Integration of Transcriptomics and Non-Targeted Metabolomics Reveals the Underlying Mechanism of Skeletal Muscle Development in Duck during Embryonic Stage

Integrating metabolomics and transcriptomics to analyze the differences of breast muscle quality and flavor formation between Daweishan mini chicken and broiler

The quality and flavor of chicken are affected by muscle metabolites and related regulatory genes, and the molecular regulation mechanism of meat quality is different among different breeds of chicken. In this study, 40 one-day-old Daweishan mini chicken (DM) and Cobb broiler (CB) were selected from each group, with 4 replicates and 10 chickens in each replicate. The chickens were reared until 90 d of age under the same management conditions. Then, metabolomics and transcriptomics data of 90-day-old DM (n = 4) and CB (n = 4) were integrated to analyze metabolites affecting breast muscle quality and flavor, and to explore the important genes regulating meat quality and flavor related metabolites. The results showed that a total of 38 significantly different metabolites (SDMs) and 420 differentially expressed genes (DEGs) were detected in the breast muscle of the 2 breeds. Amino acid and lipid metabolism may be the cause of meat quality and flavor difference between DM and CB chickens, involving metabolites such as L-methionine, betaine, N6, N6, N6-Trimethyl-L-lysine, L-anserine, glutathione, glutathione disulfide, L-threonine, N-Acetyl-L-aspartic acid, succinate, choline, DOPC, SOPC, alpha-linolenic acid, L-palmitoylcarnitine, etc. Important regulatory genes with high correlation with flavor amino acids (GATM, GSTO1) and lipids (PPARG, LPL, PLIN1, SCD, ANGPTL4, FABP7, GK, B4GALT6, UGT8, PLPP4) were identified by correlation analysis, and the gene-metabolite interaction network of breast muscle mass and flavor formation in DM chicken was constructed. This study showed that there were significant differences in breast metabolites between DM and CB chickens, mainly in amino acid and lipid metabolites. These 2 kinds of substances may be the main reasons for the difference in breast muscle quality and flavor between the 2 breeds. In general, this study could provide a theoretical basis for further research on the molecular regulatory mechanism of the formation of breast muscle quality and flavor differences between DM and CB chickens, and provide a reference for the development, utilization and genetic breeding of high-quality meat chicken breeds.

Phenotypic Identification, Genetic Characterization, and Selective Signal Detection of Huitang Duck

The Huitang duck (HT), a long-domesticated elite local breed from Hunan Province, China, with excellent meat quality, has not had its population genetic structure and genomic selective sweeps extensively studied to date. This study measured the phenotypic characteristics of HT and conducted comparative analysis between HT and 16 different duck breeds, including wild, indigenous, and meat breeds, to characterize its population structure and genetic potential. The results revealed that HT is a dual-purpose indigenous breed with a genetic background closely related to the Youxian sheldrake and Linwu ducks. In the selective sweep analysis between HT and Linwu ducks, genes such as PLCG2, FN1, and IGF2BP2, which are associated with muscle growth and development, were identified near the 27 selection signals. The comparison between HT and Jinding ducks revealed 68 selective signals that contained important genes associated with ovarian development (GRIK4, MAP3K8, and TGIF1) and egg-laying behaviors (ERBB4). Selective sweep analysis between HT and Youxian sheldrake ducks found 93 selective regions covering genes related to both meat (IGF1R and IGFBP5) and egg-production (FOXO3 and ITPR1) traits. Our study may provide novel knowledge for exploring the population structure and genetic potential of HT, offering a theoretical basis for its breeding strategies in the future.

Integrated transcriptomics and metabolomics study of embryonic breast muscle of Jiaji ducks

Because number of matured muscle fibers in poultry does not increase after birth, the meat yield is mainly determined during embryogenesis. We previously indicated breast muscle grew rapidly from 18th day after hatching (E18) to E27, and almost stopped from E27 to E34 of Jiaji ducks, while the mechanism is unclear. This study utilized RNA-seq to explore the related genes of muscle development and their relationship with small molecule metabolites at E18, E27 and E34 of Jiaji ducks. Several thousand differentially expressed genes (DEGs) were detected among E18, E27 and E34. DEGs expression profiles included 8 trend maps, among which trend 1 was opposite to and trend 6 was consistent with breast muscle development trend of Jiaji ducks. Through joint analysis between trend 1 of DEGs and trend 1 of differential metabolites (DEMs), protein digestion and absorption pathway stood out. The decrease of COL8A2 gene expression will lead to the decrease of arginine content, which will inhibit the development of breast muscle in embryonic Jiaji duck. Similarly, joint analysis between trend 6 of DEGs and trend 6 of DEMs indicated the increase of GAMT gene expression will cause the increase of proline content, and then promote the development of breast muscle of Jiaji duck in embryonic period. These results will be helpful for further understanding the mechanism of muscle yields of Jiaji ducks.

Causal relationship between genetically determined plasma metabolites and skin cancer: a two-sample Mendelian randomization study

We aimed to unveil the underlying pathogenic mechanisms of skin cancer in relation to metabolic factors and pathway mechanisms. This study utilized the TwoSample Mendelian randomization (MR) method to investigate the causal relationship between 1400 plasma metabolites and skin cancer. The primary method employed was the inverse variance weighting (IVW). Through IVW analysis, we found 105 plasma metabolites associated with Basal Cell Carcinoma (BCC), with the highest association observed for Prolylglycine levels (OR [95% CI]: 1.1902 [1.0274, 1.3788]). For Malignant Melanoma of Skin (MSS), 68 plasma metabolites were linked, with the highest causal relationship seen for 3-Hydroxybutyrate levels (OR [95% CI]: 1.0030 [1.0013, 1.0048]). Regarding actinic keratosis (AK), and the highest association observed for Hexadecadienoate (16:2n6) levels (OR [95% CI]: 1.3302 [1.0333, 1.7125]). Glycerol to palmitoylcarnitine (16: n6) levels (OR [95% CI]: 1.3302 [1.0333, 1.125]) were found to be significant for BCC and AK. Palmitoylcarnitine (C16) had the most positive causal effect for BCC (OR [95% CI]: 1.1777 [1.0493, 1.3218]), while 5-hydroxy-2-methylpyridine sulfate levels had the highest effect for AK (OR [95% CI]: 1.1788 [1.0295, 1.3498]). And 4-guanidinobutanoate levels had the largest positive causal effect (OR [95% CI]: 1.0857 [1.0417, 1.1317]) for BCC, and X-11880 levels for MSS (OR [95% CI]: 1.0013 [1.0000, 1.0025]). The study revealed a positive association between hereditary Glycerol to palmitoylcarnitine (C16) and 5-hydroxy-2-methylpyridine sulfate levels with the risk of developing BCC and AK. Additionally, 4-guanidinobutanoate levels and X 11880 levels were found to be positively associated with the risk of BCC and MMS.

Transcriptome and lipidome integration unveils mechanisms of fatty liver formation in Shitou geese

Geese evolved from migratory birds, and when they consume excessive high-energy feed, glucose is converted into triglycerides. A large amount of triglyceride deposition can induce incomplete oxidation of fatty acids, leading to lipid accumulation in the liver and the subsequent formation of fatty liver. In the Chaoshan region of Guangdong, China, Shitou geese develop a unique form of fatty liver through 24 h overfeeding of brown rice. To investigate the mechanisms underlying the formation of fatty liver in Shitou geese, we collected liver samples from normally fed and overfed geese. The results showed that the liver size in the treatment group was significantly larger, weighing 3.5 times more than that in the control group. Extensive infiltration of lipid droplets was observed in the liver upon staining of tissue sections. Biochemical analysis revealed that compared to the control group, the treatment group showed significantly elevated levels of total cholesterol (T-CHO), triglycerides (TG), and glycogen in the liver. However, no significant differences were observed in the levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST), which are common indicators of liver damage. Furthermore, we performed a combined transcriptomic and lipidomic analysis of the liver samples and identified 1,510 differentially expressed genes (DEGs) and 1,559 significantly differentially abundant metabolites (SDMs). The enrichment analysis of the DEGs revealed their enrichment in metabolic pathways, cellular process-related signaling pathways, and specific lipid metabolism pathways. We also conducted KEGG enrichment analysis of the SDMs and compared them with the enriched signaling pathways obtained from the DEGs. In this study, we identified 3 key signaling pathways involved in the formation of fatty liver in Shitou geese, namely, the biosynthesis of unsaturated fatty acids, glycerol lipid metabolism, and glycerophospholipid metabolism. In these pathways, genes such as glycerol-3-phosphate acyltransferase, mitochondrial (GPAM), 1-acylglycerol-3-phosphate O-acyltransferase 2 (AGPAT2), diacylglycerol O-acyltransferase 2 (DGAT2), lipase, endothelial (LIPG), lipoprotein lipase (LPL), phospholipase D family member 4 (PLD4), and phospholipase A2 group IVF (PLA2G4F) may regulate the synthesis of metabolites, including triacylglycerol (TG), phosphatidate (PA), 1,2-diglyceride (DG), phosphatidylethanolamine (PE), and phosphatidylcholine (PC). These genes and metabolites may play a predominant role in the development of fatty liver, ultimately promoting the accumulation of TG in the liver and leading to the progression of fatty liver.

Insights into the mechanism of L-malic acid on drip loss of chicken meat under commercial conditions

BACKGROUND

A deterioration in the meat quality of broilers has attracted much more attention in recent years. L-malic acid (MA) is evidenced to decrease meat drip loss in broilers, but the underlying molecular mechanisms are still unclear. It's also not sure whether the outputs obtained under experimental conditions can be obtained in a commercial condition. Here, we investigated the effects and mechanisms of dietary MA supplementation on chicken meat drip loss at large-scale rearing.

RESULTS

Results showed that the growth performance and drip loss were improved by MA supplementation. Meat metabolome revealed that L-2-aminoadipic acid, β-aminoisobutyric acid, eicosapentaenoic acid, and nicotinamide, as well as amino acid metabolism pathways connected to the improvements of meat quality by MA addition. The transcriptome analysis further indicated that the effect of MA on drip loss was also related to the proper immune response, evidenced by the enhanced B cell receptor signaling pathway, NF-κB signaling pathway, TNF signaling pathway, and IL-17 signaling pathway.

CONCLUSIONS

We provided evidence that MA decreased chicken meat drip loss under commercial conditions. Metabolome and transcriptome revealed a comprehensive understanding of the underlying mechanisms. Together, MA could be used as a promising dietary supplement for enhancing the water-holding capacity of chicken meat.

The Integration of Genome-Wide DNA Methylation and Transcriptomics Identifies the Potential Genes That Regulate the Development of Skeletal Muscles in Ducks

DNA methylation is a pivotal epigenetic regulatory mechanism in the development of skeletal muscles. Nonetheless, the regulators responsible for DNA methylation in the development of embryonic duck skeletal muscles remain unknown. In the present study, whole genome bisulfite sequencing (WGBS) and transcriptome sequencing were conducted on the skeletal muscles of embryonic day 21 (E21) and day 28 (E28) ducks. The DNA methylation pattern was found to fall mainly within the cytosine-guanine (CG) context, with high methylation levels in the intron, exon, and promoter regions. Overall, 7902 differentially methylated regions (DMRs) were identified, which corresponded to 3174 differentially methylated genes (DMGs). By using integrative analysis of both WGBS with transcriptomics, we identified 1072 genes that are DMGs that are negatively associated with differentially expressed genes (DEGs). The gene ontology (GO) analysis revealed significant enrichment in phosphorylation, kinase activity, phosphotransferase activity, alcohol-based receptors, and binding to cytoskeletal proteins. The Kyoto Encyclopedia of Genes and Genomes (KEGGs) analysis showed significant enrichment in MAPK signaling, Wnt signaling, apelin signaling, insulin signaling, and FoxO signaling. The screening of enriched genes showed that hyper-methylation inhibited the expression of Idh3a, Got1, Bcl2, Mylk2, Klf2, Erbin, and Klhl38, and hypo-methylation stimulated the expression of Col22a1, Dnmt3b, Fn1, E2f1, Rprm, and Wfikkn1. Further predictions showed that the CpG islands in the promoters of Klhl38, Klf2, Erbin, Mylk2, and Got1 may play a crucial role in regulating the development of skeletal muscles. This study provides new insights into the epigenetic regulation of the development of duck skeletal muscles.