: the Control group (fed a basal diet) and the Gln group (fed a basal diet supplemented with 0.81% Gln). Blood, gut, and muscle samples were collected from all piglets on Day 20 of the trial. Compared with the Control group, the supplementation of Gln increased (p < 0.05) the villus height, villus width, villus surface area, and villus height/crypt depth ratio of the small intestine. Furthermore, the supplementation of Gln increased (p < 0.05) total protein, total protein/DNA, and RNA/DNA in both the jejunum and ileum. It also increased (p < 0.05) the concentrations of carnosine and citrulline in the jejunal mucosa, as well as citrulline and cysteine concentrations in the ileum. Conversely, Gln supplementation decreased (p < 0.05) Gln concentrations in both the jejunum and ileum, along with β-aminoisobutyric acid and 1-Methylhistidine concentrations, specifically in the ileum. Subsequent research revealed that Gln supplementation increased (p < 0.05) the mRNA levels for glutathione-S-transferase omega 2 and interferon-β in the duodenum. In addition, Gln supplementation led to an increase (p < 0.05) in the number of Lactobacillus genus in the colon, but a decrease (p < 0.05) in the level of HSP70 in the jejunum and the activity of diamine oxidase in plasma. Also, Gln supplementation reduced (p < 0.05) the mRNA levels of glutathione-S-transferase omega 2 and interferon stimulated genes, such as MX1, OAS1, IFIT1, IFIT2, IFIT3, and IFIT5 in both the jejunum and ileum, and the numbers of Clostridium coccoides, Enterococcus genus, and Enterobacterium family in the colon. Moreover, Gln supplementation enhanced (p < 0.05) the concentrations of total protein, RNA/DNA, and total protein/DNA ratio in the longissimus dorsi muscle, the concentrations of citrulline, ornithine, arginine, and hydroxyproline, and the mRNA level of peptide transporter 1, while reducing the contents of hydrogen peroxide and malondialdehyde and the mRNA level of glutathione-S-transferase omega 2 in the longissimus dorsi muscle. In conclusion, dietary Gln supplementation can improve the intestinal function of piglets and promote the growth of the longissimus dorsi muscle.

Food is generally prepared and vacuum-sealed in a water bath, then heated to a precise temperature and circulated in a sous vide machine. Due to its affordability and ease of use, this cooking method is becoming increasingly popular in homes and food service businesses. However, suggestions from manufacturers and chefs for long-term, low-temperature sous vide cooking raise questions about food safety in the media. In this study, heat treatment with different times and wild thyme essential oil (EO) in sous vide-processed rabbit longissimus dorsi muscle were found to inactivate Salmonella enterica. The rabbit meat samples were vacuum-packed in control groups, in the second group the rabbit meat samples were injected with S. enterica, and in the third group were meat samples infected with S. enterica with Thymus serpylum EO additive. The vacuum-packed samples were cooked sous vide for the prescribed time at 55, 60, and 65 °C. At 5, 15, 30, and 60 min, the quantities of S. enterica, total bacterial counts, and coliform bacteria were measured in groups of sous vide rabbit meat. Microbiological analyses of rabbit meat samples on days 1 and 7 were evaluated. In this study, total viable counts, coliforms bacteria, and number of Salmonella spp. were identified. After incubation, isolates from different groups of microorganisms were identified by the mass spectrometry technique. For each day measured, the test group exposed to a temperature of 55 °C for 5 min had a greater number of total microbiota. The most isolated microorganisms by MALDI-TOF MS Biotyper from the control and treated groups were Lactococcus garvieae and in the treated groups also S. enterica. Based on our analysis of sous vide rabbit meat samples, we discovered that adding 1% of thyme essential oil to the mixture reduced the amount of Salmonella cells and increased the overall and coliform bacterial counts. The microbiological quality of sous vide rabbit meat that was kept for seven days was positively impacted by the addition of thyme essential oil.

UNASSIGNED: Pig growth is an important economic trait that involves the co-regulation of multiple genes and related signaling pathways. High-throughput sequencing has become a powerful technology for establishing the transcriptome profiles and can be used to screen genome-wide differentially expressed genes (DEGs). In order to elucidate the molecular mechanism underlying muscle growth, this study adopted RNA sequencing (RNA-seq) to identify and compare DEGs at the genetic level in the longissimus dorsi muscle (LDM) between two indigenous Chinese pig breeds (Diannan small ears [DSE] pig and Wujin pig [WJ]) and one introduced pig breed (Landrace pig [LP]).
UNASSIGNED: Animals under study were from two Chinese indigenous pig breeds (DSE pig, n = 3; WJ pig, n = 3) and one introduced pig breed (LP, n = 3) were used for RNA sequencing (RNA-seq) to identify and compare the expression levels of DEGs in the LDM. Then, functional annotation, Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and Protein-Protein Interaction (PPI) network analysis were performed on these DEGs. Then, functional annotation, Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and Protein-Protein Interaction (PPI) network analysis were performed on these DEGs.
UNASSIGNED: The results revealed that for the DSE, WJ, and LP libraries, more than 66, 65, and 71 million clean reads were generated by transcriptome sequencing, respectively. A total of 11,213 genes were identified in the LDM tissue of these pig breeds, of which 7,127 were co-expressed in the muscle tissue of the three samples. In total, 441 and 339 DEGs were identified between DSE vs. WJ and LP vs. DSE in the study, with 254, 193 up-regulated genes and 187, 193 down-regulated genes in DSE compared to WJ and LP. GO analysis and KEGG signaling pathway analysis showed that DEGs are significantly related to contractile fiber, sarcolemma, and dystrophin-associated glycoprotein complex, myofibril, sarcolemma, and myosin II complex, Glycolysis/Gluconeogenesis, Propanoate metabolism, and Pyruvate metabolism, etc. In combination with functional annotation of DEGs, key genes such as ENO3 and JUN were identified by PPI network analysis.
UNASSIGNED: In conclusion, the present study revealed key genes including DES, FLNC, PSMD1, PSMD6, PSME4, PSMB4, RPL11, RPL13A, ROS23, RPS29, MYH1, MYL9, MYL12B, TPM1, TPM4, ENO3, PGK1, PKM2, GPI, and the unannotated new gene ENSSSCG00000020769 and related signaling pathways that influence the difference in muscle growth and could provide a theoretical basis for improving pig muscle growth traits in the future.