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

Abstract

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.

Keywords: amino acid; flavor compound; lipid; native chicken; regulation mechanism.

Figure 1

Quality control analysis of breast muscle metabolomics (n = 4). (A) PCA analysis in positive ion mode. (B) PCA analysis in negative ion mode. (C) OPLS-DA analysis in positive ion mode. (D) OPLS-DA analysis in negative ion mode. (E) The permutation test of OPLS-DA in positive ion mode. (F) The permutation test of OPLS-DA in negative ion mode.

Figure 2

Analysis of SDMs in breast muscle of DM vs. CB group (n = 4). (A) Clustering heatmap of SDMs in positive ion mode, where red represents up-regulation and blue represents down-regulation. (B) Clustering heatmap of SDMs in negative ion mode, where red represents up-regulation and blue represents down-regulation. (C) Significant KEGG metabolic pathways of SDMs.

Figure 3

Analysis of DEGs in breast muscle of DM vs. CB group (n = 4). (A) The number of upward and downward DEGs. (B) Clustering heatmap of DEGs, where red represents up-regulation and blue represents down-regulation. (C) Significant KEGG signaling pathway analysis of DEGs. (D) qRT-PCR analysis of DEGs. MMP9, Matrix metallopeptidase 9; SLC46A3, Solute carrier family 46 member 3; GATM, Glycine amidinotransferase; COL19A1, Collagen, type XIX, alpha 1; PNOC, Prepronociceptin; LPL, Lipoprotein lipase.

Figure 4

Correlation analysis of SDMs and DEGs related to meat quality and flavor. (A) Venn diagram for KEGG of SDMs and DEGs. (B) Heatmap of correlation between amino acids and their derivatives and DEGs. Red indicates a positive correlation and blue indicates a negative correlation. (C) Heatmap of correlation between lipids and their derivatives and DEGs. Red indicates a positive correlation and blue indicates a negative correlation. (D) Interaction networks of amino acids and their derivatives with DEGs. The red circles represent amino acids and their derivatives, and the green circles represent DEGs, which are associated with amino acid metabolism. The red line shows a positive correlation and the green line shows a negative correlation. (E) Interaction networks of lipids and their derivatives with DEGs. The red circles represent lipids and the green circles represent DEGs, which are associated with lipid metabolism. The red line shows a positive correlation and the green line shows a negative correlation. AANAT: Aralkylamine N-acetyltransferase; ABCG4: ATP binding cassette subfamily G member 4; ANGPTL4: Angiopoietin-like protein 4; ATP6AP1: ATPase H+ transporting accessory protein 1; ATP6V0D2: ATPase, H+ transporting, lysosomal V0 subunit D2; ATP6V1C2: ATPase H+ transporting V1 subunit C2; AWAT1: Acyl-CoA wax alcohol acyltransferase 1; B4GALT6: Beta-1,4-galactosyltransferase 6; DEGS2: Delta 4-desaturase, sphingolipid 2; ENO2: Enolase 2; FABP7: Fatty acid-binding protein 7; GALC: Galactosylceramidase; GATM: Glycine amidinotransferase; GK: Glucokinase; GNE: Glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase; GSTO1: Glutathione S-transferase omega-1; HEXA: Hexosaminidase subunit alpha; LIPML5: Lipase member M-like 5; LPL: Lipoprotein lipase; NEU4: Sialidase 4; PGM3: Phosphoglucomutase 3; PIK3CB: Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta; PLIN1: Perilipin 1; PLPP4: Phospholipid phosphatase 4; PPARG: Peroxisome proliferator-activated receptor gamma; PRODH: Proline dehydrogenase 1; SCD: Stearoyl-CoA desaturase; TCIRG1: T-cell immune regulator 1; UGT8: UDP glycosyltransferase 8; WNT11B: Wingless-type MMTV integration site family, member 11b; WNT16: Wnt family member 16.

Figure 5

Analysis of key pathways, metabolites and genes that may regulate meat quality and flavor formation of DM chicken through the KEGG pathways.